diff --git a/.gitignore b/.gitignore index 73cd9f97..1586d8c8 100755 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ +migration/ +cache.*.json +user-quotas.json build/ build_qadocs/ log.lsf.txt @@ -5,6 +8,7 @@ log.txt ssl/ commits/ user/ +drafts/ image.batches.yaml iter.batches.yaml diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 28280ef6..ce2ce2c5 100755 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -56,7 +56,7 @@ variables: .deploy: &deploy stage: deploy script: - - ssh qa "bash -c \"cd $(pwd) && source .envrc && docker-compose -f docker-compose.yml -f production.yml -f sirc.yml up -d --build\"" + - ssh $DOCKER_HOST "bash -c \"cd $(pwd) && source .envrc && ./at-sirc-before-up.py && docker-compose -f docker-compose.yml -f production.yml -f sirc.yml up -d --build\"" deploy:production: <<: *deploy diff --git a/backend/Dockerfile b/backend/Dockerfile index b035977c..76f4d7d0 100644 --- a/backend/Dockerfile +++ b/backend/Dockerfile @@ -26,9 +26,14 @@ RUN apt-get update -qq \ # https://www.psycopg.org/docs/install.html#install-from-source # https://www.psycopg.org/docs/faq.html#faq-compile RUN apt-get update \ + # postgresql and toolchain && apt-get install -y libpq-dev gcc \ + # login packages + && apt-get install -y libsasl2-dev libldap2-dev libssl-dev \ && apt-get clean +# At SIRC we need to be able to turn into any user to delete their output files +RUN apt-get update && apt-get install -y sudo # If we want uwsgi's routing support # https://uwsgi-docs.readthedocs.io/en/latest/InternalRouting.html @@ -83,7 +88,7 @@ CMD ["/qaboard/backend/init.sh"] # Where we keep a cache of application data (e.g. git clones) VOLUME /var/qaboard - +RUN mkdir -p /var/qaboard && chmod -R 777 /var/qaboard # TODO: diff --git a/backend/README.md b/backend/README.md index 9330b3e1..d726e8d1 100755 --- a/backend/README.md +++ b/backend/README.md @@ -2,10 +2,23 @@ QA-Board's backend built as a [flask](https://flask.pocoo.org) application. It exposes an HTTP API used to read/write all the metadata on QA-Board's runs. ## How to start a development backend +1. First get the code: ```bash git clone git@gitlab-srv:common-infrastructure/qaboard.git cd qaboard +``` + +2. If you want to run a frontend, [go to the README](../webapp/README.md) and without docker run `npm install`. + +3. Edit at the top-level of the repository _development.yml_, and replace `arthurf` with your user. Edit _services/backend/passwd_ and add a line with your user, looking like `arthurf:*:11611:10:Arthur Flam:/home/arthurf:/bin/tcsh`. You can get it with `getent passwd | grep arthurf`. + +4. Start the server: + +```bash docker-compose -f docker-compose.yml -f development.yml up -d + +# for more build logs +export BUILDKIT_PROGRESS=plain ``` > **Tip:** If you called `npm install` in the *webapp/*, (see the [README](../webapp)), a frontend connected to the dev backend will also be up on port 3000. @@ -23,6 +36,10 @@ Consult also: - [Troubleshooting Guide](https://samsung.github.io/qaboard/docs/backend-admin/troubleshooting). - To learn how to restore from a backup, read the [upgrade guide](https://samsung.github.io/qaboard/docs/backend-admin/host-upgrades). +At SIRC: +```bash +sudo sysctl -w net.core.somaxconn=65536 +``` ## Overview [sqlalchemy](http://docs.sqlalchemy.org/en/latest/orm/tutorial.html) maps our classes (defined in [/models](models/)) to database tables: diff --git a/backend/backend/__init__.py b/backend/backend/__init__.py index dfd235e6..1673a90f 100755 --- a/backend/backend/__init__.py +++ b/backend/backend/__init__.py @@ -6,9 +6,9 @@ from flask_cors import CORS app = Flask(__name__) -# This would be needed to use flask's sessions (e.g. display flash messages after redirects...) -# However we never used this feature as (1) the backend is stateless and (2) the client uses an API, now generated views. -# app.secret_key = os.environ.get('QABOARD_FLASK_SECRET_KEY', 'xxxxxxxxxxx') +# This key will be used to sign session cookies +# To generate a key: python -c 'import os; print(os.urandom(16))' +app.secret_key = os.environ.get('SECRET_KEY', 'please-generate-your-own-secret-key') # Provide easy access to our git repositories from .git_utils import Repos @@ -24,15 +24,27 @@ def shutdown_session(exception=None): db_session.remove() import backend.api.api +import backend.api.commit +import backend.api.batch +import backend.api.outputs import backend.api.webhooks import backend.api.integrations import backend.api.tuning import backend.api.export_to_folder import backend.api.auto_rois import backend.api.milestones +import backend.api.auth # Enable cross-origin requests to avoid development headcaches # cors = CORS(app, resources={r"/api/*": {"origins": "*"}}) CORS(app) -Base.metadata.create_all(engine) \ No newline at end of file +Base.metadata.create_all(engine) + +# Avoids errors +# > sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) lost synchronization with server: got message type " " +# https://docs.sqlalchemy.org/en/13/core/pooling.html#pooling-multiprocessing +# https://stackoverflow.com/questions/43648075/uwsgi-flask-sqlalchemy-intermittent-postgresql-errors-with-warning-there-is-al +# https://uwsgi-docs.readthedocs.io/en/latest/articles/TheArtOfGracefulReloading.html#preforking-vs-lazy-apps-vs-lazy +# https://stackoverflow.com/questions/41279157/connection-problems-with-sqlalchemy-and-multiple-processes +engine.dispose() diff --git a/backend/backend/api/api.py b/backend/backend/api/api.py index 9c848101..f5578c37 100755 --- a/backend/backend/api/api.py +++ b/backend/backend/api/api.py @@ -1,27 +1,22 @@ """ -Simple REST API to list the objects in our database. +Access data related to Projects. """ -import sys -import datetime import pytz -import subprocess import json -from pathlib import Path +import datetime import ujson -from gitdb.exc import BadName -from flask import request, jsonify, make_response, redirect +from flask import request, jsonify, make_response from sqlalchemy import func, and_, asc, or_ -from sqlalchemy.orm import joinedload, selectinload -from sqlalchemy.orm.exc import NoResultFound, MultipleResultsFound +from sqlalchemy.orm import selectinload + from sqlalchemy.orm.attributes import flag_modified from sqlalchemy.sql import label from backend import app, db_session from ..models import Project, CiCommit, Batch, Output -from ..models import latest_successful_commit - +from ..utils import profiled to_datetime = lambda s: timezone.localize(datetime.datetime.strptime(s, '%Y-%m-%dT%H:%M:%S.%fZ')) @@ -61,17 +56,20 @@ def get_commits(branch=None): from_date = min(latest_authored_datetime - (to_date - from_date), from_date) from_date = from_date - datetime.timedelta(hours=3) # timezones as above - - ci_commits = (db_session - .query(CiCommit) - .options(selectinload(CiCommit.batches).selectinload(Batch.outputs)) - .filter( - CiCommit.authored_datetime >= from_date, - CiCommit.authored_datetime <= to_date, - CiCommit.project_id == project_id, - ) - .order_by(CiCommit.authored_datetime.desc()) - ) + with_outputs = False if request.args.get('with_outputs', 'false')=='false' else True + ci_commits = db_session.query(CiCommit) + if True: # with_outputs: do this when we pre-aggregated counts of Outputs per status... + ci_commits = ci_commits.options(selectinload(CiCommit.batches).selectinload(Batch.outputs)) + else: + ci_commits = ci_commits.options(selectinload(CiCommit.batches)) + ci_commits = (ci_commits + .filter( + CiCommit.authored_datetime >= from_date, + CiCommit.authored_datetime <= to_date, + CiCommit.project_id == project_id, + ) + .order_by(CiCommit.authored_datetime.desc()) + ) if committer_name: ci_commits = ci_commits.filter_by(committer_name=committer_name) @@ -80,6 +78,9 @@ def get_commits(branch=None): metrics_to_aggregate = json.loads(request.args.get('metrics', '{}')) + if project_id.startswith("CDE-Users/HW_ALG"): # too many results to be fast... + with_aggregation = {} + with_batches = None batch = request.args.get('batch', None) if batch: @@ -88,11 +89,16 @@ def get_commits(branch=None): only_ci_batches = False if request.args.get('only_ci_batches', 'false')=='false' else True if only_ci_batches: with_batches = ['default'] - with_outputs = False if request.args.get('with_outputs', 'false')=='false' else True - # from ..utils import profiled + serializable_commits = [] # with profiled(): - serializable_commits = [c.to_dict(with_aggregation=metrics_to_aggregate, with_batches=with_batches, with_outputs=with_outputs) - for c in ci_commits] + for c in ci_commits.limit(1000): + if not c.batches: + continue + serializable_commits.append(c.to_dict( + with_aggregation=metrics_to_aggregate, + with_batches=with_batches, + with_outputs=with_outputs + )) response = make_response(ujson.dumps(serializable_commits)) response.headers['Content-Type'] = 'application/json' return response @@ -110,7 +116,6 @@ def get_branches(): return jsonify([b[0] for b in branches]) - @app.route("/api/v1/projects") def get_projects(): projects = (db_session @@ -151,147 +156,4 @@ def get_project(): return jsonify(project.data) -@app.route("/api/v1/output/", methods=['GET', 'DELETE']) -@app.route("/api/v1/output//", methods=['GET', 'DELETE']) -def crud_output(output_id): - output = Output.query.filter(Output.id==output_id).one() - if request.method == 'GET': - return jsonify(output.to_dict()) - if request.method == 'DELETE': - if output.is_pending: - return {"error": "Please wait for the Output to finish running before deleting it"}, 500 - output.delete(soft=False) - db_session.delete(output) - db_session.commit() - return {"status": "OK"} - -@app.route("/api/v1/output//manifest", methods=['GET']) -@app.route("/api/v1/output//manifest/", methods=['GET']) -def get_output_manifest(output_id): - output = Output.query.filter(Output.id==output_id).one() - if output.is_running or request.args.get('refresh'): - manifest = output.update_manifest(compute_hashes=False) - return jsonify(manifest) - else: - return redirect(f"{output.output_dir_url}/manifest.outputs.json", code=302) - - - - - -@app.route("/api/v1/commit", methods=['GET', 'POST']) -@app.route("/api/v1/commit/", methods=['GET', 'POST']) -@app.route("/api/v1/commit/", methods=['GET', 'POST']) -def api_ci_commit(commit_id=None): - if request.method == 'POST': - hexsha = request.json.get('commit_sha', request.json['git_commit_sha']) if not commit_id else commit_id - try: - commit = CiCommit.get_or_create( - session=db_session, - hexsha=hexsha, - project_id=request.json['project'], - data=request.json, - ) - except: - return f"404 ERROR:\n ({request.json['project']}): There is an issue with your commit id ({request.json['git_commit_sha']})", 404 - if not commit.data: - commit.data = {} - # Clients can store any metadata with each commit. - # We've been using it to store code quality metrics per subproject in our monorepo, - # Then we use other tools (e.g. metabase) to create dashboards. - commit_data = request.json.get('data', {}) - commit.data = {**commit.data, **commit_data} - flag_modified(commit, "data") - if commit.deleted: - commit.deleted = False - db_session.add(commit) - db_session.commit() - return jsonify({"status": "OK"}) - - - project_id = request.args['project'] - if not commit_id: - commit_id = request.args.get('commit', None) - try: - project = Project.query.filter(Project.id==project_id).one() - default_branch = project.data['qatools_config']['project']['reference_branch'] - except: - default_branch = 'master' - branch = request.args.get('branch', default_branch) - ci_commit = latest_successful_commit(db_session, project_id=project_id, branch=branch, batch_label=request.args.get('batch')) - if not ci_commit: - return jsonify({'error': f'Sorry, we cant find any commit with results for the {project_id} on {branch}.'}), 404 - else: - try: - ci_commit = (db_session - .query(CiCommit) - .options( - joinedload(CiCommit.batches). - joinedload(Batch.outputs) - ) - .filter( - CiCommit.project_id==project_id, - CiCommit.hexsha.startswith(commit_id), - ) - .one() - ) - except NoResultFound: - try: - # TODO: This is a valid use case for having read-rights to the repo, - # we can identify a commit by the tag/branch - # To replace this without read rights, we should listen for push events and build a database - project = Project.query.filter(Project.id==project_id).one() - commit = project.repo.tags[commit_id].commit - try: - commit = project.repo.commit(commit_id) - except: - try: - commit = project.repo.refs[commit_id].commit - except: - commit = project.repo.tags[commit_id].commit - ci_commit = CiCommit(commit, project=project) - db_session.add(ci_commit) - db_session.commit() - except: - return jsonify({'error': f'Sorry, we could not find any data on commit {commit_id} in project {project_id}.'}), 404 - except BadName: - return jsonify({f'error': f'Sorry, we could not understand the commid ID {commit_id} for project {project_id}.'}), 404 - except Exception as e: - raise(e) - return jsonify({'error': 'Sorry, the request failed.'}), 500 - - batch = request.args.get('batch', None) - with_batches = [batch] if batch else None # by default we show all batches - with_aggregation = json.loads(request.args.get('metrics', '{}')) - response = make_response(ujson.dumps(ci_commit.to_dict(with_aggregation, with_batches=with_batches, with_outputs=True))) - response.headers['Content-Type'] = 'application/json' - return response - - -@app.route("/api/v1/commit/save-artifacts/", methods=['POST']) -@app.route("/api/v1/commit/save-artifacts", methods=['POST']) -def commit_save_artifacts(): - hexsha = request.json.get('hexsha') - try: - ci_commits = (db_session - .query(CiCommit) - .filter( - CiCommit.hexsha == hexsha, - ) - ) - except: - return f"404 ERROR:\n ({request.json['project']}): There is an issue with your commit id ({hexsha})", 404 - for ci_commit in ci_commits.all(): - if not request.json['project'].startswith(ci_commit.project_id): - print(f'skip {ci_commit.project_id}') - continue - print(f"[save-artifacts] {ci_commit}") - # FIXME: in the clean crontab we remove commits without runs - # if we rely on artifacts from a subproject without runs, it will cause issues... - # we should use the git info to find the qatools.yaml - ci_commit.save_artifacts() - ci_commit.deleted = False - db_session.add(ci_commit) - db_session.commit() - return 'OK' diff --git a/backend/backend/api/auth.py b/backend/backend/api/auth.py new file mode 100644 index 00000000..eb4d5267 --- /dev/null +++ b/backend/backend/api/auth.py @@ -0,0 +1,193 @@ +""" +Authentication for qaboard users and LDAP. +""" +import os + +import ldap +from flask import request, jsonify +from flask_login import LoginManager, login_user, logout_user, current_user +from werkzeug.security import generate_password_hash, check_password_hash + +from backend import app, db_session +from ..models import User + + +ldap_enabled = os.getenv('QABOARD_LDAP_ENABLED') +if ldap_enabled: + # Server hostname (including port) + ldap_host = os.environ['QABOARD_LDAP_HOST'] + # Server port, usually 389 or 636 if SSL is used. + ldap_port = os.environ.get('QABOARD_LDAP_PORT', 389) + # Search base for users. (Will not be searched recursively) + ldap_user_base = os.environ['QABOARD_LDAP_USER_BASE'] + # The Distinguished Name to bind as, this user will be used to lookup information about other users. + ldap_bind_dn = os.environ['QABOARD_LDAP_BIND_DN'] + # The password to bind with for the lookup user. + ldap_password = os.environ['QABOARD_LDAP_PASSWORD'] + # "User lookup filter, the placeholder {login} will be replaced by the user supplied login. (e.g. `(&(objectClass=inetOrgPerson)(|(uid={login})(mail={login})))`, or `(&(objectClass=user)(|(sAMAccountName={login})))`) + ldap_user_filter = os.environ['QABOARD_LDAP_USER_FILTER'] + # User attributes + ldap_attr_email = os.environ.get('QABOARD_LDAP_ATTRIBUTE_EMAIL', "mail") + ldap_attr_common_name = os.environ.get('QABOARD_LDAP_ATTRIBUTE_COMMON_NAME', "cn") + + +login_manager = LoginManager(app) + + +@app.route('/api/v1/user/signup/', methods=['POST']) +def signup(): + try: + user = create_user({ + "email": request.form.get('email'), + "user_name": request.form.get('user_name'), + "password": request.form.get('password'), + }) + except Exception as e: + print(f"[signup] Error when creating new user with {request.form}: {e}") + return f"ERROR: The email or user name already exists", 403 + return jsonify({"id": user.id}) # FIXME: return more info ? + + +@app.route('/api/v1/user/auth/', methods=['POST']) +def auth_post(): + if current_user.is_authenticated: + logout_user() + username = request.form['username'] + password = request.form['password'] + user_info = auth(username, password) + if not user_info["login_success"]: + print(f"[auth] Failed Login @{username}") + return jsonify({"error": user_info["error"]}), 403 + + user = User.query.filter_by(user_name=username).one() + login_user(user) + print(f"[auth] Login @{username}") + return jsonify(user_info) + + +@app.route('/api/v1/user/me/', methods=['GET']) +def get_current_user(): + # https://flask-login.readthedocs.io/en/latest/#your-user-class + is_authenticated = current_user.is_authenticated + info = { + "is_authenticated": is_authenticated, + "is_anonymous": current_user.is_anonymous, + "is_active": current_user.is_active, + } + if is_authenticated: + info.update({ + "user_id": current_user.id, + "user_name": current_user.user_name, + "full_name": current_user.full_name, + "email": current_user.email, + "is_ldap": current_user.is_ldap, + }) + return jsonify(info) + + +@app.route('/api/v1/user/logout/', methods=['POST']) +def logout(): + if current_user.is_authenticated: + logout_user() + return jsonify({"status": "OK"}) + + +@login_manager.user_loader +def load_user(user_id): + return User.query.get(user_id) + +def create_user(info): + user = User( + user_name=info["user_name"], + full_name=info["full_name"], + email=info["email"], + is_ldap=info["is_ldap"], + # TODO: use a slower hash, currently the default is pbkdf2:sha256 + # https://werkzeug.palletsprojects.com/en/1.0.x/utils/#werkzeug.security.generate_password_hash + password= generate_password_hash(info["password"]) if "password" in info else None, + ) + db_session.add(user) + db_session.commit() + print(f"Created {user}") + return user + + +def auth(username, password): + user = User.query.filter_by(user_name=username).first() # if this returns a user, then the user_name already exists in database + # FIXME: check we render the error field in JS, not invalid_passord=True.. + if ldap_enabled and (not user or user.is_ldap): + return auth_ldap(username, password) + else: + return auth_local(username, password) + + +def auth_local(username, password): + info = { + "username": username, + "is_ldap": False, + "login_success": False, + } + user = User.query.filter_by(user_name=username).one_or_none() + if not user: + info["error"] = "invalid-username" + elif not check_password_hash(user.password, password): + info["error"] = "invalid-password" + else: + info["login_success"] = True + info["id"] = user.id + info["full_name"] = user.full_name + info["user_name"] = user.user_name + info["email"] = user.email + return info + +def auth_ldap(user_name, password): + if not ldap_enabled: + raise Exception("LDAP is not enabled") + user_info = { + "user_name": user_name, + "is_ldap": True, + "login_success": False, + } + # TODO: support for secure LDAP + ldap_uri = f"ldap://{ldap_host}" if not ldap_port else f"ldap://{ldap_host}:{ldap_port}" + ldap_connect = ldap.initialize(ldap_uri) + ldap_connect.set_option(ldap.OPT_REFERRALS, 0) + ldap_connect.simple_bind_s(ldap_bind_dn, ldap_password) + + # check if the user exists + ldap_search = ldap_user_filter.replace("{login}", user_name) + certificate = ldap_connect.search_s( + ldap_user_base, + ldap.SCOPE_SUBTREE, + ldap_search, + ['distinguishedName'], + )[0][0] + + if certificate: + # check the password and get the full user info + try: + ldap_connect.set_option(ldap.OPT_REFERRALS, 0) + ldap_connect.simple_bind_s(certificate, password) + details = ldap_connect.search_s( + ldap_user_base, + ldap.SCOPE_SUBTREE, + ldap_search, + [ldap_attr_common_name, 'mail'], + ) + user_ldap = details[0][1] + user_info["login_success"] = True + user_info["full_name"] = str(user_ldap[ldap_attr_common_name][0], 'utf-8') + user_info["email"] = str(user_ldap[ldap_attr_email][0], 'utf-8') + except (ldap.INVALID_CREDENTIALS, ldap.OPERATIONS_ERROR): + user_info["error"] = "invalid-password" + else: + user_info["error"] = "invalid-username" + ldap_connect.unbind_s() + + if user_info["login_success"]: + user = User.query.filter_by(user_name=user_name).one_or_none() + if not user: + user = create_user(user_info) + user_info["id"] = user.id + return user_info + diff --git a/backend/backend/api/auto_rois.py b/backend/backend/api/auto_rois.py index ebd5426d..55a82809 100755 --- a/backend/backend/api/auto_rois.py +++ b/backend/backend/api/auto_rois.py @@ -5,6 +5,7 @@ from pathlib import Path import time # for Debugging purpose from math import sqrt, ceil +from functools import lru_cache import numpy as np from skimage import io @@ -14,12 +15,100 @@ from requests.utils import unquote from flask import request, jsonify +from PIL import Image from qaboard.api import url_to_dir from backend import app from ..models import Output +@lru_cache(maxsize=2) +def cached_read_image(image_path): + """ + Simple LRU cache - the downside is that our images are huge so with 8 workers each saving 2 image, each 300MB, it's bad... + """ + image_pil = Image.open(str(file)) + image = np.array(image_pil) + meta = { + # https://pillow.readthedocs.io/en/5.1.x/handbook/concepts.html#concept-modes + "mode": image_pil.mode + } + return image, meta + + +# TODO: - add locking when working with flask +# import threading # Lock, Semaphore +# - check locking works ok with uwsgi +try: + import uwsgi + under_uwsgi = True +except: + under_uwsgi = False + +import json +import time +import hashlib + +from backend.config import qaboard_data_dir +image_cache_dir = qaboard_data_dir / 'cache' / 'images' +image_cache_dir = Path('/algo/qa_db/image_cache') # TODO: remove for the open-source version +image_cache_dir.mkdir(exist_ok=True, parents=True) + +def clear_memmapped_cache_dir(): + cache_size = 20 + file_data = list(image_cache_dir.glob('*.dat')) + file_data.sort(key=lambda f: -f.stat().st_mtime) # oldest last + for file in file_data[cache_size:]: + print(f"RM {file}") + file.unlink() + file_info = file.with_suffix('.json') + if file_info.exists(): + file_info.unlink() + +def memmapped_read_image(image_path): + key = f"{image_path}-{image_path.stat().st_mtime}" + hash = hashlib.sha1(key.encode()).hexdigest() + image_cache_data = image_cache_dir / f"{hash}.dat" + image_cache_info = image_cache_dir / f"{hash}.json" + if not (image_cache_data.exists() and image_cache_info.exists()): + clear_memmapped_cache_dir() + # if under_uwsgi: + # # worst case the 1st requests will write multiple times that file... + # uwsgi.lock() + # print(f'MISS {image_path}') + image, meta = read_image(image_path) + # print(f'READ') + with image_cache_info.open('w') as fmeta: + json.dump({"meta": meta, "shape": image.shape, "dtype": str(image.dtype)}, fmeta) + fp = np.memmap(image_cache_data, dtype=image.dtype, mode='w+', shape=image.shape) + fp[:] = image[:] + fp.flush() # write to disk + # print(f'WRITE') + # if under_uwsgi: + # uwsgi.unlock() + return fp, meta + else: + # print(f'HIT {hash}') + with image_cache_info.open() as f: + info = json.load(f) + fp = np.memmap(image_cache_data, dtype=info['dtype'], mode='r', shape=tuple(info['shape'])) + return fp, info['meta'] + + +@app.route("/api/v1/output/image/pixel", methods=['GET', 'POST']) +def get_pixel(): + x = int(request.args['x'])-1 + y = int(request.args['y'])-1 + image_path = url_to_dir(request.args['image_url']) + # We work with huge images (100-200MP). Loading them each request can be very slow (~seconds). + # Since the frontend may request 5-10 pixel values per second, we need some form of caching. + image, meta = memmapped_read_image(Path(image_path)) + # image, meta = cached_read_image(Path(image_path)) + return jsonify({ + "value": image[y,x].tolist(), + "meta": meta, + }) + @app.route("/api/v1/output/diff/image", methods=['GET', 'POST']) def get_images(): diff --git a/backend/backend/api/batch.py b/backend/backend/api/batch.py new file mode 100644 index 00000000..906a2f9e --- /dev/null +++ b/backend/backend/api/batch.py @@ -0,0 +1,168 @@ +import json + +from flask import request, jsonify +from sqlalchemy.orm.attributes import flag_modified + +from backend import app, db_session +from ..models import CiCommit, Batch +from .export_to_folder import filter_outputs + + + + +@app.route('/api/v1/batch', methods=['POST']) +@app.route('/api/v1/batch/', methods=['POST']) +def update_batch(): + data = request.get_json() + try: + ci_commit = CiCommit.get_or_create( + session=db_session, + hexsha=request.json['git_commit_sha'], + project_id=request.json['project'], + data=data, + ) + except: + return f"404 ERROR:\n ({request.json['project']}): There is an issue with your commit id ({request.json['git_commit_sha']})", 404 + + batch = ci_commit.get_or_create_batch(data['batch_label']) + # prefix_output_dir for backward-compatibility + batch.batch_dir_override = data.get("batch_dir", data.get("prefix_output_dir")) + + # Clients can store any metadata in each batch. + # Currently it's used by `qa optimize` to store info on iterations + if not batch.data: + batch.data = {} + batch_data = request.json.get('data', {}) + # And each batch can have changes vs its commit's config and metrics. + # The use case is usually working locally with `qa --share` and + # seeing updated visualizations and metrics. + if "qaboard_config" in data and data["qaboard_config"] != ci_commit.data["qatools_config"]: + batch.data["config"] = data["qaboard_config"] + if "qaboard_metrics" in data and data["qaboard_metrics"] != ci_commit.data["qatools_metrics"]: + batch.data["qatools_metrics"] = data["qaboard_metrics"] + batch.data = {**batch.data, **batch_data} + + # Save info on each "qa batch" command in the batch, mainly to list them in logs + command = request.json.get('command') + if command: + batch.data["commands"] = {**batch.data.get('commands', {}), **command} + flag_modified(batch, "data") + + # It's a `qa optimzize` experiment + if batch_data.get('optimization'): + if batch_data.get('is_best_iter'): + # we will save the outputs from the best iteration in the batch, + # so first we need to remove any previous best results + for o in batch.outputs: + if o.output_type != 'optim_iteration': + print(f" DELETE {o}") + o.delete(soft=False) + db_session.delete(o) + db_session.add(batch) + db_session.commit() + + # Move results from the best iteration in this batch + batch_batch_label = batch_data['iteration_label'] + best_batch = ci_commit.get_or_create_batch(batch_batch_label) + for o in best_batch.outputs: + o.batch = batch + db_session.add(o) + db_session.commit() + + # delete past iterations (we can have "future iters when running in parallel") + # results from the best iter are already in the "main" batch + optim_prefix = f"{data['batch_label']}|iter" + for b in ci_commit.batches: + if not b.label.startswith(optim_prefix): + continue + iteration = int(b.label.replace(optim_prefix, "")) + if iteration <= batch_data['iteration']: + print(f'Deleting iteration {iteration} in {b.label}') + b.delete(db_session) + db_session.delete(b) + + db_session.add(batch) + db_session.commit() + return jsonify({"status": "OK", "id": batch.id}) + + + +@app.route('/api/v1/batch/stop', methods=['POST']) +@app.route('/api/v1/batch/stop/', methods=['POST']) +def stop_batch(): + data = request.get_json() + try: + batch = Batch.query.filter(Batch.id == data['id']).one() + except: + return f"404 ERROR:\n Not found", 404 + status = batch.stop() + return jsonify(status), 200 if not "error" in status else 500 + +@app.route('/api/v1/batch/redo', methods=['POST']) +@app.route('/api/v1/batch/redo/', methods=['POST']) +def redo_batch(): + data = request.get_json() + try: + batch = Batch.query.filter(Batch.id == data['id']).one() + except: + return f"404 ERROR:\n Not found", 404 + success = batch.redo( + only_failed=data.get('only_failed', False), + only_deleted=data.get('only_deleted', False), + ) + if success: + return '{"status": "OK"}' + else: + return jsonify({"status": "Some runs failed to start. Check the 'redo.log' files in the output directories to know more."}), 500 + +@app.route('/api/v1/batch/rename', methods=['POST']) +@app.route('/api/v1/batch/rename/', methods=['POST']) +def rename_batch(): + data = request.get_json() + try: + batch = Batch.query.filter(Batch.id == data['id']).one() + except: + return '{"error":"not found"}', 404 + try: + assert all([b.label != data['label'] for b in batch.ci_commit.batches]) + except: + return '{"error":"already exists {e}"}', 403 + status = batch.rename(label=data['label'], db_session=db_session) + return '{"status": "OK"}' + +# Check move: existing, delete if empty, filter + +@app.route('/api/v1/batch/move', methods=['POST']) +@app.route('/api/v1/batch/move/', methods=['POST']) +def move_batch(): + data = request.get_json() + try: + batch = Batch.query.filter(Batch.id == data['id']).one() + except: + return f"404 ERROR:\n Not found", 404 + dst_batch = batch.ci_commit.get_or_create_batch(data['label']) + for o in filter_outputs(data.get('filter'), batch.outputs): + o.batch = dst_batch + db_session.add(o) + if not batch.outputs: + batch.delete(session=db_session) + db_session.commit() + return '{"status": "OK"}' + + +@app.route('/api/v1/batch/', methods=['DELETE']) +@app.route('/api/v1/batch//', methods=['DELETE']) +def delete_batch(batch_id): + try: + batch = Batch.query.filter(Batch.id == batch_id).one() + except: + return f"404 ERROR:\nNot found", 404 + stop_status = batch.stop() + if "error" in stop_status: + return jsonify(stop_status), 500 + soft = request.args.get('soft') == 'true' + only_failed = request.args.get('only_failed') == 'true' + batch.delete(session=db_session, soft=soft, only_failed=only_failed) + return {"status": "OK"} + + diff --git a/backend/backend/api/commit.py b/backend/backend/api/commit.py new file mode 100644 index 00000000..b9e14a3a --- /dev/null +++ b/backend/backend/api/commit.py @@ -0,0 +1,131 @@ +import json + +from gitdb.exc import BadName +import ujson +from flask import request, jsonify, make_response + +from sqlalchemy.orm import joinedload +from sqlalchemy.orm.exc import NoResultFound +from sqlalchemy.orm.attributes import flag_modified + +from backend import app, db_session +from ..models import Project, CiCommit, latest_successful_commit, Batch + + + +@app.route("/api/v1/commit", methods=['GET', 'POST']) +@app.route("/api/v1/commit/", methods=['GET', 'POST']) +@app.route("/api/v1/commit/", methods=['GET', 'POST']) +def api_ci_commit(commit_id=None): + if request.method == 'POST': + hexsha = request.json.get('commit_sha', request.json['git_commit_sha']) if not commit_id else commit_id + try: + commit = CiCommit.get_or_create( + session=db_session, + hexsha=hexsha, + project_id=request.json['project'], + data=request.json, + ) + except: + return f"404 ERROR:\n ({request.json['project']}): There is an issue with your commit id ({request.json['git_commit_sha']})", 404 + if not commit.data: + commit.data = {} + # Clients can store any metadata with each commit. + # We've been using it to store code quality metrics per subproject in our monorepo, + # Then we use other tools (e.g. metabase) to create dashboards. + commit_data = request.json.get('data', {}) + commit.data = {**commit.data, **commit_data} + flag_modified(commit, "data") + if commit.deleted: + commit.deleted = False + db_session.add(commit) + db_session.commit() + return jsonify({"status": "OK"}) + + + project_id = request.args['project'] + if not commit_id: + commit_id = request.args.get('commit', None) + try: + project = Project.query.filter(Project.id==project_id).one() + default_branch = project.data['qatools_config']['project']['reference_branch'] + except: + default_branch = 'master' + branch = request.args.get('branch', default_branch) + ci_commit = latest_successful_commit(db_session, project_id=project_id, branch=branch, batch_label=request.args.get('batch')) + if not ci_commit: + return jsonify({'error': f'Sorry, we cant find any commit with results for the {project_id} on {branch}.'}), 404 + else: + try: + ci_commit = (db_session + .query(CiCommit) + .options( + joinedload(CiCommit.batches). + joinedload(Batch.outputs) + ) + .filter( + CiCommit.project_id==project_id, + CiCommit.hexsha.startswith(commit_id), + ) + .one() + ) + except NoResultFound: + try: + # TODO: This is a valid use case for having read-rights to the repo, + # we can identify a commit by the tag/branch + # To replace this without read rights, we should listen for push events and build a database + project = Project.query.filter(Project.id==project_id).one() + commit = project.repo.tags[commit_id].commit + try: + commit = project.repo.commit(commit_id) + except: + try: + commit = project.repo.refs[commit_id].commit + except: + commit = project.repo.tags[commit_id].commit + ci_commit = CiCommit(commit, project=project) + db_session.add(ci_commit) + db_session.commit() + except: + return jsonify({'error': f'Sorry, we could not find any data on commit {commit_id} in project {project_id}.'}), 404 + except BadName: + return jsonify({f'error': f'Sorry, we could not understand the commid ID {commit_id} for project {project_id}.'}), 404 + except Exception as e: + raise(e) + return jsonify({'error': 'Sorry, the request failed.'}), 500 + + batch = request.args.get('batch', None) + with_batches = [batch] if batch else None # by default we show all batches + with_aggregation = json.loads(request.args.get('metrics', '{}')) + response = make_response(ujson.dumps(ci_commit.to_dict(with_aggregation, with_batches=with_batches, with_outputs=True))) + response.headers['Content-Type'] = 'application/json' + return response + + +@app.route("/api/v1/commit/save-artifacts/", methods=['POST']) +@app.route("/api/v1/commit/save-artifacts", methods=['POST']) +def commit_save_artifacts(): + hexsha = request.json.get('hexsha') + try: + ci_commits = (db_session + .query(CiCommit) + .filter( + CiCommit.hexsha == hexsha, + ) + ) + except: + return f"404 ERROR:\n ({request.json['project']}): There is an issue with your commit id ({hexsha})", 404 + for ci_commit in ci_commits.all(): + if not request.json['project'].startswith(ci_commit.project_id): + print(f'skip {ci_commit.project_id}') + continue + print(f"[save-artifacts] {ci_commit}") + # FIXME: in the clean crontab we remove commits without runs + # if we rely on artifacts from a subproject without runs, it will cause issues... + # we should use the git info to find the qatools.yaml + ci_commit.save_artifacts() + if ci_commit.deleted: + ci_commit.deleted = False + db_session.add(ci_commit) + db_session.commit() + return 'OK' diff --git a/backend/backend/api/export_to_folder.py b/backend/backend/api/export_to_folder.py index 371533c2..f72ac797 100755 --- a/backend/backend/api/export_to_folder.py +++ b/backend/backend/api/export_to_folder.py @@ -12,11 +12,10 @@ from flask import request, jsonify, make_response from sqlalchemy import func, and_, asc, or_ from sqlalchemy.orm import joinedload -from sqlalchemy.orm.exc import NoResultFound from sqlalchemy.sql import label from qaboard.utils import copy -from qaboard.conventions import deserialize_config, serialize_config +from qaboard.conventions import serialize_config from backend import app, db_session from ..models import Project, CiCommit, Batch, slugify_hash @@ -143,6 +142,7 @@ def key(x): @app.route("/api/v1/export/") def export_to_folder(): project_id = request.args['project'] + ref_project_id = request.args.get('ref_project', project_id) new_commit = load_commit(project_id, request.args['new_commit_id']) if not new_commit: @@ -151,7 +151,7 @@ def export_to_folder(): new_outputs = new_batch.outputs if request.args.get('ref_commit_id'): - ref_commit = load_commit(project_id, request.args['ref_commit_id']) + ref_commit = load_commit(ref_project_id, request.args['ref_commit_id']) if not ref_commit: return f"ERROR: Commit {request.args['ref_commit_id']} not found", 404 ref_batch = ref_commit.get_or_create_batch(request.args.get('batch_ref', 'default')) @@ -174,7 +174,10 @@ def export_to_folder(): query_string = f"{project_id} {new_commit.hexsha} {ref_commit.hexsha if ref_commit else ''} {new_batch.id} {ref_batch.id if ref_batch else ''} {filter_new} {filter_ref}" m = hashlib.md5(query_string.encode('utf-8')).hexdigest() export_dir = new_commit.repo_outputs_dir / 'share' / m[:8] - export_dir.mkdir(parents=True, exist_ok=True) + try: + export_dir.mkdir(parents=True, exist_ok=True) + except: + return json.dumps({"error": f"permission denied: '{export_dir}'"}), 403 output_refs = {} for output in new_outputs: diff --git a/backend/backend/api/integrations.py b/backend/backend/api/integrations.py index e3834c71..8ec7dce6 100755 --- a/backend/backend/api/integrations.py +++ b/backend/backend/api/integrations.py @@ -4,6 +4,8 @@ import os import re import time +import json +from urllib.parse import urlparse from flask import request, jsonify, make_response import requests @@ -12,28 +14,101 @@ from requests.auth import HTTPBasicAuth from backend import app - - -# FIXME: Currently we rely on environment variables for the gitlab/jenkins credentials -# We only allow 1 single instance of each, with a single auth. -# TODO: - Short term, we can at least read from os.environ["QABOARD_SECRETS"]=/etc/qaboard_secrets.json -# { -# secrets: [ -# { -# "host": "http://jensirc:8080", -# "auth": ("user", "token"), -# "headers": {"Jenkins-User-Crumb": "xxxxxxx"} -# }, -# ... -# ] -# } -# TODO: - Longer-term, we should use a centralized per user/project secret store +from ..config import qaboard_data_dir # We love our proxies import urllib3 urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning) + +# TODO: Currently all users/projects share gitlab/jenkins credentials. +# Longer-term, we should use a centralized per user/project secret store + + + + +def gitlab_session_cookie(hostname, user, password, user_type="user"): + """ + There is not way to get a session cookie via the gitlab API, but we need them.... + Beware this function is likely fragile and may break with future gitlab updates. + user_type: can be "user" for gitlab default users, or ldap_user with LDAP. There are likely other valid options... + """ + # https://stackoverflow.com/questions/47948887/login-to-gitlab-with-username-and-password-using-curl + with requests.Session() as s: + s = requests.Session() + # curl for the login page to get a session cookie and the sources with the auth tokens + r = s.get(f'{hostname}/users/sign_in') + matches = re.findall(r'", methods=['GET', 'PUT', 'DELETE']) +@app.route("/api/v1/output//", methods=['GET', 'PUT', 'DELETE']) +def crud_output(output_id): + output = Output.query.filter(Output.id==output_id).one() + if request.method == 'GET': + return jsonify(output.to_dict()) + + if request.method == 'PUT': + data = request.get_json() + if 'is_pending' in data: + output.is_pending = data['is_pending'] + if 'is_running' in data: + output.is_running = data['is_running'] + if 'is_failed' in data: + output.is_failed = data['is_failed'] + if 'data' in data: + output.data = {**output.data, **data['data']} + flag_modified(output, "data") + if 'metrics' in data: + output.metrics = {**output.metrics, **data['metrics']} + flag_modified(output, "metrics") + db_session.add(output) + db_session.commit() + return jsonify(output.to_dict()) + + if request.method == 'DELETE': + if output.is_pending: + return {"error": "Please wait for the Output to finish running before deleting it"}, 500 + soft = request.args.get('soft') == 'true' + output.delete(soft=soft) + if not soft: + db_session.delete(output) + db_session.commit() + return {"status": "OK"} + + + + + +@app.route("/api/v1/output//manifest", methods=['GET']) +@app.route("/api/v1/output//manifest/", methods=['GET']) +def get_output_manifest(output_id): + output = Output.query.filter(Output.id==output_id).one() + manifest_path = output.output_dir / "manifest.outputs.json" + if output.is_running or request.args.get('refresh') or not manifest_path.exists(): + manifest = output.update_manifest(compute_hashes=False) + return jsonify(manifest) + else: + # FIXME: in dev it will return http://backend/ and break the frontend who cannot connect + # in 2021 it seems the spec allow returning relative urls... + # Maybe we should return the manifest content instead... + # return redirect(dir_to_url(manifest_path), code=302) + response = make_response(manifest_path.read_text()) + response.headers['Content-Type'] = 'application/json' + return response + + + + + + + + +@app.route('/api/v1/output', methods=['POST']) +@app.route('/api/v1/output/', methods=['POST']) +def new_output_webhook(): + """Updates the database when we get new results.""" + data = request.get_json() + hexsha = data.get('commit_sha', data['git_commit_sha']) + # We get a handle on the Commit object related to our new output + try: + ci_commit = CiCommit.get_or_create( + session=db_session, + hexsha=hexsha, + project_id=data['project'], + data=data, + ) + except Exception as e: + return jsonify({"error": f"Could not find your commit ({data['git_commit_sha']}). {e}"}), 404 + + ci_commit.project.latest_output_datetime = datetime.datetime.utcnow() + ci_commit.latest_output_datetime = datetime.datetime.utcnow() + + # We make sure the Test on which we ran exists in the database + test_input_path = data.get('rel_input_path', data.get('input_path')) + if not test_input_path: + return jsonify({"error": "the input path was not provided"}), 400 + test_input = TestInput.get_or_create( + db_session, + path=test_input_path, + database=data['database'], + ) + + # We save the basic information about our result + batch = ci_commit.get_or_create_batch(data['batch_label']) + if not batch.data: + batch.data = {} + batch.data.update({"type": data['job_type']}) + if data.get('input_metadata'): + test_input.data['metadata'] = data['input_metadata'] + flag_modified(test_input, "data") + + platform = data['platform'] + # for backward-compat with old clients + if platform == 'lsf': + platform = 'linux' + + configurations = deserialize_config(data['configuration']) if 'configuration' in data else data['configurations'] + output = Output.get_or_create(db_session, + batch=batch, + platform=platform, + configurations=configurations, + extra_parameters=data['extra_parameters'], + test_input=test_input, + ) + output.output_type = data.get('input_type', '') + + output.data = data.get('data', {}) # e.g. storage, job_options + output.data["user"] = data['user'] + # we can only trust CI outputs to run on the exact code from the commit + output.data["ci"] = data['job_type'] == 'ci' + if output.deleted: + output.deleted = False + + # prefix_output_dir for backward-compatibility + ci_commit.commit_dir_override = data.get('artifacts_commit', data.get('commit_ci_dir')) + if not ci_commit.commit_dir_override.startswith('/'): # or "some-protocol://" + ci_commit.commit_dir_override = None # just ignore... + output.output_dir_override = data['output_directory'] + + # We update the output's status + output.is_running = data.get('is_running', False) + if output.is_running: + output.is_pending = True + else: + output.is_pending = data.get('is_pending', False) + + # We save the output's metrics + if not output.is_pending: + metrics = data.get('metrics', {}) + output.metrics = metrics + output.is_failed = data.get('is_failed', False) or metrics.get('is_failed') + + db_session.add(ci_commit) + db_session.add(output) + db_session.commit() + return jsonify(output.to_dict()) + diff --git a/backend/backend/api/tuning.py b/backend/backend/api/tuning.py index c4693a7b..0309e4f9 100755 --- a/backend/backend/api/tuning.py +++ b/backend/backend/api/tuning.py @@ -8,7 +8,6 @@ import datetime import itertools import subprocess -from pathlib import Path import yaml from flask import request, jsonify diff --git a/backend/backend/api/webhooks.py b/backend/backend/api/webhooks.py index 4eca5209..14f68a79 100755 --- a/backend/backend/api/webhooks.py +++ b/backend/backend/api/webhooks.py @@ -5,139 +5,14 @@ """ import sys import json -import yaml -import datetime -import traceback -import subprocess -from pathlib import Path from flask import request, jsonify -from sqlalchemy.orm.exc import NoResultFound from sqlalchemy.orm.attributes import flag_modified -from backend import app, repos, db_session -from ..models import Project, CiCommit, Batch, Output, TestInput +from backend import app, db_session +from ..models import CiCommit, Output from ..models.Project import update_project -from qaboard.conventions import deserialize_config - - -@app.route('/api/v1/batch', methods=['POST']) -@app.route('/api/v1/batch/', methods=['POST']) -def update_batch(): - data = request.get_json() - try: - ci_commit = CiCommit.get_or_create( - session=db_session, - hexsha=request.json['git_commit_sha'], - project_id=request.json['project'], - data=data, - ) - except: - return f"404 ERROR:\n ({request.json['project']}): There is an issue with your commit id ({request.json['git_commit_sha']})", 404 - - batch = ci_commit.get_or_create_batch(data['batch_label']) - # prefix_output_dir for backward-compatibility - batch.batch_dir_override = data.get("batch_dir", data.get("prefix_output_dir")) - - # Clients can store any metadata in each batch. - # Currently it's used by `qa optimize` to store info on iterations - if not batch.data: - batch.data = {} - batch_data = request.json.get('data', {}) - # And each batch can have changes vs its commit's config and metrics. - # The use case is usually working locally with `qa --share` and - # seeing updated visualizations and metrics. - if "qaboard_config" in data and data["qaboard_config"] != ci_commit.data["qatools_config"]: - batch.data["config"] = data["qaboard_config"] - if "qaboard_metrics" in data and data["qaboard_metrics"] != ci_commit.data["qatools_metrics"]: - batch.data["qatools_metrics"] = data["qaboard_metrics"] - batch.data = {**batch.data, **batch_data} - - # Save info on each "qa batch" command in the batch, mainly to list them in logs - command = request.json.get('command') - if command: - batch.data["commands"] = {**batch.data.get('commands', {}), **command} - flag_modified(batch, "data") - - # It's a `qa optimzize` experiment - if batch_data.get('optimization'): - if 'best_iter' in batch_data: - # we will save the outputs from the best iteration in the batch, - # so first we need to remove any previous best results - for o in batch.outputs: - if o.output_type != 'optim_iteration': - o.delete(soft=False) - db_session.add(batch) - db_session.commit() - # Move results from the best iteration in this batch - batch_batch_label = batch_data['last_iteration_label'] - best_batch = ci_commit.get_or_create_batch(batch_batch_label) - for o in best_batch.outputs: - o.output_dir_override = str(o.output_dir) - o.batch = batch - db_session.add(o) - db_session.commit() - - for b in ci_commit.batches: - if b.label.startswith(f"{data['batch_label']}|iter") and b.label != batch_data['last_iteration_label']: - print(f'Deleting previous iteration {b.label}') - if b.label != batch_data['last_iteration_label']: - db_session.delete(b) - - db_session.add(batch) - db_session.commit() - return jsonify({"status": "OK", "id": batch.id}) - - - -@app.route('/api/v1/batch/stop', methods=['POST']) -@app.route('/api/v1/batch/stop/', methods=['POST']) -def stop_batch(): - data = request.get_json() - try: - batch = Batch.query.filter(Batch.id == data['id']).one() - except: - return f"404 ERROR:\n Not found", 404 - status = batch.stop() - return jsonify(status), 200 if not "error" in status else 500 - -@app.route('/api/v1/batch/redo', methods=['POST']) -@app.route('/api/v1/batch/redo/', methods=['POST']) -def redo_batch(): - data = request.get_json() - try: - batch = Batch.query.filter(Batch.id == data['id']).one() - except: - return f"404 ERROR:\n Not found", 404 - status = batch.redo(only_deleted=data.get('only_deleted', False)) - return '{"status": "OK"}' - -@app.route('/api/v1/batch/rename', methods=['POST']) -@app.route('/api/v1/batch/rename/', methods=['POST']) -def rename_batch(): - data = request.get_json() - try: - batch = Batch.query.filter(Batch.id == data['id']).one() - except: - return f"404 ERROR:\n Not found", 404 - status = batch.rename(label=data['label'], db_session=db_session) - return '{"status": "OK"}' - - -@app.route('/api/v1/batch/', methods=['DELETE']) -@app.route('/api/v1/batch//', methods=['DELETE']) -def delete_batch(batch_id): - try: - batch = Batch.query.filter(Batch.id == batch_id).one() - except: - return f"404 ERROR:\nNot found", 404 - stop_status = batch.stop() - if "error" in stop_status: - return jsonify(stop_status), 500 - batch.delete(session=db_session, only_failed=request.args.get('only_failed', False)) - return {"status": "OK"} - @app.route('/api/v1/commit///batches', methods=['DELETE']) @app.route('/api/v1/commit///batches/', methods=['DELETE']) @@ -152,100 +27,18 @@ def delete_commit(commit_id, project_id=None): except Exception as e: return f"404 ERROR {e}: {commit_id} in {project_id}", 404 for ci_commit in ci_commits: + print("DELETING", ci_commit) if ci_commit.hexsha in ci_commit.project.milestone_commits: return f"403 ERROR: Cannot delete milestones", 403 - return "OK" for batch in ci_commit.batches: + print(f" > {batch}") stop_status = batch.stop() if "error" in stop_status: return jsonify(stop_status), 500 batch.delete(session=db_session) - return {"status": "OK"} - - - - -@app.route('/api/v1/output', methods=['POST']) -@app.route('/api/v1/output/', methods=['POST']) -def new_output_webhook(): - """Updates the database when we get new results.""" - data = request.get_json() - hexsha = data.get('commit_sha', data['git_commit_sha']) - # We get a handle on the Commit object related to our new output - try: - ci_commit = CiCommit.get_or_create( - session=db_session, - hexsha=hexsha, - project_id=data['project'], - data=data, - ) - except Exception as e: - return jsonify({"error": f"Could not find your commit ({data['git_commit_sha']}). {e}"}), 404 - - ci_commit.project.latest_output_datetime = datetime.datetime.utcnow() - ci_commit.latest_output_datetime = datetime.datetime.utcnow() - - # We make sure the Test on which we ran exists in the database - test_input_path = data.get('rel_input_path', data.get('input_path')) - if not test_input_path: - return jsonify({"error": "the input path was not provided"}), 400 - test_input = TestInput.get_or_create( - db_session, - path=test_input_path, - database=data['database'], - ) - - # We save the basic information about our result - batch = ci_commit.get_or_create_batch(data['batch_label']) - if not batch.data: - batch.data = {} - batch.data.update({"type": data['job_type']}) - if data.get('input_metadata'): - test_input.data['metadata'] = data['input_metadata'] - flag_modified(test_input, "data") - - platform = data['platform'] - # for backward-compat with old clients - if platform == 'lsf': - platform = 'linux' - - configurations = deserialize_config(data['configuration']) if 'configuration' in data else data['configurations'] - output = Output.get_or_create(db_session, - batch=batch, - platform=platform, - configurations=configurations, - extra_parameters=data['extra_parameters'], - test_input=test_input, - ) - output.output_type = data.get('input_type', '') - - output.data = data.get('data', {}) - # we can only trust CI outputs to run on the exact code from the commit - output.data["ci"] = data['job_type'] == 'ci' - if output.deleted: - output.deleted = False - - # prefix_output_dir for backward-compatibility - ci_commit.commit_dir_override = data.get('artifacts_commit', data.get('commit_ci_dir')) - output.output_dir_override = data['output_directory'] - - # We update the output's status - output.is_running = data.get('is_running', False) - if output.is_running: - output.is_pending = True - else: - output.is_pending = data.get('is_pending', False) - - # We save the output's metrics - if not output.is_pending: - metrics = data.get('metrics', {}) - output.metrics = metrics - output.is_failed = data.get('is_failed', False) or metrics.get('is_failed') + return {"status": "OK"} + return f"404 ERROR: Cannot find commit", 404 - db_session.add(ci_commit) - db_session.add(output) - db_session.commit() - return jsonify(output.to_dict()) diff --git a/backend/backend/clean.py b/backend/backend/clean.py index d8ec9a31..0501346e 100755 --- a/backend/backend/clean.py +++ b/backend/backend/clean.py @@ -32,34 +32,129 @@ """ import re +import sys +import json import datetime +import subprocess +from pathlib import Path import click from click import secho -from sqlalchemy import func, and_, asc, or_ +from sqlalchemy import func, and_, asc, or_, not_ from .database import db_session, Session +from .fs_utils import rmtree from .models import Project, CiCommit, Batch, Output now = datetime.datetime.utcnow() +# TODO: remove __all__ the output folders for deleted results +3months +# TODO: remove all files in artifacts by fixing permission issues + +def clean_untracked_hwalg_artifacts(): + """ + WARNING: don't run this unless you know what you are doing + """ + from .git_utils import git_pull + cache_path = Path('cache.milestones.json') + if cache_path.exists(): + secho("WARNING: Using CACHED MILESTONES commits", fg='yellow') + milestone_commits = set(json.loads(cache_path.read_text())) + else: + milestone_commits = set() + projects = (db_session + .query(Project) + .filter(Project.id.startswith('CDE-Users/HW_ALG')) + .filter(not_(Project.id.startswith('CDE-Users/HW_ALG/ALG_GEN'))) + ) + for project in projects: + print(project) + milestone_commits.update(set(project.milestone_commits)) + with cache_path.open('w') as f: + json.dump(list(milestone_commits), f) + secho(f"Protecting {len(milestone_commits)} commits", fg='blue') + + hwalg = db_session.query(Project).filter(Project.id == 'CDE-Users/HW_ALG').one() + git_pull(hwalg.repo) + artifacts_root = Path('/stage/algo_data/ci/CDE-Users/HW_ALG/commits') # 3. add parsing for the commits in this + # artifacts_root = Path('/stage/algo_data/ci/CDE-Users/HW_ALG') # 2. try this too... + artifacts_root = Path('/algo/CIS_artifacts/CDE-Users/HW_ALG') # 1. + def iter_hashsha_dir(): + # artifacts_root = Path('/stage/algo_data/ci/CDE-Users/HW_ALG/commits') + # for directory in artifacts_root.iterdir(): + # hexsha = directory.name.split('__')[-1] + # yield hexsha, directory + # return? + # artifacts_root = Path('/stage/algo_data/ci/CDE-Users/HW_ALG') + artifacts_root = Path('/algo/PSP_2x_artifacts/CDE-Users/HW_ALG') + artifacts_root = Path('/algo/KITT_ISP_artifacts/CDE-Users/HW_ALG') + artifacts_root = Path('/algo/CIS_artifacts/CDE-Users/HW_ALG') + for hash2 in artifacts_root.iterdir(): + if len(hash2.name) != 2: + continue + for hash16 in hash2.iterdir(): + hexsha = hash2.name + hash16.name + yield hexsha, hash16 + + for hexsha, artifact_dir in iter_hashsha_dir(): + try: + commit = hwalg.repo.commit(hexsha) + created_datetime = commit.authored_datetime + except: # force pushes, rebases... some commits won't be fetched + ctime = artifact_dir.stat().st_ctime + created_datetime = datetime.datetime.fromtimestamp(ctime).astimezone() + is_old = created_datetime < now.astimezone() - parse_time('3weeks') + if is_old and not any([c.startswith(commit.hexsha) for c in milestone_commits]): + print('DELETE', artifact_dir, created_datetime) + ci_commit = CiCommit( + hexsha=hexsha, + project=hwalg, + ) + try: + nb_manifests_dir = 0 + for qatools_path in artifact_dir.rglob('manifests'): + nb_manifests_dir += 1 + ci_commit.commit_dir_override = qatools_path.parent + print(ci_commit.commit_dir_override) + ci_commit.delete() + if not nb_manifests_dir: + ci_commit.commit_dir_override = artifact_dir + print(ci_commit.commit_dir_override) + ci_commit.delete() + except Exception as e: # empty parent folders will be deleted, including the folder we iterate in... + # __pycache__ can be owned by a different user that the one that created the folder... + print(e) + # return + + @click.command() @click.option('--project', 'project_ids', help="Regular expressions to match projects", multiple=True) @click.option('--before', help="Overwrites what's defined in the project config. 1month, 3days..") @click.option('--can-delete-reference-branch', is_flag=True, help="Allows deleting results on the reference branch (e.g. master/develop). The latest commit will be kept.") +@click.option('--can-delete-outputs/--cannot-delete-outputs', is_flag=True, default=True, help="Allows deleting artifacts.") @click.option('--can-delete-artifacts', is_flag=True, help="Allows deleting artifacts.") @click.option('--dryrun', is_flag=True) @click.option('--verbose', is_flag=True) -def clean(project_ids, before, can_delete_reference_branch, can_delete_artifacts, dryrun, verbose): +def clean(project_ids, before, can_delete_reference_branch, can_delete_outputs, can_delete_artifacts, dryrun, verbose): + if '--verbose' in sys.argv: + clean_untracked_hwalg_artifacts() + exit(0) + # if '--verbose' in sys.argv: + # from .clean_big_files import main + # main() + # exit(0) + if before and not project_ids: secho('[ERROR] when using --before you need to use --project', fg='red') exit(1) - projects = db_session.query(Project) + projects = db_session.query(Project) #.filter(Project.id == 'CDE-Users/HW_ALG/CIS') for project in projects: + if project.data.get("legacy"): + continue if project_ids and not any([re.match(project_id, project.id) for project_id in project_ids]): continue secho(project.id, fg='blue', bold=True) @@ -91,12 +186,19 @@ def clean(project_ids, before, can_delete_reference_branch, can_delete_artifacts commits = commits.filter(CiCommit.branch.notin_(project.protected_refs)) for commit in commits.all(): + # if '/algo/' not in str(commit.artifacts_dir): + # continue + # print(commit.artifacts_dir) + # cis_dir = str(self.artifacts_dir).replace("KITT_ISP", "CIS") + # continue secho(f"@{commit.project_id} {commit.branch} {commit.hexsha} {commit.authored_datetime}", fg='cyan') outputs = (db_session.query(Output).join(Batch).filter(Batch.ci_commit_id == commit.id)) nb_outputs = 0 nb_outputs_deleted = 0 for o in outputs: + if not can_delete_outputs: + continue nb_outputs += 1 if o.deleted: continue @@ -116,12 +218,15 @@ def clean(project_ids, before, can_delete_reference_branch, can_delete_artifacts gc_config_artifacts = gc_config.get('artifacts', {}) if gc_config_artifacts.get('delete') == True or can_delete_artifacts: secho(f" Deleting artifacts", fg='cyan', dim=True) - commit.delete(keep=gc_config_artifacts.get('keep', []), dryrun=dryrun) - + try: + commit.delete(keep=gc_config_artifacts.get('keep', []), dryrun=dryrun) + except Exception as e: + print(e) + continue if not dryrun: if nb_outputs_deleted: db_session.add(commit) - if not nb_outputs: + if not nb_outputs and can_delete_outputs: print(f"DELETE {commit}") db_session.delete(commit) db_session.commit() diff --git a/backend/backend/clean_big_files.py b/backend/backend/clean_big_files.py new file mode 100644 index 00000000..7667675a --- /dev/null +++ b/backend/backend/clean_big_files.py @@ -0,0 +1,57 @@ +#!/usr/bin/env python +import sys +import datetime +import subprocess +from pathlib import Path + +from sqlalchemy import func, and_, asc, or_, not_ + +from .database import db_session, Session +from .models import Output + + + +now = datetime.datetime.utcnow() +from .clean import parse_time +query_start = now - parse_time('6months') +# query_start = now - parse_time('1day') + + +def main(): + outputs = (db_session + .query(Output) + .filter(Output.created_date > query_start) + .order_by(Output.created_date.desc()) + ) + print(outputs.count()) + nb_bad_files = 0 + total_size = 0 + errors = [] + for output in outputs.all(): + if not output.output_dir.exists(): + continue + if not (output.output_dir / 'manifest.outputs.json').exists(): + output.update_manifest() + for path in output.output_dir.rglob('*'): + size = path.stat().st_size + if size > 1_000_000_000: + nb_bad_files += 1 + total_size += size + print(nb_bad_files, path, size) + try: + path.unlink() + except: + errors.append(path) + # exit(0) + # exit(0) + print(f"{nb_bad_files} files for {total_size}") + if errors: + print(f"ERRORS!") + for e in errors: + print(e) + # 237 + with Path('/home/arthurf/errors.txt').open('w') as f: + for e in errors: + print(e, file=f) + +main() \ No newline at end of file diff --git a/backend/backend/fs_utils.py b/backend/backend/fs_utils.py new file mode 100644 index 00000000..5b5fead0 --- /dev/null +++ b/backend/backend/fs_utils.py @@ -0,0 +1,143 @@ +""" +Deal with filesystem common needs and issues + +# delete a file with +# python backend/fs_utils.py 11611:10 ~/test.yaml +""" +import os +import pwd +import sys +import pickle +import shutil +import tempfile +import traceback +import subprocess +from pathlib import Path + + + + +def rmtree(path: Path) -> int: + nb_deleted = 0 + if path.is_dir(): # delete the children first + for p in path.iterdir(): + nb_deleted += rmtree(p) + + print("RM", path) + try: + if path.is_file(): + path.unlink() + else: + path.rmdir() + return 1 + except: + # Already deleted? + if not path.exists(): + return 0 + + # Permission issues? + # we need to be able to delete files owned by any user + # since we don't have access to the real NFS root, we need to su as the owner of each file + stat = path.stat() + try: + try: # the user running the server needs SETUID/SETGID capabilities + as_user(f"{stat.st_uid}:{stat.st_gid}", rmtree, path) + return 1 + except: # as a fallback, we can try to use sudo... + command = ["sudo", "-tt", "python", __file__, f"{stat.st_uid}:{stat.st_gid}", str(path)] + print(command) + subprocess.run(command, check=True) + return 1 + except Exception as e: + message = f"ERROR {e}: Could not remove: {path}" + print(message) + raise Exception(message) + + + + +def rm_empty_parents(path: Path): + for parent in path.parents: + is_empty = not any(parent.iterdir()) + if is_empty: + rmtree(parent) + else: + break + + +def as_user(user, f, *args, **kwargs): + """Call a function as a given user, assuming the current user can setuid/setgid (~root)""" + tf = tempfile.NamedTemporaryFile(delete=False) + Path(tf.name).chmod(0o777) + pid = os.fork() + if pid == 0: + # child - do the work and exit + try: + if ":" in user: + uid, gid = user.split(':') + uid = int(uid) + gid = int(gid) + else: + pwnam = pwd.getpwnam(user) + assert user == pwnam.pw_name + uid = pwnam.pw_uid + gid = pwnam.pw_gid + + os.setegid(gid) + os.seteuid(uid) + # print(user, os.geteuid(), os.getegid()) + print("as:", user) + # print("f:", f) + # print("args:", args) + # print("kargs:", kwargs) + try: + result = f(*args, **kwargs) + except Exception as e: + result = e + # print("result:", result) + pickle.dump(result, open(tf.name, 'wb'), pickle.HIGHEST_PROTOCOL) + # print("from child:", tf.name, Path(tf.name).read_bytes()) + except Exception as e: + print(f"ERROR in child process: {e}") + traceback.print_exc(file=sys.stdout) + finally: + os._exit(0) + # parent - wait for the child to do its work and keep going as root + pid, status = os.waitpid(pid, 0) + # print(pid, status) + if status != 0: + print(f"ERROR: Child ({pid}) exited with {status}") + os._exit(1) + # print("from parent", tf.name) + # print(Path(tf.name).read_bytes()) + # print(pickle.load(open(tf.name, 'rb'))) + return_value = pickle.load(open(tf.name, 'rb')) + if isinstance(return_value, Exception): + raise return_value + return return_value + + +# Before using setuid to delete files as their user, we would try more complicated things... +# This assumes all users are mapped in /etc/passwd, but it's annoying to maintain! +# from pwd import getpwnam +# def open_permissions(path): +# owner = path.owner() +# # FIXME: wrap the whole ssh arg with '' +# if owner == 'sircdevops': +# subprocess.run(f'ssh sircdevops@sircdevops-vdi chmod -R 777 "{path}"', shell=True, check=True) +# else: +# pwname = getpwnam(owner) +# owner = f"{pwname.pw_uid}:{pwname.pw_uid}" # TODO: need passwd up to date.. +# subprocess.run(f'ssh arthurf-vdi drun --cpu --skip_resources -v "{path}:{path}" --no-lsf -v /home/arthurf/gosu-i386:/usr/local/bin/gosu:ro ubuntu:trusty gosu {owner} chmod -R 777 "{path}"', shell=True, check=True) + + +if __name__ == "__main__": + if len(sys.argv) > 3 or len(sys.argv) == 1: + raise ValueError("Usage: [uid:gid] path-to-delete") + if len(sys.argv) == 2: + path = Path(sys.argv[1]) + rmtree(path) + else: + uid_gid = sys.argv[1] + path = Path(sys.argv[2]) + as_user(uid_gid, rmtree, path) diff --git a/backend/backend/git_utils.py b/backend/backend/git_utils.py index 3be41d17..d9ca4d21 100644 --- a/backend/backend/git_utils.py +++ b/backend/backend/git_utils.py @@ -4,6 +4,7 @@ from git import RemoteProgress from git.exc import NoSuchPathError +from .fs_utils import as_user class Repos(): """Holds data for multiple repositories.""" diff --git a/backend/backend/models/Batch.py b/backend/backend/models/Batch.py index 74f97c1b..f79f517a 100755 --- a/backend/backend/models/Batch.py +++ b/backend/backend/models/Batch.py @@ -1,8 +1,7 @@ """ -Represents SLAM runs belonging to the same commit. +Represents runs belonging to the same commit. It might by a CI job, or tuning experiments. """ -import re import datetime import json import subprocess @@ -25,7 +24,7 @@ class Batch(Base): __tablename__ = 'batches' id = Column(Integer, primary_key=True) - created_date = Column(DateTime, default=datetime.datetime.utcnow) + created_date = Column(DateTime, default=datetime.datetime.utcnow, nullable=False) data = Column(JSON(), nullable=False, default=dict, server_default='{}') ci_commit_id = Column(Integer(), ForeignKey('ci_commits.id'), index=True) @@ -57,9 +56,23 @@ def to_dict(self, with_outputs=False, with_aggregation=None): if with_outputs: outputs = {'outputs': {o.id: o.to_dict() for o in self.outputs}} else: - # we don't even supply a key, to make it easier for the JS code to - # just update the batch properties when it get the full version outputs = {} + valid_outputs = 0 + pending_outputs = 0 + running_outputs = 0 + failed_outputs = 0 + deleted_outputs = 0 + for o in self.outputs: + if not o.is_failed and not o.is_pending: + valid_outputs += 1 + if o.is_pending: + pending_outputs += 1 + if o.is_running: + running_outputs += 1 + if o.is_failed: + failed_outputs += 1 + if o.deleted: + deleted_outputs += 1 return { 'id': self.id, 'commit_id': self.ci_commit.hexsha, @@ -69,11 +82,11 @@ def to_dict(self, with_outputs=False, with_aggregation=None): 'batch_dir_url': dir_to_url(self.batch_dir), 'aggregated_metrics': aggregated_metrics(self.outputs, metrics_to_aggregate), - 'valid_outputs': len([o for o in self.outputs if not o.is_failed and not o.is_pending]), - 'pending_outputs': len([o for o in self.outputs if o.is_pending]), - 'running_outputs': len([o for o in self.outputs if o.is_running]), - 'failed_outputs': len([o for o in self.outputs if o.is_failed]), - 'deleted_outputs': len([o for o in self.outputs if o.deleted]), + 'valid_outputs': valid_outputs, + 'pending_outputs': pending_outputs, + 'running_outputs': running_outputs, + 'failed_outputs': failed_outputs, + 'deleted_outputs': deleted_outputs, **outputs, } @@ -84,23 +97,25 @@ def __repr__(self): def rename(self, label, db_session): assert not any([o.is_pending for o in self.outputs]) - # For now we could be computing those dirs based on the label... - # We avoid moving moving anything... - for output in self.outputs: - output.output_dir_override = str(output.output_dir) + # Note that the output directories will still be based on the old label, we don't move/copy anything self.label = label db_session.add(self) db_session.commit() - def redo(self, only_deleted=False): + def redo(self, only_failed=False, only_deleted=False): + success = True # in case it was deleted without QA-Board being made aware if not self.ci_commit.artifacts_dir.exists(): print("Restoring artifacts") self.ci_commit.save_artifacts() for output in self.outputs: + if only_failed and not output.is_failed: + continue if only_deleted and not output.deleted: continue - output.redo() + output_success = output.redo() + success = success and output_success + return success def stop(self): if not any([o.is_pending for o in self.outputs]): @@ -124,17 +139,22 @@ def stop(self): else: return {} - def delete(self, session, only_failed=False): + def delete(self, session, soft=False, only_failed=False): """ - Hard delete the batch and all related outputs. - Note: You should call .stop() before + Delete the batch and all related outputs. + By default it will be a "hard" delete where the metadata+files are deleted from the database/disk. + With soft deletes, only the files are deleted. + Note: You should call .stop() before. """ + still_has_outputs = False for output in self.outputs: if only_failed and not output.is_failed: + still_has_outputs = True continue - output.delete(soft=False) - session.delete(output) - if not only_failed: + output.delete(soft=soft) + if not soft: + session.delete(output) + if not still_has_outputs and not soft: session.delete(self) session.commit() diff --git a/backend/backend/models/CiCommit.py b/backend/backend/models/CiCommit.py index 6571efb8..5de81c51 100755 --- a/backend/backend/models/CiCommit.py +++ b/backend/backend/models/CiCommit.py @@ -19,7 +19,8 @@ from qaboard.api import dir_to_url from backend.models import Base, Batch, Output -from ..utils import get_users_per_name, rm_empty_parents +from ..utils import get_users_per_name +from ..fs_utils import rm_empty_parents, rmtree from ..git_utils import find_branch @@ -133,9 +134,8 @@ def outputs_dir(self): def __repr__(self): - outputs = f"ci_batch.outputs={len(self.ci_batch.outputs)}" if len(self.ci_batch.outputs) else '' branch = re.sub('origin/', '', self.branch) if self.branch else 'None' - return f"" + return f"" @@ -153,7 +153,8 @@ def __init__(self, hexsha, *, project, branch=None, message=None, parents=None, def save_artifacts(self): - # note: it won't restore binaries, users are expected to redo their CI on their own + # Restores the artifacts that are defined in the source code + # It won't restore binaries, users are expected to redo their CI on their own import tempfile import git from ..git_utils import git_pull @@ -162,10 +163,9 @@ def save_artifacts(self): git_pull(self.project.repo) self.project.repo.git.worktree("add", tmp_dir_path, self.hexsha) tmp_repo = git.Repo(tmp_dir_path) - if self.commit_dir_override: - subprocess.run(['qa', 'save-artifacts', '--out', str(self.repo_artifacts_dir)], cwd=tmp_dir_path / self.project.id_relative) - else: - subprocess.run(['qa', 'save-artifacts'], cwd=tmp_dir_path / self.project.id_relative) + command = ['qa', 'save-artifacts', '--out', str(self.artifacts_dir)] + print(command) + subprocess.run(command, cwd=tmp_dir_path / self.project.id_relative, check=True) def delete(self, ignore=None, keep=None, dryrun=False): """ @@ -203,7 +203,7 @@ def delete(self, ignore=None, keep=None, dryrun=False): if not dryrun: try: if file_to_delete.exists(): - file_to_delete.unlink() + rmtree(file_to_delete) rm_empty_parents(file_to_delete) nb_deleted += 1 except: @@ -212,16 +212,14 @@ def delete(self, ignore=None, keep=None, dryrun=False): # raise ValueError if not has_error: try: # FIXME: umask 0 when writing the manifest file! - manifest.unlink() + rmtree(manifest) except: pass delete_errors = delete_errors or has_error if not nb_manifests: print(f"[{self.authored_datetime}] No artifact manifests found. Deleting everything in {self.artifacts_dir}") - p = subprocess.run(f'rm -rf "{self.artifacts_dir}"', shell=True) + nb_deleted = rmtree(self.artifacts_dir) rm_empty_parents(self.artifacts_dir) - nb_deleted = 1 if p.returncode == 0 else 0 - print("nb_deleted", nb_deleted) if not delete_errors and nb_deleted: self.deleted = True @@ -331,8 +329,12 @@ def to_dict(self, with_aggregation=None, with_batches=None, with_outputs=False): "data": self.data, 'outputs_url': dir_to_url(self.outputs_dir), 'artifacts_url': self.artifacts_url, - 'batches': {b.label: b.to_dict(with_outputs=with_outputs, with_aggregation=with_aggregation) - for b in self.batches if not with_batches or b.label in with_batches}, + 'repo_artifacts_url': self.repo_artifacts_url, + 'batches': { + b.label: b.to_dict(with_outputs=with_outputs, with_aggregation=with_aggregation) + for b in self.batches + if not with_batches or b.label in with_batches + }, } if with_outputs: out["data"] = self.data diff --git a/backend/backend/models/Output.py b/backend/backend/models/Output.py index cb8dd270..559b9ec1 100755 --- a/backend/backend/models/Output.py +++ b/backend/backend/models/Output.py @@ -1,18 +1,20 @@ """ Describes an Output from `qa run`. """ +import os import re -import datetime -import hashlib import json +import hashlib import fnmatch +import datetime +import subprocess from pathlib import Path from requests.utils import quote from sqlalchemy import Column, ForeignKey, Index from sqlalchemy.orm import relationship from sqlalchemy.orm.exc import NoResultFound, MultipleResultsFound -from sqlalchemy import and_, Integer, String, Float, Boolean, DateTime, JSON +from sqlalchemy import text, and_, Integer, String, Float, Boolean, DateTime, JSON from sqlalchemy.dialects.postgresql import JSONB from qaboard.conventions import slugify, slugify_hash, make_hash, serialize_config @@ -20,6 +22,7 @@ from qaboard.api import dir_to_url from backend.models import Base +from backend.fs_utils import rmtree @@ -40,7 +43,7 @@ class Output(Base): # It is easier if there is a centralized way of storing results, but # we let people override this to use disk with different quotas # or even random folder (like for the CIS projects) - output_dir_override = Column(String()) + output_dir_override = Column(String(), index=True) #### What we ran # Different output types (slam/6dof, cis/siemens...) are visualized differently output_type = Column(String()) @@ -56,6 +59,10 @@ class Output(Base): # CREATE INDEX CONCURRENTLY idx_outputs_configurations ON outputs (configurations) # CREATE INDEX CONCURRENTLY idx_outputs_extra_parameters ON outputs (extra_parameters) __table_args__ = ( + # https://stackoverflow.com/questions/30885846/how-to-create-jsonb-index-using-gin-on-sqlalchemy + # https://www.postgresql.org/docs/8.3/indexes-opclass.html + # CREATE INDEX idx_outputs_data_user ON outputs((data -> 'user')); + Index('idx_outputs_data_user', text("(data->'user')")),#, postgresql_ops={'user': 'text_pattern_ops'}), Index('idx_outputs_filter', "batch_id", "test_input_id", "platform"), # we can't create an btree index on everything because JSON values can be big # https://github.com/doorkeeper-gem/doorkeeper/wiki/How-to-fix-PostgreSQL-error-on-index-row-size @@ -124,7 +131,6 @@ def __repr__(self): f"filename='{self.test_input.filename}' /]") def to_dict(self): - print() cols = [ 'id', 'output_type', @@ -198,19 +204,35 @@ def get_or_create(session, **kwargs): def redo(self): extra_parameters = json.dumps(self.extra_parameters, sort_keys=True) + job_options = self.data.get("job_options", {}) + job_options_cli = "" + if not job_options: + # for backward compatibility, it's a good defaut at SIRC + job_options_cli = "--lsf-max-memory 20000" + elif job_options['type'] == "lsf": + # TODO: support other runners... maybe create an ad-hoc functions in their classes... + if 'queue' in job_options: + job_options_cli += f"--lsf-queue '{job_options['queue']}'" + if 'max_memory' in job_options and job_options['max_memory'] != 0: + job_options_cli += f"--lsf-max-memory '{job_options['max_memory']}'" + if 'resources' in job_options and job_options['resources']: + job_options_cli += f"--lsf-resources '{job_options['resources']}'" + if 'max_threads' in job_options and job_options['max_threads'] != 0: + job_options_cli += f"--lsf-threads '{job_options['max_threads']}'" command = ' '.join([ 'qa', f'--label "{self.batch.label}"', f"--configuration '{self.configuration}'", f"--database '{self.test_input.database}'", + f"--type '{self.output_type}'", f"--tuning '{extra_parameters}'", 'batch', '--no-wait', - "--lsf-memory 12000", # TODO: not hardcoded? + job_options_cli, '--action-on-existing=run', '--action-on-pending=run', - # '--list', f'"{self.test_input.path}"', + # FIXME: if forwarded_args in parsed(self.configuration), add it.. ]) script = '\n'.join([ '#!/bin/bash', @@ -220,9 +242,11 @@ def redo(self): f"export GIT_COMMIT='{self.batch.ci_commit.hexsha}';", f"export QA_OUTPUTS_COMMIT='{self.batch.ci_commit.outputs_dir}'", f"export QABOARD_TUNING=true;", - f'export QA_BATCH_COMMAND_HIDE_LOGS=true' + f'export QA_BATCH_COMMAND_HIDE_LOGS=true', "", # get the env right + f'umask 0', + f'mkdir -p "{self.batch.ci_commit.artifacts_dir}"', f'cd "{self.batch.ci_commit.artifacts_dir}"', 'set +ex', '[[ -f ".envrc" ]] && source .envrc', @@ -234,13 +258,14 @@ def redo(self): ]) if not self.output_dir.exists(): self.output_dir.mkdir(parents=True) + logs_path = self.output_dir / 'log.txt' script_path = self.output_dir / 'redo.sh' with script_path.open('w') as f: f.write(script) - # print(script) print(f'"{script_path}"') - import os - os.system(f'bash "{script_path}"') + p = subprocess.run(f'bash "{script_path}" > "{logs_path}" 2>&1', shell=True) + success = p.returncode == 0 + return success def delete(self, soft=True, ignore=None, dryrun=False): @@ -256,7 +281,7 @@ def delete(self, soft=True, ignore=None, dryrun=False): return if not soft: - from shutil import rmtree + print(output_dir) rmtree(output_dir) else: # If a run crashes, or in case of network issues, the manifests may not be updated... @@ -270,17 +295,18 @@ def delete(self, soft=True, ignore=None, dryrun=False): if ignore: if any([fnmatch.fnmatch(file, i) for i in ignore]): continue - print(f'{output_dir / file}') + output_file = output_dir / file + if not output_file.exists(): + continue + print(f'{output_file}') if not dryrun: - try: - (output_dir / file).unlink() - except: # already deleted? - print(f"WARNING: Could not remove: {output_dir / file}") + rmtree(output_dir) self.deleted = True def update_manifest(self, compute_hashes=True): qatools_config = self.batch.ci_commit.project.data.get('qatools_config', {}) + os.umask(0) return save_outputs_manifest(self.output_dir, config=qatools_config, compute_hashes=compute_hashes) def update_metrics(self, filepath=None): diff --git a/backend/backend/models/Project.py b/backend/backend/models/Project.py index 4a6c5c4e..79574da0 100755 --- a/backend/backend/models/Project.py +++ b/backend/backend/models/Project.py @@ -41,10 +41,11 @@ def storage_roots(self): The locations where we save outputs and artifacts for this project. """ id_git = self.id_git - outputs_root, artifacts_root = storage_roots(self.data.get('qatools_config', {}), Path(self.id), Path(self.id_relative)) + qaboard_config = self.data.get('qatools_config', {}) try: - outputs_root, artifacts_root = storage_roots(self.data.get('qatools_config', {}), Path(self.id), Path(self.id_relative)) - except: + outputs_root, artifacts_root = storage_roots(qaboard_config, Path(self.id), Path(self.id_relative)) + except Exception as e: + print(e) outputs_root = default_outputs_root artifacts_root = default_artifacts_root return { @@ -220,6 +221,7 @@ def parsed_content(commit_id, path): session=db_session, hexsha=commit_id, project_id=project_id, + data={"commit_branch": branch}, ) except Exception as e: exc_type, exc_value, exc_traceback = sys.exc_info() diff --git a/backend/backend/models/TestInput.py b/backend/backend/models/TestInput.py index a3ac85ce..0f1aeb2c 100644 --- a/backend/backend/models/TestInput.py +++ b/backend/backend/models/TestInput.py @@ -37,8 +37,8 @@ class TestInput(Base): def output_folder(self): """returns test path without any extension""" input_dir = Path(self.path).with_suffix('') - if len(input_dir.as_posix()) > 90: - input_dir = Path(slugify_hash(input_dir.as_posix(), maxlength=90)) + if len(input_dir.as_posix()) > 70: + input_dir = Path(slugify_hash(input_dir.as_posix(), maxlength=70)) return input_dir diff --git a/backend/backend/models/User.py b/backend/backend/models/User.py new file mode 100644 index 00000000..59d4793c --- /dev/null +++ b/backend/backend/models/User.py @@ -0,0 +1,28 @@ +import datetime + +from flask_login import UserMixin +from sqlalchemy import Column, Integer, String, DateTime, Boolean + +from backend.models import Base + + +class User(Base, UserMixin): + __tablename__ = 'users' + + id = Column(Integer, primary_key=True) + created_date = Column(DateTime, default=datetime.datetime.utcnow, nullable=False) + + user_name = Column(String(), unique=True) + full_name = Column(String(), unique=True) + email = Column(String(), unique=True) + + password = Column(String()) + is_ldap = Column(Boolean(), default=False) + + def __repr__(self): + return (f" /home/arthurf/add_storage.log 2>&1 +Usage: +- docker-compose -f docker-compose.yml -f development.yml -f sirc.yml run --no-deps backend bash +- [arthurf] python backend/scripts/add_output_data_storage.py - run staging - deloy new cli @@ -8,61 +12,62 @@ - migrate json->jsonb - sql! """ +import os import json import time import datetime from sqlalchemy.orm.attributes import flag_modified from sqlalchemy import text -from qaboard.utils import total_storage, save_outputs_manifest +from qaboard.utils import total_storage, save_outputs_manifest, outputs_manifest from backend.models import Output from backend.database import db_session, Session db_session.autoflush = False +os.umask(0) -db_session batch_size = 1_000 output_total = 1_700_000 # est. start = time.time() -print('Adding storage info') def get_storage(output): manifest_path = output.output_dir / 'manifest.outputs.json' - if not manifest_path.exists(): - if not output.output_dir.exists(): - return 0 - else: - manifest = save_outputs_manifest(output.output_dir) - else: + if not output.output_dir.exists(): + return 0 + try: with manifest_path.open() as f: - try: - manifest = json.load(f) - except: # hello corrupted file - manifest = save_outputs_manifest(output.output_dir) - return total_storage(manifest) + manifest = json.load(f) + except: # e.g. if the manifest does not exist, if it is corrupted... + manifest = outputs_manifest(output.output_dir) + try: + with manifest_path.open('w') as f: + json.dump(manifest, f, indent=2) + except Exception as e: + print(f"[WARNING] Could not write the manifest: {e}") + finally: + return total_storage(manifest) def migrate(): batch = [] - batch_size = 500 - batch_size = 70000 - print(f'TOTAL {db_session.query(Output).count()}') - output_total = db_session.query(Output).filter(text("(data->'storage') is null")).filter(Output.is_pending==False).count() + batch_size = 500 + output_total = db_session.query(Output).filter(text("(data->'storage') is null")).count() start_batch = time.time() - print(f'without storage {output_total}') + print(f'Without storage {output_total}') outputs = (db_session.query(Output) .filter(text("(data->'storage') is null")) - .filter(Output.is_pending==False) + # .filter(Output.is_pending==False) + # .filter(text("outputs.created_date < now() - '15 days'::interval")) .order_by(Output.created_date.desc()) # .limit(10000) # .yield_per(batch_size) - .enable_eagerloads(False) + .enable_eagerloads(False) ) updated = 0 now = time.time() @@ -74,9 +79,18 @@ def migrate(): # continue try: + print(o.output_dir) + if "C:\\" in str(o.output_dir): + o.output_dir_override = o.output_dir_override.replace("\\", "/").replace("C:/netapp/algo_data", "/stage/algo_data") + if not o.output_dir_override.startswith("/stage/algo_data"): + continue + else: + db_session.add(o) + db_session.commit() storage = get_storage(o) + print(f" Storage: {storage/1024/1024:.2f}MB at {o.output_dir}") except Exception as e: - print("error", o, e) + print("[Error-Skipping]", o, e) continue if storage is None: continue @@ -98,60 +112,61 @@ def migrate(): batch = [] # break - print(f"DONE, now committing configurations [elapsed time: {now - start:.1f}s]") + print(f"DONE, now committing storage [elapsed time: {now - start:.1f}s]") db_session.bulk_update_mappings(Output, batch) db_session.flush() db_session.commit() return updated -while migrate(): - print('Still results to update...') -exit(0) +if __name__ == '__main__': + print('Adding storage info') + while migrate(): + print('Still results to update...') + exit(0) + print("Starting migration") + def query(since): + print(since) + return (db_session.query(Output) + .enable_eagerloads(False) + .filter(Output.created_date > since) + .order_by(Output.created_date.desc()) + # .limit(batch_size) + # .all() + # .yield_per(batch_size) + ) - -print("Starting migration") -def query(since): - print(since) - return (db_session.query(Output) - .enable_eagerloads(False) - .filter(Output.created_date > since) - .order_by(Output.created_date.desc()) - # .limit(batch_size) - # .all() - # .yield_per(batch_size) - ) - -print("Starting updates") -most_recent = datetime.datetime.now() - datetime.timedelta(days=7) -for idx, output in enumerate(query(most_recent)): - if output.is_pending: - continue - if output.data.get('storage'): - continue - - manifest_path = output.output_dir / 'manifest.outputs.json' - if not manifest_path.exists(): - if not output.output_dir.exists(): - output.data['storage'] = 0 - db_session.add(output) - flag_modified(output, "data") + print("Starting updates") + most_recent = datetime.datetime.now() - datetime.timedelta(days=7) + for idx, output in enumerate(query(most_recent)): + if output.is_pending: + continue + if output.data.get('storage'): continue + + manifest_path = output.output_dir / 'manifest.outputs.json' + if not manifest_path.exists(): + if not output.output_dir.exists(): + output.data['storage'] = 0 + db_session.add(output) + flag_modified(output, "data") + continue + else: + manifest = save_outputs_manifest(output.output_dir) else: - manifest = save_outputs_manifest(output.output_dir) - else: - with manifest_path.open() as f: - manifest = json.load(f) + with manifest_path.open() as f: + manifest = json.load(f) + manifest_path.chmod(0o777) - output.data['storage'] = total_storage(manifest) - flag_modified(output, "data") - db_session.add(output) + output.data['storage'] = total_storage(manifest) + flag_modified(output, "data") + db_session.add(output) - if idx % batch_size == 0: - print(f"{idx/output_total:.1%}", output, f"{output.data['storage']/1024/1024:.01f} MB") + if idx % batch_size == 0: + print(f"{idx/output_total:.1%}", output, f"{output.data['storage']/1024/1024:.01f} MB") -db_session.commit() + db_session.commit() diff --git a/backend/backend/scripts/add_output_data_user.py b/backend/backend/scripts/add_output_data_user.py new file mode 100644 index 00000000..75c7969e --- /dev/null +++ b/backend/backend/scripts/add_output_data_user.py @@ -0,0 +1,107 @@ +""" +python add_storage_info.py + +Usage: +- docker-compose -f docker-compose.yml -f development.yml -f sirc.yml run --no-deps backend bash +- [arthurf] python backend/scripts/add_output_data_storage.py + +- run staging +- deloy new cli +- run on prod +- migrate json->jsonb +- sql! +""" +import json +import time +import datetime + +from sqlalchemy.orm.attributes import flag_modified +from sqlalchemy import text +from qaboard.utils import total_storage, save_outputs_manifest, outputs_manifest + +from backend.models import Output +from backend.database import db_session, Session + +db_session.autoflush = False + + +db_session +batch_size = 1_000 + + +start = time.time() + + +def get_user(output): + if output.output_dir.exists(): + return output.output_dir.owner() + # TODO: fix the changed location with (output.output_dir.parent / input_path.name) + # if output.batch.ci_commit.artifacts_dir.exists(): + # return output.batch.ci_commit.artifacts_dir.owner() + # TODO: 1. batch command 2. committer + return None + +def migrate(): + batch = [] + batch_size = 2_000 + # batch_size = 70000 + output_total = db_session.query(Output).filter(text("(data->'user') is null")).count() + start_batch = time.time() + print(f'Without username {output_total}') + + outputs = (db_session.query(Output) + .filter(text("(data->'user') is null")) + .order_by(Output.created_date.desc()) + .enable_eagerloads(False) + .limit(10000) + ) + updated = 0 + now = time.time() + for idx, o in enumerate(outputs): + # print(o) + if o.data is None: + o.data = {} + # if '/' in o.batch.ci_commit.hexsha: + # continue + + try: + print(o.output_dir) + user = get_user(o) + print(f" User: {user}") + # exit(0) + except Exception as e: + print("[Error-Skipping]", o, e) + continue + if not user: + continue + updated += 1 + batch.append({ + "id": o.id, + "data": { + **o.data, + "user": user, + }, + }) + if idx and idx % batch_size == 0: + print(o) + now = time.time() + print(f"{idx/output_total:.1%} [{batch_size/(now - start_batch):.1f}/s] [est. total left {(now - start_batch) * ((output_total-idx)/batch_size) / 3600:.2f}h] [elapsed time: {now - start:.1f}s]") + start_batch = now + db_session.bulk_update_mappings(Output, batch) + db_session.flush() + batch = [] + # break + + print(f"DONE, now committing users [elapsed time: {now - start:.1f}s]") + db_session.bulk_update_mappings(Output, batch) + db_session.flush() + db_session.commit() + return updated + + + +if __name__ == '__main__': + print('Adding user info') + while migrate(): + print('Still work to do...') + exit(0) diff --git a/backend/backend/scripts/debug_missing_storage.py b/backend/backend/scripts/debug_missing_storage.py new file mode 100644 index 00000000..dfbf71e7 --- /dev/null +++ b/backend/backend/scripts/debug_missing_storage.py @@ -0,0 +1,113 @@ +import json +from datetime import datetime +from pathlib import Path + +from backend.models import Output +from backend.database import db_session, Session + +user = 'itamarp' +user = 'omera' + +# find /algo/HM6/outputs -user itamarp > itamarp.txt +owned_files_path = Path(f'/home/arthurf/qaboard/{user}.txt') +owned_files_info_path = owned_files_path.with_suffix('.info.txt') + +# NFS used 65536 blocks, but empty blocks don't count in the quotas +# so we can use the underlying FS block size +f_frsize = 4096 + +def update(): + nb_folders = 0 + nb_files = 0 + total_size = 0 + total_storage = 0 + files = [] + for line in owned_files_path.read_text().splitlines(): + nb_files += 1 + path = Path(line.strip()) + if not path.exists(): + print("missing", path) + continue + if path.is_dir(): + nb_folders += 1 + continue + size = path.stat().st_size + total_size += size + storage = (size // f_frsize) * f_frsize + f_frsize if size % f_frsize != 0 else 0 + total_storage += storage + files.append((str(path), size, storage)) + print(f"total_size {total_size/1024/1024:.3f}MB ({total_size})") + print(f"storage {total_storage/1024/1024:.3f}MB ({total_storage})") + print("nb_folders", nb_folders) + print("nb_files", nb_files) + total_size += nb_folders * 8 * 1024 + total_storage += nb_folders * 8 * 1024 + # total_storage += (nb_files - nb_folders) * 4096 + # inode? + print(f"total_size {total_size/1024/1024:.3f}MB ({total_size})") + print(f"storage {total_storage/1024/1024:.3f}MB ({total_storage})") + with owned_files_info_path.open('w') as f: + json.dump(files, f) + +refresh = False +# refresh = True +if not owned_files_info_path.exists() or refresh: + update() +with owned_files_info_path.open() as f: + files = json.load(f) +files_info = [(Path(path), size, storage) for path, size, storage in files] + +def filter_files(filter): + import re + files = [(path, size, storage) for path, size, storage in files_info if re.search(filter, str(path))] + total_storage = 0 + # files.sort(key=lambda x: -x[1]) + for path, size, storage in files[:50]: + print(f"{storage/1024/1024:.2f}MB", path) + total_storage += storage + print(f"filtered {filter} storage {total_storage/1024/1024:.3f}MB ({total_storage})") +# filter_files('(log(.lsf)?.txt|manifest)') +# filter_files('/share/') # 12G +# exit(0) + +# todo: check for files 1 parent is a dir with manifest.outputs.json + + +files = [path for path, size, storage in files_info] +# the manifest output files may end up owned by arthurf +output_dirs = set([path.parent for path in files if path.name == 'run.json']) + +def is_in_output_dirs(path): + return any([parent in output_dirs for parent in path.parents]) + +# for file in files: +# if file.is_file() and not is_in_output_dirs(file): +# # when tuning those files are created +# is_batch_related = file.name in ['start.sh', 'log.txt', 'qa_batch.sh'] +# is_from_export = '/share/' in str(file) +# if not is_batch_related and not is_from_export: +# print(file) +# exit(0) + + +print(len(output_dirs), "output directories") +max_ctime = 0 +output_dirs_missing = [] +for output_dir in output_dirs: + # find all run.json, check parentin + output = db_session.query(Output).filter(Output.output_dir_override==str(output_dir)).one_or_none() + if not output: + output_dirs_missing.append(output_dir) + ctime = output_dir.stat().st_ctime + print(datetime.fromtimestamp(ctime)) + if ctime > max_ctime: + max_ctime = ctime + print(output_dir) + # exit(0) + + +print(len(output_dirs), "output directories on disk") +print(len(output_dirs_missing), "missing in QA-Board - seems fine to delete") +print(max_ctime, "latest") +print(datetime.datetime.fromtimestamp(max_ctime)) +# TODO: check in DB wtf where is it? like dir ... \ No newline at end of file diff --git a/backend/backend/scripts/delete_orphan_output_dir.py b/backend/backend/scripts/delete_orphan_output_dir.py new file mode 100644 index 00000000..a869958b --- /dev/null +++ b/backend/backend/scripts/delete_orphan_output_dir.py @@ -0,0 +1,65 @@ +""" +docker-compose -f docker-compose.yml -f development.yml -f sirc.yml run --user=root --rm --no-deps -v /home/arthurf/qaboard/services/backend/passwd:/etc/passwd -e QABOARD_DATA_GIT_DIR=/home/arthurf -e MIGRATION_PROJECT backend python /qaboard/backend/backend/scripts/delete_orphan_output_dir.py +""" +import os +import sys +import shutil +from pathlib import Path + +from backend.models import Output +from backend.database import db_session, Session +from backend.fs_utils import as_user, rm_empty_parents, rmtree + + + + +root = Path("/algo/HP1/outputs") +# root = Path("/algo/HM6/outputs/omera/CDE-Users/HW_ALG/81/96978392ec9c86/CIS/tests/products/HM6/output") +root = Path("/algo/CIS/outputs/sircdevops") + +# output_dir_file = "run.json" +# output_dir_file = "kiwi_log.txt" +output_dir_file = "manifest.outputs.json" + +def delete(output_dir: Path): + for path in output_dir.iterdir(): + if path.name == output_dir_file: + continue + owner = path.owner() + def _delete(path): + if path.is_dir(): + shutil.rmtree(path) + else: + path.unlink() + try: + _delete(path) + except: + as_user(owner, _delete, path) + as_user((output_dir / output_dir_file).owner(), lambda p: p.unlink(), output_dir / output_dir_file) + # it causes the glob to fail... + # rm_empty_parents(path) + +directories = list(root.rglob(output_dir_file)) +print(f"{len(directories)} directories will be checked") +errors = [] +for run_json in directories: + output_dir = run_json.parent + output = None + try: + output = db_session.query(Output).filter(Output.output_dir_override==str(output_dir)).one_or_none() + except Exception as e: + print("ERROR:", output_dir) + print(e) + if not output: + print(f"? {output_dir}") + try: + rmtree(output_dir) + except: + errors.append(output_dir) +for error in errors: + print(error) + +# in algo/hm6/omera still more that what should be... +# find /algo/HM6/outputs -name omera > omera.txt + +# ? data folder / version \ No newline at end of file diff --git a/backend/backend/scripts/delete_remaining_data_from_deleted_outputs.py b/backend/backend/scripts/delete_remaining_data_from_deleted_outputs.py new file mode 100644 index 00000000..92379513 --- /dev/null +++ b/backend/backend/scripts/delete_remaining_data_from_deleted_outputs.py @@ -0,0 +1,83 @@ +""" +cd qaboard +docker-compose -f docker-compose.yml -f development.yml -f sirc.yml run --rm --user=root --no-deps -v /home/arthurf/qaboard/services/backend/passwd:/etc/passwd backend python /qaboard/backend/backend/scripts/delete_remaining_data_from_deleted_outputs.py +""" +import sys +import time +import shutil +import traceback + +import click + +from backend.models import Output +from backend.database import db_session, Session + +from migration_utils import get_username +from backend.fs_utils import as_user +from migration_utils import rm_files_not_listed_in_manifests + +dryrun = '--dry-run' in sys.argv +# Progress will be printed every batch/100 +batch_size = 10_000 +start = time.time() + + +def check_output(output): + try: + output_dir_exists = output.output_dir.exists() + except: + output_dir_exists = False + if output_dir_exists: + print(f"[{output.id}]", output.output_dir) + try: + output.delete(soft=False) + except: + delete = lambda o: o.delete(soft=False) + owner = output.output_dir.owner() + as_user(owner, delete, output) + + + +def run_delete(min_id): + deleted_outputs = (db_session + .query(Output) + .filter(Output.deleted==True) + ) + if min_id: + deleted_outputs = deleted_outputs.filter(Output.id >= min_id) + deleted_outputs = (deleted_outputs + .order_by(Output.created_date.asc()) + .enable_eagerloads(False) + ) + output_total = deleted_outputs.count() + click.secho(f'- outputs to check: {output_total}', bold=True, fg='blue') + should_continue = output_total > batch_size + + start_batch = time.time() + updated = 0 + now = time.time() + + for idx, o in enumerate(deleted_outputs.limit(batch_size)): + # o, batch, commit = result + check_output(o) + if idx and idx % batch_size/100 == 0: + print(o) + print(o.batch.ci_commit) + now = time.time() + print(f"{idx/output_total:.1%} [{batch_size/(now - start_batch):.1f}/s] [est. total left {(now - start_batch) * ((output_total-idx)/batch_size) / 3600:.2f}h] [elapsed time: {now - start:.1f}s]") + start_batch = now + return updated, o.id, should_continue + + +def main(): + # Optionnally, you can give an id to start from... + last_id = 3457400 # None + + should_continue = True + while should_continue: + click.secho('Deleting...', bold=True, fg='blue') + nb_updated, last_id, should_continue = run_delete(last_id) + click.secho(f"nb_updated={nb_updated}, last_id={last_id}, should_continue={should_continue}", fg='blue') + click.secho('DONE', fg='green') + +main() diff --git a/backend/backend/scripts/fix-nobody-manifest.py b/backend/backend/scripts/fix-nobody-manifest.py new file mode 100644 index 00000000..6892a055 --- /dev/null +++ b/backend/backend/scripts/fix-nobody-manifest.py @@ -0,0 +1,77 @@ +""" +Usage: +- docker-compose -f docker-compose.yml -f development.yml -f sirc.yml run --no-deps backend bash +- [arthurf] python backend/scripts/fix-nobody-manifest.py +""" +import os +import json +import time +import datetime +from pathlib import Path + +from sqlalchemy.orm.attributes import flag_modified +from sqlalchemy import text +from qaboard.utils import total_storage, save_outputs_manifest, outputs_manifest + +from backend.models import Output +from backend.database import db_session, Session + +db_session.autoflush = False + +os.umask(0) + + + +def get_storage(output): + manifest_path = output.output_dir / 'manifest.outputs.json' + if not output.output_dir.exists(): + return 0 + try: + with manifest_path.open() as f: + manifest = json.load(f) + except: # e.g. if the manifest does not exist, if it is corrupted... + manifest = outputs_manifest(output.output_dir) + try: + with manifest_path.open('w') as f: + json.dump(manifest, f, indent=2) + except Exception as e: + print(f"[WARNING] Could not write the manifest: {e}") + finally: + return total_storage(manifest) + + +def migrate(): + outputs = (db_session.query(Output) + .filter(text("outputs.created_date > now() - '2 days'::interval")) + .order_by(Output.created_date.desc()) + .enable_eagerloads(False) + ) + updated = 0 + now = time.time() + for idx, o in enumerate(outputs): + # try: + manifest_path = o.output_dir / 'manifest.outputs.json' + if 'C:\\' in str(manifest_path): + continue + if not manifest_path.exists() or manifest_path.owner() == 'nobody' or manifest_path.owner() == 'arthurf': + print(o.id, o.output_dir) + if manifest_path.exists(): + manifest_path.unlink() + storage = get_storage(o) + o.data['storage'] = storage + db_session.add(o) + flag_modified(o, "data") + db_session.commit() + # except Exception as e: + # print("[Error-Skipping]", o, e) + # continue + + + return updated + + +if __name__ == '__main__': + while migrate(): + print('Still results to update...') + + diff --git a/backend/backend/scripts/fix_bad_output_dir_name.py b/backend/backend/scripts/fix_bad_output_dir_name.py new file mode 100644 index 00000000..b84d1f73 --- /dev/null +++ b/backend/backend/scripts/fix_bad_output_dir_name.py @@ -0,0 +1,124 @@ +#!/usr/bin/env python +""" +Fix stuff. +docker-compose -f docker-compose.yml -f development.yml -f sirc.yml run --rm --no-deps -v /home/arthurf/qaboard/services/backend/passwd:/etc/passwd -e QABOARD_DATA_GIT_DIR=/home/arthurf backend python /qaboard/backend/backend/scripts/fix_bad_output_dir_name.py +""" +import os +import sys +import time +import shutil +import traceback +from pathlib import Path + +import click +import requests +from sqlalchemy.orm.attributes import flag_modified +from sqlalchemy import text + +from backend.models import Project, CiCommit, Batch, Output +from backend.database import db_session, Session + +from migration_utils import get_username + + +# Progress will be printed every batch/100 +batch_size = 10_000 +start = time.time() + + +# TODO +# ? go over all deleted outputs +# make sure deleted, delete parents + + +def migrate_output(output): + if output.output_dir.exists(): + return + + tentative_output_dir = output.output_dir.parent / Path(output.test_input.path).with_suffix('').name + if not tentative_output_dir.exists(): + click.secho(f" ? {output.output_dir_override}") + click.secho(f" {output}") + click.secho(f" {output.test_input}") + return + + output.output_dir_override = str(tentative_output_dir) + output.data["user"] = tentative_output_dir.owner() + click.secho(f" ✔ {output.data['user']} {output.output_dir_override}", fg='green') + # exit(0) + + + flag_modified(output, "data") + db_session.add(output) + db_session.commit() + # click.secho(" 🆗", fg='green') + # exit(0) + + +def migrate(min_id): + # it's an aweful join... + all_outputs = (db_session + .query(Output) + ) + if min_id: + all_outputs = all_outputs.filter(Output.id >= min_id) + outputs = (all_outputs + # .filter(text("(outputs.data->'migrated') is null")) + .filter(text("outputs.output_dir_override is not null")) + .filter(text("outputs.output_dir_override like '/algo%'")) + # .filter(text("outputs.created_date < now() - '15 days'::interval")) + # .filter(text("output_dir_override like '/stage/algo_data/ci/CDE-Users/HW_ALG/%/CIS/output%'")) + # .filter(Output.is_pending==False) + # .filter(Output.deleted==False) + .order_by(Output.created_date.asc()) + .enable_eagerloads(False) + ) + click.secho(f'- outputs total: {all_outputs.count()}', bold=True, fg='blue') + output_total = outputs.count() + click.secho(f'- outputs to migrate: {output_total}', bold=True, fg='blue') + should_continue = output_total > batch_size + start_batch = time.time() + updated = 0 + now = time.time() + + if not output_total: + for result in all_outputs.limit(1): + o = result + # o, batch, commit = result + print(o) + print(o.output_dir) + return updated, None, should_continue + + for idx, result in enumerate(outputs.limit(batch_size)): + o = result + # print(o, batch, commit) + if o.data is None: + o.data = {} + ## legacy outputs from the previous CI + # if '/' in o.batch.ci_commit.hexsha: + # continue + + migrate_output(o) + if idx and idx % batch_size/100 == 0: + print(o) + print(o.batch.ci_commit) + now = time.time() + print(f"{idx/output_total:.1%} [{batch_size/(now - start_batch):.1f}/s] [est. total left {(now - start_batch) * ((output_total-idx)/batch_size) / 3600:.2f}h] [elapsed time: {now - start:.1f}s]") + start_batch = now + return updated, o.id, should_continue + + +def main(): + # Optionnally, you can give an id to start from... + # it helps if there are many non-migrated runs that fail because of whatever and + # you don't want to wait until the migration fails to migrate them again! + last_id = None #1245250 # None + + should_continue = True + while should_continue: + click.secho('Migrating...', bold=True, fg='blue') + nb_updated, last_id, should_continue = migrate(last_id) + click.secho(f"nb_updated={nb_updated}, last_id={last_id}, should_continue={should_continue}", fg='blue') + click.secho('DONE', fg='green') + +main() diff --git a/backend/backend/scripts/gen_parallel_migration.py b/backend/backend/scripts/gen_parallel_migration.py new file mode 100755 index 00000000..a28f5904 --- /dev/null +++ b/backend/backend/scripts/gen_parallel_migration.py @@ -0,0 +1,82 @@ +#!/usr/bin/env python +""" +Usage: + cd qaboard + ./backend/backend/scripts/gen_parallel_migration.py CDE-Users/HW_ALG/CIS 10 + ./backend/backend/scripts/gen_parallel_migration.py --all 10 + bash migration/start.sh + +Needs a server to sync user quotas.. +- python backend/backend/scripts/user_storage_server.py +- update the server location in migrate.py with QUOTA_SERVER + +Note: +- Best not run this on the production server, just in case +""" +import os +import sys +from pathlib import Path + + +def gen_script(project, parallel_jobs, start=False): + yamls = "-f docker-compose.yml -f development.yml -f sirc.yml" + start_script = "" + migration_dir = Path('migration') + migration_dir.mkdir(exist_ok=True) + + for i in range(parallel_jobs): + project_name = project.split('/')[-1] + logs = migration_dir / f"{project_name}-{i:02}.txt" + script = migration_dir / f"{project_name}-{i:02}.sh" + with script.open('w') as f: + f.write(f"""#!/bin/bash +set -x +export MIGRATION_PROJECT={project} +export MIGRATION_JOBS={parallel_jobs} +export MIGRATION_INDEX={i} + +# Avoid "Too many levels of symbolic links" errors +./at-sirc-before-up.py --shallow > /dev/null + +docker-compose {yamls} pull backend +docker-compose {yamls} run --rm --user=root --no-deps -v /home/arthurf/qaboard/services/backend/passwd:/etc/passwd -e QABOARD_DATA_GIT_DIR=/home/arthurf -e MIGRATION_PROJECT -e MIGRATION_INDEX -e MIGRATION_JOBS backend /qaboard/backend/backend/scripts/migrate.py +# docker-compose {yamls} down -v +""") + command = f" bsub -q alg_isp_q -P migration -o {logs} bash {script}" + start_script += f"{command}\n" + + start_script_path = migration_dir / f"{project_name}-start.sh" + with start_script_path.open('w') as f: + f.write(start_script) + start_command = f"bash {start_script_path}" + print("# To start the migration, run:") + print(start_command) + os.system(start_command) + + +if len(sys.argv) < 2: + print("ERROR: Usage is gen_parallel_migration.py $project [nb_parallel_jobs=1]") + sys.exit(1) +parallel_jobs = int(sys.argv[2]) if len(sys.argv) > 2 else 1 + +project = sys.argv[1] +if project != "--all": + gen_script(project, parallel_jobs=parallel_jobs) +else: + # import requests + # projects = requests.get("https://qa/api/v1/projects", verify=False).json() + projects = [ + # "CDE-Users/HW_ALG/CIS/tests/products/HM2", 8T 38k . + # "CDE-Users/HW_ALG/CIS/tests/products/HM3", 18T 126k + # "CDE-Users/HW_ALG/CIS/tests/products/HP1", 13T 57k + # "CDE-Users/HW_ALG/PSP_2x", 3.8T 270k . + # "CDE-Users/HW_ALG/PSP_2x/tests/products/ASPv43", 1T 20k . + # "LSC/Calibration", + # "tof/swip_tof", + # "tof/python_isp_chain", + # "dvs/SIRC-VINS", + ] + for project in projects: + if "HW_ALG" in project: + print(f"Migrating {project}") + gen_script(project, parallel_jobs=parallel_jobs, start=True) diff --git a/backend/backend/scripts/migrate.py b/backend/backend/scripts/migrate.py new file mode 100755 index 00000000..a432c050 --- /dev/null +++ b/backend/backend/scripts/migrate.py @@ -0,0 +1,386 @@ +#!/usr/bin/env python +""" +Migrates a projects' outputs to their default location. + +Usage: +0. Clean old results.. + ssh qa + docker-compose -f docker-compose.yml -f development.yml -f sirc.yml exec -T backend qaboard_clean --project 'CDE-Users/HW_ALG/CIS$' --before 3months --can-delete-reference-branch # --can-delete-artifacts +1. Save the remote user list + $ getent --service=sss passwd >> ./services/backend/passwd + Manually remove those entries and redo if needed... +2. Needs a server to sync user quotas.. + $ python backend/backend/scripts/user_storage_server.py + # update the server location in migrate.py with QUOTA_SERVER +3. You'll run the gen_parallel_migration.py in the end... + +-- how much left to migrate? +SQL STORAGE +select + projects.id, + to_char(sum((outputs.data->>'storage')::text::numeric/1000000000), '9999999999999.99') as storage_GB, + count(*) as nb +from outputs + left join batches on batches.id=outputs.batch_id + left join ci_commits on ci_commits.id=batches.ci_commit_id + left join projects on projects.id=ci_commits.project_id +where + -- outputs.data->'migrated' is null + "output_dir_override" is not null + -- and outputs.created_date < now() - '14 days'::interval + -- and outputs.deleted=false + and ("output_dir_override" not like '/algo%') + -- and ("output_dir_override" like '/stage/algo_data/ci/CDE-Users/HW_ALG/%/KITT_ISP/output%') + -- and ("output_dir_override" like '/stage/algo_data/ci/CDE-Users/HW_ALG/%/KITT_ISP/output%' or "output_dir_override" like '/algo/KITT_ISP%') + -- and projects.data->>'legacy' is null + and (projects.id like '%HW%' or projects.id like '%dvs%' or projects.id like '%tof%') +group by projects.id; +--limit 10; + + +-- 2 264 674 at 23:30 +-- 2 050 619 at 09:08 + + + + + + +select to_char(sum((data->>'storage')::text::numeric/1000000000), '9.9') as storage from outputs where ("output_dir_override" like '/stage/algo_data/ci/CDE-Users/HW_ALG/%/CIS/output%') limit 10; + +-- wtf... +select count(*) from outputs where "output_dir_override" is NULL limit 10; +select * from outputs where "output_dir_override" is NULL and deleted=false order by created_date desc limit 100; + + +Usage: + migrate.py PROJECT [--dry-run] + e.g. + migrate.py CDE-Users/HW_ALG/CIS --dry-run + + +Note: +- Best not run this on the production server, just in case +""" +import os +import re +import sys +import time +import random +import shutil +import traceback +from pathlib import Path +from add_output_data_storage import get_storage + +import click +import requests +from sqlalchemy.orm.attributes import flag_modified +from sqlalchemy import text + +from backend.models import Project, CiCommit, Batch, Output +from backend.database import db_session, Session +from backend.fs_utils import as_user, rm_empty_parents + +from migration_utils import get_username +from migration_utils import rm_files_not_listed_in_manifests + +# TODO +# - [TODO CHECK tmux alginfra1] remove old deleted stuff with delete_remaining_data_from_deleted_runs.py +# - [TODO] ./backend/backend/scripts/gen_parallel_migration.py --all 15 +# - [TODO] rg Missing migration +# - [TODO] add missing users in migration_utils.py +# - [TODO] ./backend/backend/scripts/gen_parallel_migration.py --all 15 +# - [TODO] add missing users in migration_utils.py +# - [TODO] check in SQL all is done! +# - remove deleted=False filter in the delete, check if there is data, if yes remove completely the folder and parents... +# /algo/CIS/outputs/nimrodn/CDE-Users/HW_ALG/ed/1f2abce82c7bb2/CIS/output/linux/RV1/tv/tv_RV1_512x256_REMOSAIC_FULL_V1 + + +# Some output directories depend on the current user. +# We'll switch user a lot, so we don't want to cache the current user. +os.environ['QABOARD_NO_CACHE_USER'] = "YES" + +# At SIRC we cannot be root on the shared storage, so +# we need to su the proper users in order to migrate their runs. +# This flag controls the extra work to get it right +# at_sirc = False +at_sirc = True + + +project = os.environ["MIGRATION_PROJECT"] if "MIGRATION_PROJECT" in os.environ else sys.argv[1] +project_name = project.split('/')[-1] +if "ALG_GEN" in project: + project_name = "CIS" +dryrun = '--dry-run' in sys.argv + +# Progress will be printed every batch/100 +batch_size = 10_000 +start = time.time() + +# We parallelize the migration, each worker handles a given idx modulo parts_nbr +parts_nbr = int(os.environ.get('MIGRATION_JOBS', 0)) +parts_idx = int(os.environ.get('MIGRATION_INDEX', 0)) +if parts_nbr: + click.secho(f"[Migration Job {parts_idx+1}/{parts_nbr}]", bold=True) + +# Everything is simpler if all folders/files are writable by everyone +# We don't have any trust issue, and everything is backed-up, so no need to bother +# Otherwise down the line it's yet more trouble +os.umask(0) + + +quota_server = os.environ.get('QUOTA_SERVER', "http://qa:3001") +def fetch_quota(user, project): + r = requests.get(f"{quota_server}/user/{user}/storage/project/{project_name}?proxies=cache-buster") + try: + return r.json() + except Exception as e: + print(r.text) + raise e + +def add_storage(user, project, storage): + return requests.get(f"{quota_server}/user/{user}/storage/project/{project_name}/add?usage={storage}").json() + + +def move_files(before_dir: Path, after_dir: Path, output: Output): + # print(before_dir, after_dir) + if before_dir.exists(): # needs_migration + try: + # /before/path/a + # /after/path/b + after_dir.parent.mkdir(parents=True, exist_ok=True) # /after/path + if before_dir.name != after_dir.name: + after_dir = after_dir.parent / before_dir.name + if not after_dir.exists(): + shutil.move(str(before_dir), str(after_dir.parent)) + else: + for path in before_dir.iterdir(): + if not (after_dir / path.relative_to(before_dir) ).exists(): + shutil.move(str(path), str(after_dir)) + rm_empty_parents(before_dir) + # # TODO: we should delete the dirs for very old outputs... + # if output.deleted: + # rm_files_not_listed_in_manifests(after_dir) + except Exception as e: + click.secho(f" ERROR: {e}", bold=True, fg='red') + traceback.print_exc(file=sys.stdout) + exit(1) + + + +users_with_max_quota = set() + +def migrate_output(output): + if not output.output_dir_override: + print("MISSING output.output_dir_override") + print("- output.id", output.id) + print("- output.batch", output.batch) + print("- output.ci_commit", output.batch.ci_commit) + print("- output.project", output.batch.ci_commit.project) + # for those... just delete we alreadt cannot reach them + return + + before_dir = output.output_dir + # we unset those to make sure we get the default value + output.output_dir_override = None + output.batch.batch_dir_override = None + output.batch.ci_commit.commit_dir_override = None + # get the committer name -> login (here we wish we had saved the email too...) + if at_sirc: + username = get_username(output.batch.ci_commit) + if not username: + return + os.environ['LOGNAME'] = username + after_dir = output.output_dir + + if 'products/HM2P/output/' in str(after_dir): + after_dir = Path(str(after_dir).replace('/stage/algo_data/ci/CDE-Users/HW_ALG', '/algo/HM2P')) + if '/HEX/' in str(after_dir): + after_dir = Path(str(after_dir).replace('/HEX/', '/HP2/')) + match = re.search("PSP_2x/tests/products/([0-9A-Za-z]+)/output", str(after_dir)) + if match: + product = match.groups(0)[0] + if product == 'ASP51': + product = "ASPv5" + after_dir = Path(str(after_dir).replace('/stage/algo_data/ci/CDE-Users/HW_ALG', f'/algo/{product}')) + if '/DVS/tests/products/' in str(after_dir): + after_dir = Path(str(after_dir).replace('/stage/algo_data/ci/CDE-Users/HW_ALG', '/algo/DVS')) + if '/tests/common/scripts/SCD/output': + after_dir = Path(str(after_dir).replace('/stage/algo_data/ci/CDE-Users/HW_ALG', '/algo/CIS')) + if '/tests/blocks/AAG/output' in str(after_dir) or '/tests/blocks/GBPC/workspace/output' in str(after_dir) or '/tests/blocks/VISION_SCD/output' in str(after_dir): + after_dir = Path(str(after_dir).replace('/stage/algo_data/ci/CDE-Users/HW_ALG', '/algo/CIS')) + if '/mnt/qaboard/igorf' in str(after_dir): + after_dir = Path(str(after_dir).replace('/mnt/qaboard/igorf', '/algo/CIS/outputs/igorf/CDE-Users/HW_ALG')) + username = 'igorf' + if '/home/arthurf/ci' in str(after_dir): + after_dir = Path(str(after_dir).replace('/home/arthurf/ci', '/algo/DVS')) + if '/home/yotama/ci' in str(after_dir): + after_dir = Path(str(after_dir).replace('/home/yotama/ci', '/algo/DVS')) + if '/stage/algo_data/ci/dvs' in str(after_dir): + after_dir = Path(str(after_dir).replace('/stage/algo_data/ci', '/algo/DVS')) + + # click.secho(str(output)) + click.secho(f"{output.id} {'[deleted]' if output.deleted else ''}") + click.secho(f" ♻ {before_dir}", dim=True) + if '/algo' not in str(after_dir): + print(after_dir) + exit(0) + + needs_migration = str(before_dir) != str(after_dir) + if not needs_migration: + click.secho(f" Looks OK!", dim=True) + + if 'storage' not in output.data: + print("missing storage...") + try: + exists = as_user("sircdevops", lambda: output.output_dir.exists()) + if not exists: + storage = 0 + else: + owner = as_user("sircdevops", lambda: output.output_dir.owner()) + # print(f"> {owner}") + # owner = output.output_dir.owner() + # print("output_dir owner:", owner) + storage = as_user(owner, get_storage, output) + except Exception as e: + print(e) + exit(0) + try: + storage = as_user('sircdevops', get_storage, output) + except: + click.secho(f" .. ERROR permission issue...", dim=True) + return + print(storage) + output.data['storage'] = storage + + storage = float(output.data['storage']) / 1024 + # print(quota, storage) + + click.secho(f" ✔ {after_dir}") + if dryrun: + return + + if not needs_migration: + return + + # ldapsearch -t -L -H ldap://dc04.transchip.com -b 'dc=transchip,dc=com' -D "cn=Ldap Query,ou=IT,ou=SIRC Users,dc=transchip,dc=com" -x -w LQstc009 -s sub "(memberOf=CN=Sensor_Algorithms,OU=Groups,OU=SIRC Users,DC=transchip,DC=com)" | grep 'sAMAccountName:' + fillers = ["dima","oded","guy","itail","arielo","haim","igal","galb","yahavs","erand","arthurf","royy","shahafd","rivkae","amichaya","shais","taeerw","royp","matand","davidn","nimrodn","eitanl","matanh","mandyr","talb","eliavm","noar","barakd","itamarp","yoavpi","shaharj","talf","elady","dannyz","yardenr","mayav","bena","eilamg","nitsanr","ronenk","org","adirm","yoramf","ilyar","naomis","ronyg","assafb","alon","adamo","rafir","vladimird","buzzm","noal","lenag","chenr","nadavo","amitkad","orens","omera","sivanm","liranh","raziela"] + def new_owner_info(): + random.shuffle(fillers) + for user in [username, *fillers]: + if user in users_with_max_quota: + continue + quota = fetch_quota(user, project_name) + print(user, "?", quota['used']/1024/1024) + if quota['used'] > quota['limit'] * 0.79: + click.secho(f" 😭 {user} full quota", dim=True) + users_with_max_quota.add(user) + continue + if storage and quota['used'] + storage > quota['limit'] * 0.8: + click.secho(f" 😭 {user} not enough quota: {storage/1024} on {quota['used']/1024/1024}/{quota['limit']/1024/1024}", dim=True) + continue + return user, quota + + try: + print(f" . Belongs to {username}") + username, quota = new_owner_info() + print(f" . Using {username}") + # exit(0) + except Exception as e: + click.secho(f" 😭😭😭😭 [{e}] skipping, no one has enough quota... ", dim=True) + exit(0) + db_session.refresh(output.batch.ci_commit) + db_session.refresh(output.batch) + try: + as_user(username, move_files, before_dir, after_dir, output) + except Exception as e: + try: # TODO: try to find as which user to retry... + as_user('sircdevops', move_files, before_dir, after_dir, output) + except Exception as e: + print(f" ERROR: {e}") + traceback.print_exc(file=sys.stdout) + exit(1) + if not output.deleted: + add_storage(username, project, storage) + + + output.output_dir_override = str(after_dir) + output.data['migrated'] = True + flag_modified(output, "data") + db_session.add(output) + db_session.commit() + click.secho(" 🆗", fg='green') + # exit(0) + + +def migrate(min_id): + # it's an aweful join... + all_outputs = (db_session + .query(Output, Batch, CiCommit) + .join(Batch.outputs)#, isouter=True) + .join(CiCommit)#, isouter=True) + .filter(CiCommit.project_id==project) + ) + if min_id: + all_outputs = all_outputs.filter(Output.id >= min_id) + if parts_nbr: + all_outputs = all_outputs.filter(Output.id % parts_nbr == parts_idx) + # ("output_dir_override" like '/stage/algo_data/ci/CDE-Users/HW_ALG%') + outputs = (all_outputs + # .filter(text("(outputs.data->'migrated') is null")) + .filter(text("outputs.output_dir_override is not null")) + .filter(text("outputs.output_dir_override not like '/algo%'")) + # .filter(text("outputs.created_date < now() - '15 days'::interval")) + # .filter(text("output_dir_override like '/stage/algo_data/ci/CDE-Users/HW_ALG/%/CIS/output%'")) + # .filter(Output.is_pending==False) + # .order_by(Output.created_date.asc()) + .enable_eagerloads(False) + ) + # click.secho(f'- outputs total: {all_outputs.count()}', bold=True, fg='blue') + output_total = outputs.count() + click.secho(f'- outputs to migrate: {output_total}', bold=True, fg='blue') + should_continue = output_total > batch_size + start_batch = time.time() + updated = 0 + now = time.time() + + if not output_total: + for result in all_outputs.limit(1): + o, batch, commit = result + print(o) + print(o.output_dir) + return updated, None, should_continue + + for idx, result in enumerate(outputs.limit(batch_size)): + o, batch, commit = result + # print(o, batch, commit) + if o.data is None: + o.data = {} + ## legacy outputs from the previous CI + # if '/' in o.batch.ci_commit.hexsha: + # continue + + migrate_output(o) + if idx and idx % batch_size/100 == 0: + print(o) + print(o.batch.ci_commit) + now = time.time() + print(f"{idx/output_total:.1%} [{batch_size/(now - start_batch):.1f}/s] [est. total left {(now - start_batch) * ((output_total-idx)/batch_size) / 3600:.2f}h] [elapsed time: {now - start:.1f}s]") + start_batch = now + return updated, o.id, should_continue + + +def main(): + # Optionnally, you can give an id to start from... + # it helps if there are many non-migrated runs that fail because of whatever and + # you don't want to wait until the migration fails to migrate them again! + last_id = None #1245250 # None + + should_continue = True + while should_continue: + click.secho('Migrating...', bold=True, fg='blue') + nb_updated, last_id, should_continue = migrate(last_id) + click.secho(f"nb_updated={nb_updated}, last_id={last_id}, should_continue={should_continue}", fg='blue') + click.secho('DONE', fg='green') + +main() diff --git a/backend/backend/scripts/migration_utils.py b/backend/backend/scripts/migration_utils.py new file mode 100644 index 00000000..84b0bbba --- /dev/null +++ b/backend/backend/scripts/migration_utils.py @@ -0,0 +1,87 @@ +import os +import pwd +import shutil +import pickle +from pathlib import Path + +import requests +import click + + + + + + +def rm_files_not_listed_in_manifests(deleted_output_dir: Path): + """Deletes files from output directories that are not listed in output-manifest files.""" + for path in deleted_output_dir.iterdir(): + if path.name in ('log.txt', 'manifest.inputs.json', 'manifest.outputs.json'): + continue + if path.is_file(): + path.unlink() + else: + shutil.rmtree(path) + + + + +def valid(username): + return Path(f"/home/{username}").exists() + + +# Some emails from git cannot be mapped to user names +# You can add more to the list...b +usernames = { + "chenrimoch@samsung.com": "chenr", + "royyam@samsung.com": "royy", + "j.y.shin@samsung.com": "sircdevops", + "heyabcd.yang@samsung.com": "sircdevops", + "heyabcd.yang@samsungds.net": "sircdevops", + "omeralon@gmail.com": "alon", + "avi.zanko@samsung.com": "aviza", + "yotamater@mail.tau.ac.il": "yotama", + "yotamater@mail.tau.ac.il": "yotama", + "$amsonite3": "ayalg", + "$amsonite2": "ayalg", + "ayal.green#samsung.com": "ayalg", + "=": "ayalg", +} + +def get_username(ci_commit): + try: + committer_email = ci_commit.project.repo.commit(ci_commit.hexsha).committer.email + except Exception as e: + click.secho(str(e), fg='red') + try: + owner = ci_commit.artifacts_dir.owner() + except: + owner = "sircdevops" + print(f"??? {owner}") + # return None if owner in ['sircdevops', 'ispq'] else owner + return owner + if committer_email in usernames: + return usernames[committer_email] + + try: + username, _ = committer_email.split('@') + except: + raise ValueError((committer_email, ci_commit.project.repo.commit(ci_commit.hexsha).committer)) + if not valid(username): + r = requests.post("http://itweb/tel/mail2user.php", {"mail": committer_email}) + username_from_it = r.text.strip() + if username_from_it: + username = username_from_it + else: + try: # try the default user naming convention at SIRC + first, second = username.split('.') + username = f"{first}{second[0]}" + except: + pass + if not valid(username): + click.secho(f"Missing username for {committer_email}", fg='red') + return None + click.secho(f"❓ {ci_commit.committer_name} -> {committer_email} -> {username}", fg='yellow') + usernames[committer_email] = username + return username + else: + return username \ No newline at end of file diff --git a/backend/backend/scripts/queries.sql b/backend/backend/scripts/queries.sql new file mode 100644 index 00000000..1bb5103d --- /dev/null +++ b/backend/backend/scripts/queries.sql @@ -0,0 +1,63 @@ +drop view storage; +create view storage as + SELECT outputs.id, + ((outputs.data ->> 'storage'::text)::double precision) / 1000::double precision / 1000::double precision / 1000::double precision AS total_storage_gb, + (outputs.data->>'user')::text as username, + outputs.created_date, + outputs.deleted, + batches.id AS batch_id, + batches.label AS batch_label, + ci_commits.hexsha, + ci_commits.branch, + ci_commits.committer_name, + projects.id AS project + FROM outputs + JOIN batches ON batches.id = outputs.batch_id + JOIN ci_commits ON ci_commits.id = batches.ci_commit_id + JOIN projects ON projects.id::text = ci_commits.project_id::text + WHERE NOT (outputs.data ->> 'storage'::text) IS NULL; + +-- WIP per batch +select + batches.id as id, + (sum(outputs.data->>'storage')::bigint) / 1000 / 1000 / 1000 as total_storage_gb, + count(*) as nb_outputs, + ci_commits.hexsha, batches.label, projects.id, ci_commits.branch +from outputs + inner join batches on batches.id = outputs.batch_id + inner join ci_commits on ci_commits.id = batches.ci_commit_id + inner join projects on projects.id = ci_commits.project_id +where + outputs.created_date > current_date - 31 +group by (outputs.batch_id, ci_commits.hexsha, ci_commits.branch, batches.label, batches.id, projects.id) +ORDER BY storage_GB DESC NULLS LAST; + + +-- per project +select + (sum((outputs.data->>'storage')::bigint) / 1000 / 1000 / 1000) as storage_GB, + count(*) as nb_outputs, + projects.id +from outputs + inner join batches on batches.id = outputs.batch_id + inner join ci_commits on ci_commits.id = batches.ci_commit_id + inner join projects on projects.id = ci_commits.project_id +where + outputs.created_date > current_date - 31 +group by (projects.id) +ORDER BY storage_GB DESC NULLS LAST; + + +-- per branch +select + (sum((outputs.data->>'storage')::bigint) / 1000 / 1000 / 1000) as storage_GB, + count(*) as nb_outputs, + projects.id, ci_commits.branch +from outputs + inner join batches on batches.id = outputs.batch_id + inner join ci_commits on ci_commits.id = batches.ci_commit_id + inner join projects on projects.id = ci_commits.project_id +where + outputs.created_date > current_date - 31 +group by (ci_commits.branch, projects.id) +ORDER BY storage_GB DESC NULLS LAST; diff --git a/backend/backend/scripts/quota.py b/backend/backend/scripts/quota.py new file mode 100644 index 00000000..b3a1ca9b --- /dev/null +++ b/backend/backend/scripts/quota.py @@ -0,0 +1,172 @@ +import sys +import ssl +import base64 + +sys.path.append("/home/arthurf/netapp/netapp") +from NaServer import * + + + +ssl._create_default_https_context = ssl._create_unverified_context + +s = NaServer("npmng.transchip.com", 1, 100) +s.set_server_type("FILER") +s.set_transport_type("HTTPS") +s.set_port(443) +s.set_style("LOGIN") +s.set_admin_user(base64.b64decode("YWRtaW4="),base64.b64decode("MmJIcWNjQFNJUkM=")) +print(s) + + +def quota(username): + resultLength = -1 + outputType = 'raw' + + api = NaElement("quota-report-iter") + api.child_add_string('max-records', '20000') + + print(api) + xo = s.invoke_elem(api) + print(xo) + print(xo.sprintf()) + if (xo.results_status() == "failed"): + print ("Error:\n") + print (xo.sprintf()) + sys.exit(1) + + print("Collecting quota information, please wait...") + + for each in xo.sprintf().split('\n'): + + if '' in each: + diskLimitList = re.findall(r'\>(.*?)\<', each) + diskLimitKB = ''.join(diskLimitList) + + elif '' in each: + diskUsedList = re.findall(r'\>(.*?)\<', each) + diskUsed = ''.join(diskUsedList) + + elif '' in each: + fileLimit = re.findall(r'\>(.*?)\<', each) + + elif '' in each: + filesUsed = re.findall(r'\>(.*?)\<', each) + + elif '' in each: + quotaTarget = re.findall(r'\>(.*?)\<', each) + + elif '' in each: + quotaType = re.findall(r'\>(.*?)\<', each) + + elif '' in each: + quotaUserId = re.findall(r'\>(.*?)\<', each) + + elif '' in each: + quotaUserName = re.findall(r'\>(.*?)\<', each) + + elif '' in each: + quotaUserType = re.findall(r'\>(.*?)\<', each) + + elif '' in each: + quotaDiskLimit = re.findall(r'\>(.*?)\<', each) + + elif '' in each: + threshold = re.findall(r'\>(.*?)\<', each) + + elif '' in each: + treeList = re.findall(r'\>(.*?)\<', each) + tree = ''.join(treeList) + + elif '' in each: + volumeList = re.findall(r'\>(.*?)\<', each) + volume = ''.join(volumeList) + + elif '' in each: + vserver = re.findall(r'\>(.*?)\<', each) + + elif '' in each: + + try: + quotaUserName + except NameError: + quotaUserName = '' + + if (username in quotaTarget or username in volume or username in quotaUserName): + # Calculate quota usage in % + try: + diskUtilization = 100 * (float(diskUsed) / float(diskLimitKB)) + # Convert to GB + diskLimit = float(int(diskLimitKB)/1024/1024) + # Calculate FREE disk space (GB) + diskFree = (float(diskLimitKB) - float(diskUsed))/1024/1024 + + + except ValueError: + pass + + try: + outputType + except: + showQuota() + else: + if outputType == 'raw': + showRawData() + elif outputType == 'web': # Show in web format + showWebQuota() + elif (outputType != 'raw') or (outputType != 'web'): + showQuota() + + + + +def showQuota(): + # Cerate & populate dictionary + thisList = {} + if round(diskUtilization, 1) >= int(resultLength): + thisList['Ut.%'] = round(diskUtilization, 1) + # If not ampty add into the Dict. + if volume != '': + thisList['Volume'] = str(volume) + else: + thisList['-'] = '' + if tree != '': + thisList['Project'] = str(tree) + else: + thisList['-'] = '' + if diskLimit != '': + thisList['Limit'] = str(diskLimit) + else: + diskLimit['-'] = '' + if diskUsed != '': + thisList['Used'] = str(diskUsed) + else: + diskLimit['-'] = '' + print(thisList) + +def showRawData(): + # Cerate & populate dictionary + thisList = {} + if round(diskUtilization, 1) >= int(resultLength): + thisList['Ut.%'] = round(diskUtilization, 1) + # If not ampty add into the Dict. + if volume != '': + thisList['Volume'] = str(volume) + else: + thisList['-'] = '' + + if tree != '': + thisList['Project'] = str(tree) + else: + thisList['-'] = '' + + if diskLimit != '': + thisList['Limit'] = str(diskLimit) + else: + diskLimit['-'] = '' + + if diskUsed != '': + thisList['Used'] = str(diskUsed) + else: + diskLimit['-'] = '' + + print(thisList) diff --git a/backend/backend/scripts/user_storage_server.py b/backend/backend/scripts/user_storage_server.py new file mode 100644 index 00000000..bf75146e --- /dev/null +++ b/backend/backend/scripts/user_storage_server.py @@ -0,0 +1,129 @@ +""" +When running a migration we need to know user quotas, and update them. +Since we need multiple server to make the migration server, we need to sync them somehow... +The IT API is very slow.. + +Test URLs +- http://qatools01:3001/user/arthurf/storage +- http://qatools01:3001/user/arthurf/storage/project/HP2 +- http://qatools01:3001/user/arthurf/storage/project/HP2/add?usage=2 +- http://qatools01:3001/user/arthurf/storage + +""" +import sys +import json +from pathlib import Path +from copy import deepcopy +from ast import literal_eval + +import requests +from flask import Flask, request, jsonify +from flask_cors import CORS + +app = Flask(__name__) +CORS(app) + +missing_quota_info = {"volume": None, "used": 0, "limit": 100*1024*1024} + +# NOTE: we assume we run with 1 thread only... +# otherwise you need a sync: simplest is always writing to disk and reading from disk.. +# or work hard with pythn, or use e.g. redis... + +# TODO: +# - we really should return a _list_ of {volume, project, quota} +# since multiple volumes can refer to a project, and things are mounted at various locations.. +# We could parse mount and get the info... +# - the API to add storage should provide a mount point only and we should figure it out... +# - Then on the frontend it also require a bit of re-work, +# we could query by project, group by volume/mount-point... + + + +def fetch_user_quota(username): + r = requests.get(f"http://itweb01/quota/index.php?username={username}&limit=-1&type=raw") + usage = {} + # The response is not an array, but 1 line per record... + for line in r.text.splitlines(): + # The type is printed between each record... + if line == 'raw': + continue + info = literal_eval(line) + # info = json.loads(line) # if only we had JSON + if 'Project' not in info: # we only care about volumes with Projects + continue + usage[info['Project']] = { + "volume": info['Volume'], + "used": float(info['Used']), + "limit": float(info['Limit']) * 1024 * 1024, + } + return usage + + +user_quota_path = Path('user-quotas.json') +if user_quota_path.exists(): + if '--no-cache' in sys.argv: + user_quota_path.unlink() + with user_quota_path.open() as f: + users_quotas = json.load(f) +else: + users_quotas = { + # "arthurf": { + # "some-volume": {"used": 10, "limit": 1024} + # } + } + + +def write_users_quotas(): + with user_quota_path.open('w') as f: + json.dump(users_quotas, f) + + +def user_quota(username): + if username not in users_quotas: + quotas = fetch_user_quota(username) + users_quotas[username] = quotas + write_users_quotas() + return users_quotas[username] + + +@app.route('/user//storage') +def all_quotas(user): + return jsonify(users_quotas) + +@app.route('/user//storage') +def all_user_storage(user): + return jsonify(user_quota(user)) + + +@app.route('/user//storage/project/') +def user_storage(user, project): + project_quota = user_quota(user).get(project, deepcopy(missing_quota_info)) + print("[get]", project_quota) + return jsonify(project_quota) + + +@app.route('/user//storage/project//add') +def add_user_storage(user, project): + project_quota = user_quota(user).get(project, deepcopy(missing_quota_info)) + project_quota['used'] += float(request.args['usage']) + write_users_quotas() + print("[after-add]", project_quota) + return jsonify(project_quota) + +@app.route('/project/') +def project_storage(project): + return jsonify({ + user: quotas[project] for user, quotas in users_quotas.items() if project in quotas + }) + + +if __name__ == '__main__': + # we want to be sure we don't have sync issues between threads... + # without involving _anything_ complicated + app.run( + host='0.0.0.0', + port=3001, + debug=None, + reloader_type='watchdog', + threaded=False, + ) diff --git a/backend/backend/utils.py b/backend/backend/utils.py index 32ffbde3..6ebdc476 100644 --- a/backend/backend/utils.py +++ b/backend/backend/utils.py @@ -95,12 +95,3 @@ def profiled(): ps.print_stats(35) ps.print_callers(35) print(s.getvalue(), file=sys.stderr) - - -def rm_empty_parents(path: Path): - for parent in path.parents: - is_empty = not any(parent.iterdir()) - if is_empty: - parent.rmdir() - else: - break diff --git a/backend/init.sh b/backend/init.sh index ee4871b0..b85f2355 100755 --- a/backend/init.sh +++ b/backend/init.sh @@ -9,6 +9,17 @@ chmod 777 /var/qaboard cd /qaboard/backend/backend alembic upgrade head || alembic downgrade head || alembic stamp head + +# At SIRC we need to be able to turn into any user to delete their output files +if [ -z ${UWSGI_UID_CAN_SUDO+x} ]; then + if [ -z ${UWSGI_UID+x} ]; then + echo "not-needed" + else + echo "$UWSGI_UID ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers + fi +fi + + # Start the server cd /qaboard/backend -uwsgi --ini /qaboard/backend/uwsgi.ini \ No newline at end of file +uwsgi --listen $UWSGI_LISTEN_QUEUE_SIZE --ini /qaboard/backend/uwsgi.ini diff --git a/backend/poetry.lock b/backend/poetry.lock index 1f3668e0..b0490f3b 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -1,104 +1,122 @@ [[package]] -category = "main" -description = "A database migration tool for SQLAlchemy." name = "alembic" +version = "1.5.8" +description = "A database migration tool for SQLAlchemy." +category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "1.4.3" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" [package.dependencies] Mako = "*" -SQLAlchemy = ">=1.1.0" python-dateutil = "*" python-editor = ">=0.3" +SQLAlchemy = ">=1.3.0" [[package]] -category = "dev" -description = "Atomic file writes." name = "atomicwrites" +version = "1.4.0" +description = "Atomic file writes." +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "1.4.0" [[package]] -category = "dev" -description = "Classes Without Boilerplate" name = "attrs" +version = "20.3.0" +description = "Classes Without Boilerplate" +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "20.2.0" [package.extras] -dev = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "sphinx-rtd-theme", "pre-commit"] -docs = ["sphinx", "sphinx-rtd-theme", "zope.interface"] -tests = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"] -tests_no_zope = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"] +docs = ["furo", "sphinx", "zope.interface"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"] +tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"] [[package]] -category = "main" -description = "Python package for providing Mozilla's CA Bundle." name = "certifi" -optional = false +version = "2020.12.5" +description = "Python package for providing Mozilla's CA Bundle." +category = "main" +optional = true python-versions = "*" -version = "2020.6.20" [[package]] -category = "main" -description = "Universal encoding detector for Python 2 and 3" name = "chardet" +version = "4.0.0" +description = "Universal encoding detector for Python 2 and 3" +category = "main" optional = true -python-versions = "*" -version = "3.0.4" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] -category = "main" -description = "Composable command line interface toolkit" name = "click" +version = "7.1.2" +description = "Composable command line interface toolkit" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -version = "7.1.2" [[package]] -category = "dev" -description = "Cross-platform colored terminal text." -marker = "sys_platform == \"win32\"" name = "colorama" +version = "0.4.4" +description = "Cross-platform colored terminal text." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -version = "0.4.4" [[package]] +name = "coverage" +version = "5.5" +description = "Code coverage measurement for Python" category = "main" -description = "Composable style cycles" +optional = true +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" + +[package.extras] +toml = ["toml"] + +[[package]] name = "cycler" +version = "0.10.0" +description = "Composable style cycles" +category = "main" optional = false python-versions = "*" -version = "0.10.0" [package.dependencies] six = "*" [[package]] +name = "dataclasses" +version = "0.6" +description = "A backport of the dataclasses module for Python 3.6" category = "main" -description = "Decorators for Humans" +optional = true +python-versions = "*" + +[[package]] name = "decorator" +version = "4.4.2" +description = "Decorators for Humans" +category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*" -version = "4.4.2" [[package]] -category = "main" -description = "A simple framework for building complex web applications." name = "flask" +version = "1.1.2" +description = "A simple framework for building complex web applications." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -version = "1.1.2" [package.dependencies] -Jinja2 = ">=2.10.1" -Werkzeug = ">=0.15" click = ">=5.1" itsdangerous = ">=0.24" +Jinja2 = ">=2.10.1" +Werkzeug = ">=0.15" [package.extras] dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"] @@ -106,54 +124,79 @@ docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx- dotenv = ["python-dotenv"] [[package]] -category = "main" -description = "A Flask extension adding a decorator for CORS support" name = "flask-cors" +version = "3.0.10" +description = "A Flask extension adding a decorator for CORS support" +category = "main" optional = false python-versions = "*" -version = "3.0.9" [package.dependencies] Flask = ">=0.9" Six = "*" [[package]] +name = "flask-login" +version = "0.5.0" +description = "User session management for Flask" category = "main" -description = "Git Object Database" +optional = false +python-versions = "*" + +[package.dependencies] +Flask = "*" + +[[package]] name = "gitdb" +version = "4.0.7" +description = "Git Object Database" +category = "main" optional = false python-versions = ">=3.4" -version = "4.0.5" [package.dependencies] -smmap = ">=3.0.1,<4" +smmap = ">=3.0.1,<5" [[package]] -category = "main" -description = "Python Git Library" name = "gitpython" +version = "3.1.14" +description = "Python Git Library" +category = "main" optional = false python-versions = ">=3.4" -version = "3.1.11" [package.dependencies] gitdb = ">=4.0.1,<5" [[package]] +name = "green" +version = "3.2.5" +description = "Green is a clean, colorful, fast python test runner." category = "main" -description = "Internationalized Domain Names in Applications (IDNA)" +optional = true +python-versions = "*" + +[package.dependencies] +colorama = "*" +coverage = "*" +lxml = "*" +unidecode = "*" + +[[package]] name = "idna" +version = "2.10" +description = "Internationalized Domain Names in Applications (IDNA)" +category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "2.10" [[package]] -category = "main" -description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats." name = "imageio" +version = "2.9.0" +description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats." +category = "main" optional = false python-versions = ">=3.5" -version = "2.9.0" [package.dependencies] numpy = "*" @@ -167,20 +210,20 @@ gdal = ["gdal"] itk = ["itk"] [[package]] -category = "main" -description = "Various helpers to pass data to untrusted environments and back." name = "itsdangerous" +version = "1.1.0" +description = "Various helpers to pass data to untrusted environments and back." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "1.1.0" [[package]] -category = "main" -description = "A very fast and expressive template engine." name = "jinja2" +version = "2.11.3" +description = "A very fast and expressive template engine." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -version = "2.11.2" [package.dependencies] MarkupSafe = ">=0.23" @@ -189,28 +232,42 @@ MarkupSafe = ">=0.23" i18n = ["Babel (>=0.8)"] [[package]] -category = "main" -description = "Lightweight pipelining: using Python functions as pipeline jobs." name = "joblib" -optional = true +version = "1.0.1" +description = "Lightweight pipelining with Python functions" +category = "main" +optional = false python-versions = ">=3.6" -version = "0.17.0" [[package]] -category = "main" -description = "A fast implementation of the Cassowary constraint solver" name = "kiwisolver" +version = "1.3.1" +description = "A fast implementation of the Cassowary constraint solver" +category = "main" optional = false python-versions = ">=3.6" -version = "1.2.0" [[package]] +name = "lxml" +version = "4.6.3" +description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." category = "main" -description = "A super-fast templating language that borrows the best ideas from the existing templating languages." +optional = true +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*" + +[package.extras] +cssselect = ["cssselect (>=0.7)"] +html5 = ["html5lib"] +htmlsoup = ["beautifulsoup4"] +source = ["Cython (>=0.29.7)"] + +[[package]] name = "mako" +version = "1.1.4" +description = "A super-fast templating language that borrows the best ideas from the existing templating languages." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "1.1.3" [package.dependencies] MarkupSafe = ">=0.9.2" @@ -220,48 +277,47 @@ babel = ["babel"] lingua = ["lingua"] [[package]] -category = "main" -description = "Safely add untrusted strings to HTML/XML markup." name = "markupsafe" +version = "1.1.1" +description = "Safely add untrusted strings to HTML/XML markup." +category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" -version = "1.1.1" [[package]] -category = "main" -description = "Python plotting package" name = "matplotlib" +version = "3.4.1" +description = "Python plotting package" +category = "main" optional = false -python-versions = ">=3.6" -version = "3.3.2" +python-versions = ">=3.7" [package.dependencies] -certifi = ">=2020.06.20" cycler = ">=0.10" kiwisolver = ">=1.0.1" -numpy = ">=1.15" +numpy = ">=1.16" pillow = ">=6.2.0" -pyparsing = ">=2.0.3,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6" -python-dateutil = ">=2.1" +pyparsing = ">=2.2.1" +python-dateutil = ">=2.7" [[package]] -category = "dev" -description = "More routines for operating on iterables, beyond itertools" name = "more-itertools" +version = "8.7.0" +description = "More routines for operating on iterables, beyond itertools" +category = "dev" optional = false python-versions = ">=3.5" -version = "8.5.0" [[package]] -category = "main" -description = "Python package for creating and manipulating graphs and networks" name = "networkx" +version = "2.5.1" +description = "Python package for creating and manipulating graphs and networks" +category = "main" optional = false python-versions = ">=3.6" -version = "2.5" [package.dependencies] -decorator = ">=4.3.0" +decorator = ">=4.3,<5" [package.extras] all = ["numpy", "scipy", "pandas", "matplotlib", "pygraphviz", "pydot", "pyyaml", "lxml", "pytest"] @@ -277,147 +333,190 @@ pyyaml = ["pyyaml"] scipy = ["scipy"] [[package]] -category = "main" -description = "NumPy is the fundamental package for array computing with Python." name = "numpy" +version = "1.20.2" +description = "NumPy is the fundamental package for array computing with Python." +category = "main" optional = false -python-versions = ">=3.6" -version = "1.19.2" +python-versions = ">=3.7" [[package]] -category = "main" -description = "Powerful data structures for data analysis, time series, and statistics" name = "pandas" +version = "1.2.3" +description = "Powerful data structures for data analysis, time series, and statistics" +category = "main" optional = false -python-versions = ">=3.6.1" -version = "1.1.3" +python-versions = ">=3.7.1" [package.dependencies] -numpy = ">=1.15.4" +numpy = ">=1.16.5" python-dateutil = ">=2.7.3" -pytz = ">=2017.2" +pytz = ">=2017.3" [package.extras] -test = ["pytest (>=4.0.2)", "pytest-xdist", "hypothesis (>=3.58)"] +test = ["pytest (>=5.0.1)", "pytest-xdist", "hypothesis (>=3.58)"] [[package]] -category = "main" -description = "Python Imaging Library (Fork)" name = "pillow" +version = "8.2.0" +description = "Python Imaging Library (Fork)" +category = "main" optional = false python-versions = ">=3.6" -version = "8.0.1" [[package]] -category = "dev" -description = "plugin and hook calling mechanisms for python" name = "pluggy" +version = "0.13.1" +description = "plugin and hook calling mechanisms for python" +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "0.13.1" [package.extras] dev = ["pre-commit", "tox"] [[package]] -category = "main" -description = "psycopg2 - Python-PostgreSQL Database Adapter" name = "psycopg2" +version = "2.8.6" +description = "psycopg2 - Python-PostgreSQL Database Adapter" +category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" -version = "2.8.6" [[package]] -category = "dev" -description = "library with cross-python path, ini-parsing, io, code, log facilities" name = "py" +version = "1.10.0" +description = "library with cross-python path, ini-parsing, io, code, log facilities" +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "1.9.0" [[package]] +name = "pyaml" +version = "20.4.0" +description = "PyYAML-based module to produce pretty and readable YAML-serialized data" category = "main" -description = "Python parsing module" +optional = false +python-versions = "*" + +[package.dependencies] +PyYAML = "*" + +[[package]] +name = "pyasn1" +version = "0.4.8" +description = "ASN.1 types and codecs" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "pyasn1-modules" +version = "0.2.8" +description = "A collection of ASN.1-based protocols modules." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +pyasn1 = ">=0.4.6,<0.5.0" + +[[package]] name = "pyparsing" +version = "2.4.7" +description = "Python parsing module" +category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" -version = "2.4.7" [[package]] -category = "dev" -description = "pytest: simple powerful testing with Python" name = "pytest" +version = "3.10.1" +description = "pytest: simple powerful testing with Python" +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "3.10.1" [package.dependencies] atomicwrites = ">=1.0" attrs = ">=17.4.0" -colorama = "*" +colorama = {version = "*", markers = "sys_platform == \"win32\""} more-itertools = ">=4.0.0" pluggy = ">=0.7" py = ">=1.5.0" -setuptools = "*" six = ">=1.10.0" [[package]] -category = "main" -description = "Extensions to the standard Python datetime module" name = "python-dateutil" +version = "2.8.1" +description = "Extensions to the standard Python datetime module" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" -version = "2.8.1" [package.dependencies] six = ">=1.5" [[package]] -category = "main" -description = "Programmatically open an editor, capture the result." name = "python-editor" +version = "1.0.4" +description = "Programmatically open an editor, capture the result." +category = "main" optional = false python-versions = "*" -version = "1.0.4" [[package]] +name = "python-ldap" +version = "3.3.1" +description = "Python modules for implementing LDAP clients" category = "main" -description = "World timezone definitions, modern and historical" +optional = false +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" + +[package.dependencies] +pyasn1 = ">=0.3.7" +pyasn1_modules = ">=0.1.5" + +[[package]] name = "pytz" +version = "2021.1" +description = "World timezone definitions, modern and historical" +category = "main" optional = false python-versions = "*" -version = "2020.1" [[package]] -category = "main" -description = "PyWavelets, wavelet transform module" name = "pywavelets" +version = "1.1.1" +description = "PyWavelets, wavelet transform module" +category = "main" optional = false python-versions = ">=3.5" -version = "1.1.1" [package.dependencies] numpy = ">=1.13.3" [[package]] -category = "main" -description = "YAML parser and emitter for Python" name = "pyyaml" -optional = true -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -version = "5.3.1" +version = "5.4.1" +description = "YAML parser and emitter for Python" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [[package]] -category = "main" -description = "" -develop = true name = "qaboard" +version = "0.8.5" +description = "Visualize and compare algorithm results. Optimize parameters. Share results and track progress." +category = "main" optional = true -python-versions = ">=3.7" -version = "0.8.6" +python-versions = ">=3.6" +develop = false [package.dependencies] click = ">=7.0" +dataclasses = "*" +green = "*" joblib = "*" pyyaml = "*" requests = "*" @@ -425,62 +524,61 @@ simplejson = "*" sklearn = "*" [package.extras] -dev = ["flake8", "green", "mypy"] -optimize = ["scikit-optimize (>=0.7.2)"] +optimize = ["skopt"] [package.source] -reference = "" type = "directory" url = ".." [[package]] -category = "main" -description = "Python HTTP for Humans." name = "requests" +version = "2.25.1" +description = "Python HTTP for Humans." +category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -version = "2.24.0" [package.dependencies] certifi = ">=2017.4.17" -chardet = ">=3.0.2,<4" +chardet = ">=3.0.2,<5" idna = ">=2.5,<3" -urllib3 = ">=1.21.1,<1.25.0 || >1.25.0,<1.25.1 || >1.25.1,<1.26" +urllib3 = ">=1.21.1,<1.27" [package.extras] security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"] -socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"] +socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] [[package]] -category = "main" -description = "Image processing in Python" name = "scikit-image" +version = "0.18.1" +description = "Image processing in Python" +category = "main" optional = false -python-versions = ">=3.6" -version = "0.17.2" +python-versions = ">=3.7" [package.dependencies] -PyWavelets = ">=1.1.1" imageio = ">=2.3.0" matplotlib = ">=2.0.0,<3.0.0 || >3.0.0" networkx = ">=2.0" -numpy = ">=1.15.1" +numpy = ">=1.16.5" pillow = ">=4.3.0,<7.1.0 || >7.1.0,<7.1.1 || >7.1.1" +PyWavelets = ">=1.1.1" scipy = ">=1.0.1" tifffile = ">=2019.7.26" [package.extras] -docs = ["sphinx (>=1.8,<=2.4.4)", "numpydoc (>=0.9)", "sphinx-gallery (>=0.3.1)", "sphinx-copybutton", "pytest-runner", "scikit-learn", "matplotlib (>=3.0.1)", "dask (>=0.15.0)", "cloudpickle (>=0.2.1)", "pandas (>=0.23.0)", "seaborn (>=0.7.1)", "pooch (>=0.5.2)"] -optional = ["simpleitk", "astropy (>=1.2.0)", "qtpy", "pyamg", "dask (>=0.15.0)", "cloudpickle (>=0.2.1)", "pooch (>=0.5.2)"] -test = ["pytest (!=3.7.3)", "pytest-cov", "pytest-localserver", "flake8", "codecov"] +data = ["pooch (>=1.3.0)"] +docs = ["sphinx (>=1.8,<=2.4.4)", "sphinx-gallery (>=0.7.0,!=0.8.0)", "numpydoc (>=1.0)", "sphinx-copybutton", "pytest-runner", "scikit-learn", "matplotlib (>=3.0.1)", "dask[array] (>=0.15.0,!=2.17.0)", "cloudpickle (>=0.2.1)", "pandas (>=0.23.0)", "seaborn (>=0.7.1)", "pooch (>=1.3.0)", "tifffile (>=2020.5.30)", "myst-parser", "ipywidgets", "plotly (>=4.10.0)"] +optional = ["simpleitk", "astropy (>=3.1.2)", "qtpy", "pyamg", "dask[array] (>=1.0.0,!=2.17.0)", "cloudpickle (>=0.2.1)", "pooch (>=1.3.0)"] +test = ["pytest (>=5.2.0)", "pytest-cov (>=2.7.0)", "pytest-localserver", "pytest-faulthandler", "flake8", "codecov", "pooch (>=1.3.0)"] [[package]] -category = "main" -description = "A set of python modules for machine learning and data mining" name = "scikit-learn" -optional = true +version = "0.24.1" +description = "A set of python modules for machine learning and data mining" +category = "main" +optional = false python-versions = ">=3.6" -version = "0.23.2" [package.dependencies] joblib = ">=0.11" @@ -489,61 +587,82 @@ scipy = ">=0.19.1" threadpoolctl = ">=2.0.0" [package.extras] -alldeps = ["numpy (>=1.13.3)", "scipy (>=0.19.1)"] +benchmark = ["matplotlib (>=2.1.1)", "pandas (>=0.25.0)", "memory-profiler (>=0.57.0)"] +docs = ["matplotlib (>=2.1.1)", "scikit-image (>=0.13)", "pandas (>=0.25.0)", "seaborn (>=0.9.0)", "memory-profiler (>=0.57.0)", "sphinx (>=3.2.0)", "sphinx-gallery (>=0.7.0)", "numpydoc (>=1.0.0)", "Pillow (>=7.1.2)", "sphinx-prompt (>=1.3.0)"] +examples = ["matplotlib (>=2.1.1)", "scikit-image (>=0.13)", "pandas (>=0.25.0)", "seaborn (>=0.9.0)"] +tests = ["matplotlib (>=2.1.1)", "scikit-image (>=0.13)", "pandas (>=0.25.0)", "pytest (>=5.0.1)", "pytest-cov (>=2.9.0)", "flake8 (>=3.8.2)", "mypy (>=0.770)", "pyamg (>=4.0.0)"] [[package]] +name = "scikit-optimize" +version = "0.8.1" +description = "Sequential model-based optimization toolbox." category = "main" -description = "SciPy: Scientific Library for Python" -name = "scipy" optional = false -python-versions = ">=3.6" -version = "1.5.3" +python-versions = "*" [package.dependencies] -numpy = ">=1.14.5" +joblib = ">=0.11" +numpy = ">=1.13.3" +pyaml = ">=16.9" +scikit-learn = ">=0.20.0" +scipy = ">=0.19.1" + +[package.extras] +plots = ["matplotlib (>=2.0.0)"] [[package]] +name = "scipy" +version = "1.6.2" +description = "SciPy: Scientific Library for Python" category = "main" -description = "Simple, fast, extensible JSON encoder/decoder for Python" +optional = false +python-versions = ">=3.7,<3.10" + +[package.dependencies] +numpy = ">=1.16.5,<1.23.0" + +[[package]] name = "simplejson" +version = "3.17.2" +description = "Simple, fast, extensible JSON encoder/decoder for Python" +category = "main" optional = true python-versions = ">=2.5, !=3.0.*, !=3.1.*, !=3.2.*" -version = "3.17.2" [[package]] -category = "main" -description = "Python 2 and 3 compatibility utilities" name = "six" +version = "1.15.0" +description = "Python 2 and 3 compatibility utilities" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" -version = "1.15.0" [[package]] -category = "main" -description = "A set of python modules for machine learning and data mining" name = "sklearn" +version = "0.0" +description = "A set of python modules for machine learning and data mining" +category = "main" optional = true python-versions = "*" -version = "0.0" [package.dependencies] scikit-learn = "*" [[package]] -category = "main" -description = "A pure Python implementation of a sliding window memory map manager" name = "smmap" +version = "4.0.0" +description = "A pure Python implementation of a sliding window memory map manager" +category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "3.0.4" +python-versions = ">=3.5" [[package]] -category = "main" -description = "Database Abstraction Library" name = "sqlalchemy" +version = "1.3.24" +description = "Database Abstraction Library" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "1.3.20" [package.extras] mssql = ["pyodbc"] @@ -552,22 +671,22 @@ mssql_pyodbc = ["pyodbc"] mysql = ["mysqlclient"] oracle = ["cx-oracle"] postgresql = ["psycopg2"] -postgresql_pg8000 = ["pg8000"] +postgresql_pg8000 = ["pg8000 (<1.16.6)"] postgresql_psycopg2binary = ["psycopg2-binary"] postgresql_psycopg2cffi = ["psycopg2cffi"] -pymysql = ["pymysql"] +pymysql = ["pymysql (<1)", "pymysql"] [[package]] -category = "main" -description = "Various utility functions for SQLAlchemy." name = "sqlalchemy-utils" +version = "0.36.8" +description = "Various utility functions for SQLAlchemy." +category = "main" optional = false python-versions = "*" -version = "0.36.8" [package.dependencies] -SQLAlchemy = ">=1.0" six = "*" +SQLAlchemy = ">=1.0" [package.extras] anyjson = ["anyjson (>=0.3.3)"] @@ -579,77 +698,85 @@ intervals = ["intervals (>=0.7.1)"] password = ["passlib (>=1.6,<2.0)"] pendulum = ["pendulum (>=2.0.5)"] phone = ["phonenumbers (>=5.9.2)"] -test = ["pytest (>=2.7.1)", "Pygments (>=1.2)", "Jinja2 (>=2.3)", "docutils (>=0.10)", "flexmock (>=0.9.7)", "mock (2.0.0)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pg8000 (>=1.12.4)", "pytz (>=2014.2)", "python-dateutil (>=2.6)", "pymysql", "flake8 (>=2.4.0)", "isort (>=4.2.2)", "pyodbc"] -test_all = ["anyjson (>=0.3.3)", "arrow (>=0.3.4)", "Babel (>=1.3)", "colour (>=0.0.4)", "cryptography (>=0.6)", "intervals (>=0.7.1)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "phonenumbers (>=5.9.2)", "pytest (>=2.7.1)", "Pygments (>=1.2)", "Jinja2 (>=2.3)", "docutils (>=0.10)", "flexmock (>=0.9.7)", "mock (2.0.0)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pg8000 (>=1.12.4)", "pytz (>=2014.2)", "python-dateutil (>=2.6)", "pymysql", "flake8 (>=2.4.0)", "isort (>=4.2.2)", "pyodbc", "python-dateutil", "furl (>=0.4.1)"] +test = ["pytest (>=2.7.1)", "Pygments (>=1.2)", "Jinja2 (>=2.3)", "docutils (>=0.10)", "flexmock (>=0.9.7)", "mock (==2.0.0)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pg8000 (>=1.12.4)", "pytz (>=2014.2)", "python-dateutil (>=2.6)", "pymysql", "flake8 (>=2.4.0)", "isort (>=4.2.2)", "pyodbc"] +test_all = ["anyjson (>=0.3.3)", "arrow (>=0.3.4)", "Babel (>=1.3)", "colour (>=0.0.4)", "cryptography (>=0.6)", "intervals (>=0.7.1)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "phonenumbers (>=5.9.2)", "pytest (>=2.7.1)", "Pygments (>=1.2)", "Jinja2 (>=2.3)", "docutils (>=0.10)", "flexmock (>=0.9.7)", "mock (==2.0.0)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pg8000 (>=1.12.4)", "pytz (>=2014.2)", "python-dateutil (>=2.6)", "pymysql", "flake8 (>=2.4.0)", "isort (>=4.2.2)", "pyodbc", "python-dateutil", "furl (>=0.4.1)"] timezone = ["python-dateutil"] url = ["furl (>=0.4.1)"] [[package]] -category = "main" -description = "threadpoolctl" name = "threadpoolctl" -optional = true -python-versions = ">=3.5" version = "2.1.0" +description = "threadpoolctl" +category = "main" +optional = false +python-versions = ">=3.5" [[package]] -category = "main" -description = "Read and write TIFF(r) files" name = "tifffile" +version = "2021.3.31" +description = "Read and write TIFF files" +category = "main" optional = false python-versions = ">=3.7" -version = "2020.10.1" [package.dependencies] numpy = ">=1.15.1" [package.extras] -all = ["imagecodecs (>=2020.5.30)", "matplotlib (>=3.2)", "lxml"] +all = ["imagecodecs (>=2021.3.31)", "matplotlib (>=3.2)", "lxml"] [[package]] -category = "main" -description = "Ultra fast JSON encoder and decoder for Python" name = "ujson" +version = "4.0.2" +description = "Ultra fast JSON encoder and decoder for Python" +category = "main" optional = false python-versions = ">=3.6" -version = "4.0.1" [[package]] +name = "unidecode" +version = "1.2.0" +description = "ASCII transliterations of Unicode text" category = "main" -description = "HTTP library with thread-safe connection pooling, file post, and more." +optional = true +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[[package]] name = "urllib3" +version = "1.26.4" +description = "HTTP library with thread-safe connection pooling, file post, and more." +category = "main" optional 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postgresql driver @@ -29,7 +31,8 @@ numpy = "=>1.17.3" # (needed by pandas - just we ensure python3.8 compat) scikit-image = "*" # image processing for auto-regions of interest uwsgi = "*" # server uwsgitop = "*" # top for uwsgi -qaboard = { path = "..", optional = true, develop = true } +qaboard = { path = "..", optional = true } #, develop = true } +scikit-optimize = "*" # needed for auto-tuning, it's specified in qaboard, normally it should be enough but.. # Makes incremental docker builds easier [tool.poetry.extras] diff --git a/backend/uwsgi.ini b/backend/uwsgi.ini index c58be654..36acb184 100755 --- a/backend/uwsgi.ini +++ b/backend/uwsgi.ini @@ -1,20 +1,38 @@ # https://uwsgi-docs.readthedocs.io/en/latest/ThingsToKnow.html # https://pythonise.com/series/learning-flask/python-flask-uwsgi-introduction # https://uwsgi-docs.readthedocs.io/en/latest/ConfigLogic.html +# https://www.techatbloomberg.com/blog/configuring-uwsgi-production-deployment/ [uwsgi] -strict = true -# default? +; FIXME: why do we need this? it complained about "listen" from the CLI not being OK... +; strict = true + protocol = uwsgi master = true module = backend:app +need-app = true processes = 1 if-env = UWSGI_PROCESSES processes = $(UWSGI_PROCESSES) endif = +; https://uwsgi-docs.readthedocs.io/en/latest/Cheaper.html#:~:text=To%20enable%20cheaper%20mode%20add,(%20workers%20or%20processes%20option). +if-env = UWSGI_CHEAPER_ALGO_BUSYNESS +cheaper-algo = busyness +processes = 64 ; Maximum number of workers allowed +cheaper = $(UWSGI_CHEAPER) ; Minimum number of workers allowed +cheaper-initial = $(UWSGI_CHEAPER_INITIAL) ; Workers created at startup +cheaper-overload = 1 ; Length of a cycle in seconds +cheaper-step = 16 ; How many workers to spawn at a time +cheaper-busyness-multiplier = 30 ; How many cycles to wait before killing workers +cheaper-busyness-min = 20 ; Below this threshold, kill workers (if stable for multiplier cycles) +cheaper-busyness-max = 70 ; Above thiss threshold, spawn new workers +cheaper-busyness-backlog-alert = 16 ; Spawn emergency workers if more than this many requests are waiting in the queue +cheaper-busyness-backlog-step = 2 ; How many emergegency workers to create if there are too many requests in the queue +endif = + if-env = UWSGI_UID uid = %(_) endif = @@ -34,6 +52,12 @@ vacuum = true # well-behaved when running with an init system like systemd die-on-term = true +# if ever need threads +# enable-threads = true + +# https://github.com/unbit/uwsgi/issues/1978 +; py-call-osafterfork = true + if-env = UWSGI_STATS memory-report = true @@ -42,6 +66,7 @@ stats = /tmp/stats.sock # stats = 127.0.0.1:3001 endif = +single-interpreter = true # timeout to kill requests -# harakiri = 300 +harakiri = 300 diff --git a/development.yml b/development.yml index e541292c..88e9a27b 100644 --- a/development.yml +++ b/development.yml @@ -22,6 +22,7 @@ services: volumes: - ./qaboard:/qaboard/qaboard - ./backend:/qaboard/backend + - ./setup.py:/qaboard/setup.py environment: - QABOARD_DB_ECHO=true - UWSGI_STATS=true @@ -32,8 +33,15 @@ services: # To use it, comment out, as well as frontent:environment below working_dir: /qaboard/backend command: flask run --host 0.0.0.0 --with-threads --port 5152 + # in same cases (NFS+squash-root), it can be useful to be a usual sudoer user... + # user: "11611:10" + # command: > + # bash -c " + # echo 'user ALL=(ALL) NOPASSWD: ALL' >> /etc/sudoers + # && su user -c 'flask run --host 0.0.0.0 --with-threads --port 5152' + # " ports: - - 5152:5152 + - "${QABOARD_DEV_BACKEND_PORT:-5152}:5152" # logging: # driver: none @@ -52,7 +60,7 @@ services: - REACT_APP_QABOARD_HOST=http://proxy:5151 command: npm start ports: - - 3000:3000 + - "${QABOARD_DEV_FRONTEND_PORT:-3000}:3000" depends_on: - proxy - backend diff --git a/docker-compose.yml b/docker-compose.yml index b9877be3..8d1bca7e 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -81,12 +81,13 @@ services: - data:/var/qaboard - /mnt/qaboard:/mnt/qaboard environment: + - SECRET_KEY - UWSGI_PROCESSES=2 + - UWSGI_LISTEN_QUEUE_SIZE=100 - QABOARD_DB_HOST - QABOARD_DB_PORT - - JENKINS_USER_NAME - - JENKINS_USER_TOKEN - - JENKINS_USER_CRUMB + - JENKINS_AUTH + - GITLAB_AUTH - GITLAB_ACCESS_TOKEN frontend: @@ -94,7 +95,7 @@ services: build: cache_from: ["arthurflam/qaboard:frontend"] context: webapp - shm_size: 4gb + shm_size: 6gb args: REACT_APP_QABOARD_DOCS_ROOT: "/" volumes: diff --git a/production.yml b/production.yml index c3c0a2ea..c2ebca0e 100644 --- a/production.yml +++ b/production.yml @@ -2,6 +2,7 @@ version: "3.5" services: db: + shm_size: 1g restart: always # volumes: # - /WHERE/TO/SAVE/BACKUPS:/backups @@ -14,11 +15,24 @@ services: backend: restart: always environment: - - UWSGI_PROCESSES=8 + # To use values beyond 128, read + # * https://stackoverflow.com/a/36452474/5993501 + # * https://uwsgi-docs.readthedocs.io/en/latest/articles/TheArtOfGracefulReloading.html#the-listen-queue + # * https://stackoverflow.com/questions/43243483/docker-container-increase-listen-queue-size-beyond-128 + # * https://serverfault.com/questions/271380/how-can-i-increase-the-value-of-somaxconn + - UWSGI_LISTEN_QUEUE_SIZE=1024 + - UWSGI_CHEAPER_ALGO_BUSYNESS=true + - UWSGI_CHEAPER_INITIAL=16 # initial number of processes + - UWSGI_PROCESSES=64 # max + - UWSGI_CHEAPER=8 # minimum + - UWSGI_STATS=true # leave an unbound port open, useful for debugging ports: - ${QABOARD_PORT_DEBUG:-5152}:3001 - + # https://github.com/compose-spec/compose-spec/blob/master/spec.md#sysctls + sysctls: + - net.core.somaxconn=1024 + proxy: restart: always cantaloupe: @@ -29,11 +43,12 @@ services: # # docker-compose run /etc/periodic/daily/backup # cron-backup-db: # image: postgres:12-alpine + # restart: always # depends_on: # - db # environment: # # https://www.postgresql.org/docs/9.3/libpq-envars.html - # PGHOST: db + # PGHOST: ${PGHOST:-db} # PGDATABASE: qaboard # PGUSER: qaboard # PGPASSWORD: password @@ -45,7 +60,8 @@ services: # # https://busybox.net/downloads/BusyBox.html # # -f: foreground # # -d: log to stderr, 0 is the most verbose, default 8 - # command: crond -f -l 0 + # command: crond -f -d 0 # volumes: # - ./services/db/backup:/etc/periodic/daily/backup:ro # - /WHERE/TO/SAVE/BACKUPS:/backups + diff --git a/qaboard/api.py b/qaboard/api.py index b7aed7e5..011378e6 100755 --- a/qaboard/api.py +++ b/qaboard/api.py @@ -12,7 +12,7 @@ import simplejson import click -from .config import config, commit_id, is_ci, available_metrics +from .config import project, config, commit_id, is_ci, available_metrics from .config import secrets qaboard_protocol = os.getenv('QABOARD_PROTOCOL', secrets.get('QABOARD_PROTOCOL', 'https')) @@ -52,7 +52,7 @@ def dir_to_url(path: Path) -> str: def print_url(ctx, status="starting"): if not ctx.obj['offline'] and not os.environ.get('QA_BATCH'): batch_label = ctx.obj["batch_label"] - commit_url = f"{qaboard_url}/{config['project']['name']}/commit/{commit_id[:10] if commit_id else ''}{f'?batch={quote(batch_label)}' if batch_label != 'default' else ''}" + commit_url = f"{qaboard_url}/{project.as_posix()}/commit/{commit_id[:10] if commit_id else ''}{f'?batch={quote(batch_label)}' if batch_label != 'default' else ''}" if is_ci or ctx.obj['share']: if status == "starting": click.echo(click.style("Results: ", bold=True) + click.style(commit_url, underline=True, bold=True), err=True) @@ -131,15 +131,15 @@ def notify_qa_database(object_type='output', **kwargs): # if object_type != "output" # le'ts be wasteful to make init easier # Will help initialize/update the commit/batch in QA-Board data.update({ - 'commit_branch': commit_branch, - 'commit_tag': commit_tag, - 'commit_committer_name': commit_committer_name, - 'commit_committer_email': commit_committer_email, - 'commit_authored_datetime': commit_authored_datetime, - 'commit_parents': commit_parents, - 'commit_message': commit_message, - "qaboard_config": serialize_paths(deepcopy(config)), - "qaboard_metrics": _metrics, + 'commit_branch': commit_branch, + 'commit_tag': commit_tag, + 'commit_committer_name': commit_committer_name, + 'commit_committer_email': commit_committer_email, + 'commit_authored_datetime': commit_authored_datetime, + 'commit_parents': commit_parents, + 'commit_message': commit_message, + "qaboard_config": serialize_paths(deepcopy(config)), + "qaboard_metrics": _metrics, }) if 'QA_VERBOSE' in os.environ: click.secho(url, fg='cyan', err=True) @@ -159,10 +159,14 @@ def notify_qa_database(object_type='output', **kwargs): except Exception as e: click.secho(f'WARNING: [{e}] Failed to update QA-Board.', fg='yellow', bold=True, err=True) click.secho(url, fg='yellow', err=True) + data = json.loads(data) + del data['qaboard_config'] + del data['qaboard_metrics'] + del data['inputs_settings'] click.secho(str(data), fg='yellow', err=True) try: click.secho(str(r.request.headers), fg='yellow', dim=True, err=True) - click.secho(str(r.request.body), fg='yellow', dim=True, err=True) + # click.secho(str(r.request.body), fg='yellow', dim=True, err=True) click.secho(f'{r.status_code}: {r.text}', fg='yellow', dim=True, err=True) except: pass @@ -184,11 +188,11 @@ def get_output(output_id): # We used to use a cache but now we want to check run statuses before/after the batch # @lru_cache() -def batch_info(reference, batch, is_branch=False): +def batch_info(reference, batch, is_branch=False, project=project): """Get data about a batch of outputs in the database""" import requests params = { - "project": config['project']['name'], + "project": str(project), "batch": batch, # the format is metric: target.... not great. "metrics": json.dumps({metric: 0 for metric in available_metrics.keys()}), @@ -200,6 +204,8 @@ def batch_info(reference, batch, is_branch=False): r = requests.get(url, params=params) if 'batches' not in r.json(): raise ValueError(f'We could not get the results for {batch} batch {reference}') + if batch not in r.json()["batches"]: + raise ValueError(f'We could not get the results for {batch} batch {reference}. Available: {list(b for b in r.json()["batches"])}') return r.json()['batches'][batch] diff --git a/qaboard/bit_accuracy.py b/qaboard/bit_accuracy.py index 5f5ef051..b2343f8b 100755 --- a/qaboard/bit_accuracy.py +++ b/qaboard/bit_accuracy.py @@ -2,19 +2,22 @@ """ Bit-accuracy test between 2 results folders """ -import os +import json import filecmp import fnmatch -import json from pathlib import Path import click -from .config import subproject, config, commit_branch +from .conventions import make_batch_conf_dir +from .iterators import iter_inputs +from .utils import PathType +from .config import commit_id, project, subproject, outputs_commit_root, outputs_commit, is_ci, default_platform, config +from .config import user, default_batches_files def cmpfiles(dir_1=Path(), dir_2=Path(), patterns=None, ignore=None): - """Bit-accuracy test between two directories. + """Bit-accuracy test between two directories. We usually use cmpmanifest only... Almost like https://docs.python.org/3/library/filecmp.html """ if not patterns: @@ -22,13 +25,24 @@ def cmpfiles(dir_1=Path(), dir_2=Path(), patterns=None, ignore=None): if not ignore: ignore = [] - mismatch = [] # not the same - match = [] # the same - only_in_1 = [] # exists in dir_1 but not in dir_2 - errors = [] # or errors accessing + mismatch = set() # not the same + match = set() # the same + only_in_1 = set() # exists in dir_1 but not in dir_2 + only_in_2 = set() # exists in dir_2 but not in dir_1 + errors = set() # or errors accessing for pattern in patterns: - for file_1 in dir_1.rglob(pattern): + files_1 = list(dir_1.rglob(pattern)) + files_2 = list(dir_2.rglob(pattern)) + + for file_2 in files_2: + if not file_2.is_file(): continue + if any(fnmatch.fnmatch(file_2.name, i) for i in ignore): continue + rel_path = file_2.relative_to(dir_2) + if not (dir_1 / rel_path).is_file(): + only_in_2.add(rel_path) + + for file_1 in files_1: if not file_1.is_file(): continue if any(fnmatch.fnmatch(file_1.name, i) for i in ignore): continue @@ -38,18 +52,19 @@ def cmpfiles(dir_1=Path(), dir_2=Path(), patterns=None, ignore=None): try: is_same = filecmp.cmp(str(file_1), str(file_2), shallow=False) if not is_same: - mismatch.append(rel_path) + mismatch.add(rel_path) else: - match.append(rel_path) + match.add(rel_path) except: - errors.append(rel_path) + errors.add(rel_path) else: - only_in_1.append(rel_path) + only_in_1.add(rel_path) return { "mismatch": mismatch, "match": match, "only_in_1": only_in_1, + "only_in_2": only_in_2, "errors": errors, } @@ -58,33 +73,48 @@ def cmpfiles(dir_1=Path(), dir_2=Path(), patterns=None, ignore=None): def cmpmanifests(manifest_path_1, manifest_path_2, patterns=None, ignore=None): """Bit-accuracy test between two manifests. Their format is {filepath: {md5, size_st}}""" - with manifest_path_1.open() as f: - manifest_1 = json.load(f) - with manifest_path_2.open() as f: - manifest_2 = json.load(f) - # print(manifest_1) - # print(manifest_2) - # print(set(manifest_1.keys()) & set(manifest_2.keys())) + def parse_json(path): + with path.open() as f: + data = f.read() + try: + return json.loads(data) + except Exception as e: + print(data) + raise Exception(f"{e} Could not parse as JSON: {path}") + manifest_1 = parse_json(manifest_path_1) + manifest_2 = parse_json(manifest_path_2) + # print("manifest_1", manifest_1) + # print("manifest_2", manifest_2) + # print("manifest inter:", set(manifest_1.keys()) & set(manifest_2.keys())) if not patterns: patterns = ['*'] if not ignore: ignore = [] - # print(patterns) + # print("patterns", patterns) mismatch = set() # not the same match = set() # the same only_in_1 = set() # exists in dir_1 but not in dir_1 + only_in_2 = set() # exists in dir_2 but not in dir_2 errors = set() # or errors accessing for pattern in patterns: pattern = f'*{pattern}' + for file_2_str in manifest_2: + if not fnmatch.fnmatch(file_2_str, pattern): + continue + if any(fnmatch.fnmatch(file_2_str, f"{i}*") for i in ignore): + continue + if file_2_str not in manifest_1: + only_in_2.add(Path(file_2_str)) + for file_1_str, meta_1 in manifest_1.items(): if not fnmatch.fnmatch(file_1_str, pattern): continue file_1 = Path(file_1_str) - if any(fnmatch.fnmatch(file_1.name, i) for i in ignore): + if any(fnmatch.fnmatch(file_1, f"{i}*") for i in ignore): continue if file_1_str in manifest_2: is_same = meta_1['md5'] == manifest_2[file_1_str]['md5'] @@ -96,15 +126,16 @@ def cmpmanifests(manifest_path_1, manifest_path_2, patterns=None, ignore=None): only_in_1.add(file_1) return { - "mismatch": list(mismatch), - "match": list(match), - "only_in_1": list(only_in_1), - "errors": list(errors), + "mismatch": mismatch, + "match": match, + "only_in_1": only_in_1, + "only_in_2": only_in_2, + "errors": errors, } -def is_bit_accurate(commit_rootproject_dir, reference_rootproject_dir, output_directories, reference_platform=None): +def is_bit_accurate(commit_rootproject_dir, reference_rootproject_dir, output_directories, strict=False, reference_platform=None): """Compares the results of the current output directory versus a reference""" from .config import config patterns = config.get("bit_accuracy", {}).get("patterns", []) @@ -117,6 +148,7 @@ def is_bit_accurate(commit_rootproject_dir, reference_rootproject_dir, output_di ignore = config.get("bit_accuracy", {}).get("ignore", []) if not (isinstance(ignore, list) or isinstance(ignore, tuple)): ignore = [ignore] + ignore.append('run.json') # qa-board data, not relevant ignore.append('log.txt') # contains timestamps ignore.append('log.lsf.txt') # contains timestamps ignore.append('metrics.json') # contains measured run time @@ -126,19 +158,24 @@ def is_bit_accurate(commit_rootproject_dir, reference_rootproject_dir, output_di click.secho("WARNING: nothing was compared", fg='yellow') return True - comparaisons = {'match': [], 'mismatch': [], 'errors': []} + missing_runs = False + comparaisons = {'match': [], 'mismatch': [], 'errors': [], 'only_in_1': [], 'only_in_2': []} for output_directory in output_directories: # print('output_directory', output_directory) dir_1 = reference_rootproject_dir / output_directory dir_2 = commit_rootproject_dir / output_directory - # it's ugly and fragile... + # FIXME: the platform named used to be part of the output dir, + # but not anymore, so this code is broken..! + # We'd need a smart refactoring, and pass RunContexts instead of output directories... + # then it would be simple to compare to runs with any attribute changed. if reference_platform: from .config import platform dir_2 = Path(str(dir_2).replace(platform, reference_platform)) - # print('dir_1', dir_1) - # print('dir_2', dir_2) + if not dir_2.exists(): + click.secho(f"ERROR: did not run {output_directory}", fg='red') + missing_runs = True if (dir_1 / 'manifest.outputs.json').exists() and (dir_2 / 'manifest.outputs.json').exists(): comparaison = cmpmanifests( manifest_path_1 = dir_1 / 'manifest.outputs.json', @@ -146,8 +183,6 @@ def is_bit_accurate(commit_rootproject_dir, reference_rootproject_dir, output_di patterns=patterns, ignore=ignore, ) - comparaisons['match'].extend(output_directory / p for p in comparaison['match']) - comparaisons['mismatch'].extend(output_directory / p for p in comparaison['mismatch']) else: comparaison = cmpfiles( dir_1=dir_1, @@ -155,32 +190,207 @@ def is_bit_accurate(commit_rootproject_dir, reference_rootproject_dir, output_di patterns=patterns, ignore=ignore, ) - comparaisons['match'].extend(output_directory / p for p in comparaison['match']) - comparaisons['mismatch'].extend(output_directory / p for p in comparaison['mismatch']) - comparaisons['errors'].extend(output_directory / p for p in comparaison['errors']) + for attr in ('match', 'mismatch', 'errors', 'only_in_1', 'only_in_2'): + comparaisons[attr].extend(output_directory / p for p in comparaison[attr]) + + if missing_runs: + return False + bit_accurate = True + if strict: + if comparaisons['only_in_1']: + for o in output_directories: + click.secho(str(o), fg='red', bold=True, err=True) + click.secho(f"ERROR: some files existing in the reference run are not present:", fg='red') + for p in comparaisons['only_in_1']: + click.secho(f'➖ {p}', fg='red', dim=True) + bit_accurate = False + if comparaisons['only_in_2']: + for o in output_directories: + click.secho(str(o), fg='red', bold=True, err=True) + click.secho(f"ERROR: some files are not present in the reference run:", fg='red') + for p in comparaisons['only_in_2']: + click.secho(f'➕ {p}', fg='red', dim=True) + # print(comparaisons) + # exit(0) + bit_accurate = False # print(comparaisons['mismatch']) nothing_was_compared = not (len(comparaisons['match']) + len(comparaisons['mismatch']) + len(comparaisons['errors']) ) if nothing_was_compared: for o in output_directories: - click.echo(click.style(str(o), fg='yellow') + click.style(' (warning: no files were found to compare)', fg='yellow', dim=True), err=True) + click.echo(click.style(str(o), fg='yellow') + click.style(' (warning: no files were compared)', fg='yellow', dim=True), err=True) - if len(comparaisons['errors']): + if comparaisons['errors']: + bit_accurate = False click.secho("ERROR: while trying to read those files:", fg='red', bold=True) for p in comparaisons['error']: - click.secho(str(p), fg='red') - return False + click.secho(f"⚠️ {p}", fg='red') - if len(comparaisons['mismatch']): + if comparaisons['mismatch']: + bit_accurate = False for o in output_directories: click.secho(str(o), fg='red', bold=True, err=True) click.secho(f"ERROR: mismatch for:", fg='red') for p in comparaisons['mismatch']: - click.secho(f' {p}', fg='red', dim=True) - return False + click.secho(f'❌ {p}', fg='red', dim=True) - bit_accurate = not len(comparaisons['mismatch']) if bit_accurate and not nothing_was_compared: for o in output_directories: click.secho(str(o), fg='green', err=True) return bit_accurate + + + +@click.command() +@click.pass_context +@click.option('--batch', '-b', 'batches', required=True, multiple=True, help="Only check bit-accuracy for this batch of inputs+configs+database.") +@click.option('--batches-file', 'batches_files', type=PathType(), default=default_batches_files, multiple=True, help="YAML file listing batches of inputs+config+database selected from the database.") +@click.option('--strict', is_flag=True, help="By default only files existing in current/ref runs are checked. This files ensure we fail if some files exist in one run and not the other.") +def check_bit_accuracy_manifest(ctx, batches, batches_files, strict): + """ + Checks the bit accuracy of the results in the current ouput directory + versus the latest commit on origin/develop. + """ + commit_dir = outputs_commit if (is_ci or ctx.obj['share']) else Path() + all_bit_accurate = True + nb_compared = 0 + for run_context in iter_inputs(batches, batches_files, ctx.obj['database'], ctx.obj['configurations'], default_platform, {}, config, ctx.obj['inputs_settings']): + if not (run_context.database / run_context.rel_input_path / "manifest.outputs.json").exists(): + click.secho(f"[WARNING] no manifest for {run_context.database / run_context.rel_input_path}", fg='yellow') + continue + nb_compared += 1 + if run_context.input_path.is_file(): + click.secho('ERROR: check_bit_accuracy_manifest only works for inputs that are folders', fg='red', err=True) + # otherwise the manifest is at + # * input_path.parent / 'manifest.json' in the database + # * input_path.with_suffix('') / 'manifest.json' in the results + # # reference_output_directory = run_context.input_path if run_context.input_path.is_folder() else run_context.input_path.parent + exit(1) + + batch_conf_dir = make_batch_conf_dir(Path(), ctx.obj['batch_label'], ctx.obj["platform"], run_context.configurations, ctx.obj['extra_parameters'], ctx.obj['share']) + if f"/{user}/" in str(commit_dir): + commit_dir = Path(str(commit_dir).replace(user, '*')) + start, *end = commit_dir.parts + start, end = Path(start), str(Path(*end)) + commit_dirs = start.glob(end) + # FIXME: the output path is not created like this if rel_input_path is long or there are configs/tuning... + commit_dirs = [d for d in commit_dirs if (d / batch_conf_dir / run_context.rel_input_path).exists()] + assert commit_dirs + for commit_dir in commit_dirs: + input_is_bit_accurate = is_bit_accurate(commit_dir / batch_conf_dir, run_context.database, [run_context.rel_input_path], strict=strict) + all_bit_accurate = all_bit_accurate and input_is_bit_accurate + else: + input_is_bit_accurate = is_bit_accurate(commit_dir / batch_conf_dir, run_context.database, [run_context.rel_input_path], strict=strict) + all_bit_accurate = all_bit_accurate and input_is_bit_accurate + + if not all_bit_accurate: + click.secho("\nError: you are not bit-accurate versus the manifest.", bg='red', underline=True, bold=True) + click.secho("Reminder: the manifest lists the expected inputs/outputs for each test. It acts as an explicit gatekeeper against changes", fg='red', dim=True) + if not run_context.database.is_absolute(): + click.secho("If that's what you wanted, update and commit all manifests.", fg='red') + # click.secho("If that's what you wanted, update all manifests using:", fg='red') + # click.secho("$ qa batch * --save-manifests-in-database", fg='red') + # click.secho("$ git add # your changes", fg='red') + # click.secho("$ git commit # now retry your CI", fg='red') + else: + click.secho("To update the manifests for all tests, run:", fg='red') + click.secho("$ qa batch --save-manifests --batch *", fg='red') + exit(1) + + if not nb_compared: + click.secho("\nWARNING: Nothing was compared! It's not likely to be what you expected...", fg='yellow', underline=True, bold=True) + + + +@click.command() +@click.pass_context +@click.option( + "--reference", + default=config.get('project', {}).get('reference_branch', 'master'), + help="Branch, tag or commit used as reference." +) +@click.option('--batch', '-b', 'batches', multiple=True, help="Only check bit-accuracy for those batches of inputs+configs+database.") +@click.option('--batches-file', 'batches_files', type=PathType(), default=default_batches_files, multiple=True, help="YAML file listing batches of inputs+config+database selected from the database.") +@click.option('--strict', is_flag=True, help="By default only files existing in current/ref runs are checked. This files ensure we fail if some files exist in one run and not the other.") +@click.option('--reference-platform', help="Compare against a difference platform.") +def check_bit_accuracy(ctx, reference, batches, batches_files, strict, reference_platform): + """ + Checks the bit accuracy of the results in the current ouput directory + versus the latest commit on origin/develop. + """ + from .config import is_in_git_repo, commit_branch, is_ci, outputs_project_root, repo_root + from .gitlab import lastest_successful_ci_commit + from .conventions import get_commit_dirs + from .git import latest_commit, git_parents + + if not is_in_git_repo: + click.secho("You are not in a git repository, maybe in an artifacts folder. `check_bit_accuracy` is unavailable.", fg='yellow', dim=True) + exit(1) + + + if is_ci and commit_branch == reference: + click.secho(f'We are on branch {reference}', fg='cyan', bold=True, err=True) + click.secho(f"Comparing bit-accuracy against this commit's ({commit_id[:8]}) parents.", fg='cyan', bold=True, err=True) + # It will work until we try to rebase merge requests. + # We really should use Gitlab' API (or our database) to ask about previous pipelines on the branch + reference_commits = git_parents(commit_id) + else: + # ideally we should do something smarter... + # https://stackoverflow.com/questions/18222634/given-a-git-refname-can-i-detect-whether-its-a-hash-tag-or-branch + if "origin" not in reference: + origin_reference = f"origin/{reference}" + origin_latest_commit = latest_commit(origin_reference) + if origin_latest_commit != origin_reference: # it was a commit + click.secho(f'Comparing bit-accuracy versus the latest remote commit of {origin_reference}', fg='cyan', bold=True, err=True) + reference_commits = [origin_latest_commit] + else: + click.secho(f'Comparing bit-accuracy versus {reference}', fg='cyan', bold=True, err=True) + reference_commits = [reference] + click.secho(f"{commit_id[:8]} versus {reference_commits}.", fg='cyan', err=True) + + # This where the new results are located + commit_dir = outputs_commit_root if (is_ci or ctx.obj['share']) else Path() + + if not batches: + output_directories = list(p.parent.relative_to(commit_dir) for p in (commit_dir / subproject / 'output').rglob('manifest.outputs.json')) + else: + output_directories = [] + for run_context in iter_inputs(batches, batches_files, ctx.obj['database'], ctx.obj['configurations'], default_platform, {}, config, ctx.obj['inputs_settings']): + batch_conf_dir = make_batch_conf_dir(subproject, ctx.obj['batch_label'], ctx.obj["platform"], run_context.configurations, ctx.obj["extra_parameters"], ctx.obj['share']) + if batch_conf_dir.is_absolute(): + try: + batch_conf_dir = batch_conf_dir.relative_to(Path().resolve()) + except: + print("TODO: fix this...") + pass + input_path = run_context.rel_input_path + output_directory = batch_conf_dir / input_path.with_suffix('') + output_directories.append(output_directory) + + for reference_commit in reference_commits: + # if the reference commit is pending or failed, we wait or maybe pick a parent + reference_commit = lastest_successful_ci_commit(reference_commit) + click.secho(f'Current directory : {commit_dir}', fg='cyan', bold=True, err=True) + reference_rootproject_ci_dir = outputs_project_root / get_commit_dirs(reference_commit, repo_root) + if f"/{user}/" in str(reference_rootproject_ci_dir): + reference_rootproject_ci_dir_ = Path(str(reference_rootproject_ci_dir).replace(user, '*')) + start, *end = reference_rootproject_ci_dir_.parts + start, end = Path(start), str(Path(*end)) + reference_rootproject_ci_dirs = start.glob(end) + all_bit_accurate = True + for reference_rootproject_ci_dir in reference_rootproject_ci_dirs: + click.secho(f"Reference directory: {reference_rootproject_ci_dir}", fg='cyan', bold=True, err=True) + for o in output_directories: + all_bit_accurate = is_bit_accurate(commit_dir, reference_rootproject_ci_dir, [o], strict=strict, reference_platform=reference_platform) and all_bit_accurate + else: + click.secho(f"Reference directory: {reference_rootproject_ci_dir}", fg='cyan', bold=True, err=True) + all_bit_accurate = True + for o in output_directories: + all_bit_accurate = is_bit_accurate(commit_dir, reference_rootproject_ci_dir, [o], strict=strict, reference_platform=reference_platform) and all_bit_accurate + if not all_bit_accurate: + click.secho(f"\nERROR: results are not bit-accurate to {reference_commits}.", bg='red', bold=True) + if is_ci: + click.secho(f"\nTo investigate, go to", fg='red', underline=True) + for reference_commit in reference_commits: + click.secho(f"https://qa/{project.as_posix()}/commit/{commit_id}?reference={reference_commit}&selected_views=bit_accuracy", fg='red') + exit(1) diff --git a/qaboard/compat.py b/qaboard/compat.py index 7b74e49f..d8d4220b 100644 --- a/qaboard/compat.py +++ b/qaboard/compat.py @@ -22,6 +22,7 @@ def ensure_cli_backward_compatibility(): ('--return-prefix-outputs-path', '--list-output-dirs'), ('--ci', '--share'), ('--dry-run', '--dryrun'), + ('--lsf-memory', '--lsf-max-memory'), ('--group', '--batch'), ('--groups-file', '--batches-file'), ('--no-qa-database', '--offline'), @@ -100,3 +101,29 @@ def windows_to_linux_path(path : Path) -> Path: def linux_to_windows_path(path : Path) -> Path: return Path(linux_to_windows(str(path))) + + +def fix_linux_permissions(path: Path): + """ + This function is meant to be only used from Samsung SIRC. + + Windows does not set file permissions correctly on the shared storage, + it does not respect umask 0: files are not world-writable. + Trying to each_file.chmod(0o777) does not work either + The only option is to make the call from linux. + We could save a list of paths and chmod them with their parent directories... + but to make things faster to code, we just "ssh linux chmod everything" + We can assume SSH to be present on Windows10 + """ + return + from getpass import getuser + click.secho("... Fixing linux file permissions", err=True) + try: + user = getuser() + ssh = f"ssh -i \\\\netapp\\raid\\users\\{user}\\.ssh\\id_rsa -oStrictHostKeyChecking=no" + hostname = f"{user}-vdi" if user != "sircdevops" else "jenkins10-srv" + chmod = f'{ssh} {user}@{hostname} \'chmod -R 777 "{windows_to_linux_path(path).as_posix()}"\'' + click.secho(chmod, err=True) + os.system(chmod) + except Exception as e: + click.secho(f'WARNING: {e}', err=True) diff --git a/qaboard/config.py b/qaboard/config.py index 9e705568..83b57a7b 100755 --- a/qaboard/config.py +++ b/qaboard/config.py @@ -60,11 +60,15 @@ def find_configs(path : Path) -> List[Tuple[Dict, Path]]: if not qatools_configsxpaths: config_has_error = True if not ignore_config_errors: - click.secho('ERROR: Could not find a `qaboard.yaml` configuration file.\nDid you run `qatools init` ?', fg='red', err=True) - click.secho( - 'Please read the tutorial or ask Arthur Flam for help:\n' - 'http://qa-docs/', - dim=True, err=True) + click.secho('ERROR: Could not find a `qaboard.yaml` configuration file.', fg='red', err=True) + if 'QABOARD_TUNING' not in os.environ: + click.secho(' If you are starting a new project, run `qatools init`.', fg='red', err=True) + else: + click.secho(f' It seems "artifacts" are missing. To save them:', fg='red', err=True) + click.secho(f' 1. cd your/project', fg='red', err=True) + click.secho(f' 2. git checkout {os.environ.get("GIT_COMMIT", "your-commit")}', fg='red', err=True) + click.secho(f' 3. # build whatever is needed', fg='red', err=True) + click.secho(f' 4. qa save-artifacts', fg='red', err=True) # take care not to mutate the root config, as its project.name is the git repo name @@ -126,15 +130,18 @@ def find_configs(path : Path) -> List[Tuple[Dict, Path]]: user = getuser() -def storage_roots(config: Dict, project: Path, subproject: Path) -> Tuple[Path, Path]: - # we do compute it twice, but it gives us some flexibility - user = getuser() +def storage_roots(config: Dict, project: Path, subproject: Path) -> Tuple[Path, Path]: + # useful when migration results to a new default location + if 'QABOARD_NO_CACHE_USER' in os.environ: + user_ = getuser() + else: + user_ = user try: if 'ci_root' in config: # click.secho('DEPRECATION WARNING: the config key "ci_root" was renamed "storage"', fg='yellow', err=True) config['storage'] = config['ci_root'] config_storage: Union[str, Dict] = os.environ.get('QA_STORAGE', config.get('storage', {})) - interpolation_vars = {"project": project, "subproject": subproject, "user": user} + interpolation_vars = {"project": project, "subproject": subproject, "user": user_} spec_artifacts = config_storage.get('artifacts', config_storage) if isinstance(config_storage, dict) else config_storage spec_outputs = config_storage.get('outputs', config_storage) if isinstance(config_storage, dict) else config_storage artifacts_root = location_from_spec(spec_artifacts, interpolation_vars) @@ -250,7 +257,11 @@ def mkdir(path: Path): repo_root = d if not commit_id or not commit_branch: if is_in_git_repo: - commit_branch, commit_id = git_head(repo_root) + commit_branch_, commit_id_ = git_head(repo_root) + if not commit_id: + commit_id = commit_id_ + if not commit_branch: + commit_branch = commit_branch_ else: if not commit_branch: commit_branch = f'' @@ -266,15 +277,19 @@ def mkdir(path: Path): commit_committer_name: Optional[str] = user commit_committer_email: Optional[str] = None -commit_authored_datetime = datetime.datetime.now(datetime.timezone.utc).isoformat() -commit_message: Optional[str] = None +commit_authored_datetime = os.environ.get("GIT_AUTHORED_DATETIME", datetime.datetime.now(datetime.timezone.utc).isoformat()) +commit_message: Optional[str] = os.environ.get("GIT_MESSAGE") commit_parents: List[str] = [] if commit_id and is_in_git_repo: fields = ['%cn', '%ce', '%aI', '%P', "%B"] try: commit_info = git_show("%n".join(fields), commit_id) fields_values = commit_info.split('\n', maxsplit=len(fields)) - commit_committer_name, commit_committer_email, commit_authored_datetime, commit_parents_str, commit_message = fields_values + commit_committer_name, commit_committer_email, commit_authored_datetime_, commit_parents_str, commit_message_ = fields_values + if not commit_authored_datetime: + commit_authored_datetime = commit_authored_datetime_ + if not commit_message: + commit_message = commit_message_ commit_parents = commit_parents_str.split() except: # may fail when working on the first commit in a repo, like in our tests @@ -376,7 +391,7 @@ def get_default_database(inputs_settings): if not ignore_config_errors: click.secho(f'ERROR: Unable to parse {metrics_file}', fg='red', err=True, bold=True) click.secho(f'{e}', fg='red', err=True) - ignore_config_errors = True + ignore_config_errors = False available_metrics = _metrics.get('available_metrics', {}) main_metrics = _metrics.get('main_metrics', []) diff --git a/qaboard/conventions.py b/qaboard/conventions.py index a8c0fa36..8d1e572e 100755 --- a/qaboard/conventions.py +++ b/qaboard/conventions.py @@ -181,7 +181,7 @@ def get_commit_dirs(commit, repo_root: Optional[Path]=None) -> Path: return repo_root.resolve() if isinstance(commit, str): # commit hexsha try: - commit_id = git_show(format='%H') + commit_id = git_show(format='%H', reference=commit) except: if repo_root is None: raise ValueError("Not enough information about the commit to know where to store its data.") diff --git a/qaboard/gitlab.py b/qaboard/gitlab.py index 80bbe97c..09717e47 100755 --- a/qaboard/gitlab.py +++ b/qaboard/gitlab.py @@ -1,118 +1,113 @@ -import os -from pathlib import Path - -import requests -import click - -from urllib.parse import quote -from .config import config, root_qatools_config, subproject, commit_branch -from .config import secrets - -# TODO: read root_qatools_config['project']['url'] -# handle git@ and http:// schemes... -# TODO: don't put credentials here... -gitlab_host = os.getenv('GITLAB_HOST', secrets.get('GITLAB_HOST', 'https://gitlab.com')) -gitlab_token = os.environ.get('GITLAB_ACCESS_TOKEN', secrets.get('GITLAB_ACCESS_TOKEN')) -gitlab_headers = { - 'Private-Token': gitlab_token, -} -gitlab_api = f"{gitlab_host}/api/v4" -gitlab_project_id = quote(root_qatools_config['project']['name'], safe='') - - -def check_gitlab_token(): - if not gitlab_token: - click.secho("WARNING: GITLAB_ACCESS_TOKEN is not defined.", fg='yellow', bold=True, err=True) - click.secho(" Please provide it as an environment variable: https://docs.gitlab.com/ee/user/profile/personal_access_tokens.html", fg='yellow', err=True) - - -def ci_commit_data(commit_id): - check_gitlab_token() - url = f"{gitlab_api}/projects/{gitlab_project_id}/repository/commits/{commit_id}" - r = requests.get(url, headers=gitlab_headers) - r.raise_for_status() - return r.json() - -def ci_commit_statuses(commit_id, **kwargs): - check_gitlab_token() - url = f"{gitlab_api}/projects/{gitlab_project_id}/repository/commits/{commit_id}/statuses" - r = requests.get(url, headers=gitlab_headers, params=kwargs) - r.raise_for_status() - return r.json() - - - -def update_gitlab_status(commit_id, state, label, description): - check_gitlab_token() - url = f"{gitlab_api}/projects/{gitlab_project_id}/statuses/{commit_id}" - name = f"QA {subproject.name}" if subproject else 'QA' - target_url = f"https://qa/{config['project']['name']}/commit/{commit_id}" - if label != "default": - name += f" | {label}" - target_url += f"?batch={label}" - params = { - "state": state, - "name": name, - "target_url": target_url, - "description": description, - # "ref": commit_branch, - } - try: - r = requests.post(url, headers=gitlab_headers, params=params) - r.raise_for_status() - # print(r.json()) - except Exception as e: - print(r) - print(url) - print(e) - pass - - - - - -def lastest_successful_ci_commit(commit_id: str, max_parents_depth=config.get('bit_accuracy', {}).get('max_parents_depth', 5)): - if not gitlab_token: - return commit_id - - from .git import git_parents - if max_parents_depth < 0: - click.secho(f'Could not find a commit that passed CI', fg='red', bold=True, err=True) - exit(1) - - failed_ci_job_name = config.get('bit_accuracy', {}).get('failed_ci_job_name') - if failed_ci_job_name and subproject: - failed_ci_job_name = f"{failed_ci_job_name} {subproject.name}", - - - wait_time = 15 # seconds - while True: - statuses = ci_commit_statuses(commit_id, ref=commit_branch, name=failed_ci_job_name) - # print(statuses) - - if statuses is None: - click.secho(f'WARNING: Could not get the CI status. You may need a different GITLAB_ACCESS_TOKEN.', fg='yellow', err=True) - return commit_id - - if failed_ci_job_name: - # print('filtering') - statuses = [s for s in statuses if s['name'] == f"{subproject.name} {failed_ci_job_name}"] - # print(statuses) - - commit_failed = any(s['status'] in ['failed', 'canceled'] and not s.get('allow_failure', False) for s in statuses) - if commit_failed: - click.secho(f"WARNING: {commit_id[:8]} failed the CI pipeline. (statuses: {set(s['status'] for s in statuses)})", fg='yellow', bold=True, err=True) - if config.get('bit_accuracy', {}).get('on_reference_failed_ci') == 'compare-first-parent': - click.secho(f"We now try to compare against its first parent.", fg='yellow', err=True) - return lastest_successful_ci_commit(git_parents(commit_id)[0], max_parents_depth=1) - else: - return commit_id - - commit_success = all(s['status'] == 'success' or s.get('allow_failure', False) for s in statuses) - if commit_success: - return commit_id - - click.secho(f"The CI pipeline for {commit_id[:8]} is not over yet (statuses: {set(s['status'] for s in statuses)}). Retrying in {wait_time}s", fg='yellow', dim=True, err=True) - # click.secho(str(statuses), fg='yellow', dim=True, err=True) - import time - time.sleep(wait_time) +import os +from pathlib import Path + +import requests +import click + +from urllib.parse import quote +from .config import config, root_qatools_config, subproject, commit_branch, commit_id +from .config import secrets + +# TODO: read root_qatools_config['project']['url'] +# handle git@ and http:// schemes... +# TODO: don't put credentials here... +gitlab_host = os.getenv('GITLAB_HOST', secrets.get('GITLAB_HOST', 'https://gitlab.com')) +gitlab_token = os.environ.get('GITLAB_ACCESS_TOKEN', secrets.get('GITLAB_ACCESS_TOKEN')) +gitlab_headers = { + 'Private-Token': gitlab_token, +} +gitlab_api = f"{gitlab_host}/api/v4" +gitlab_project_id = quote(root_qatools_config['project']['name'], safe='') + + +def check_gitlab_token(): + if not gitlab_token: + click.secho("WARNING: GITLAB_ACCESS_TOKEN is not defined.", fg='yellow', bold=True, err=True) + click.secho(" Please provide it as an environment variable: https://docs.gitlab.com/ee/user/profile/personal_access_tokens.html", fg='yellow', err=True) + + +def ci_commit_data(commit_id): + check_gitlab_token() + url = f"{gitlab_api}/projects/{gitlab_project_id}/repository/commits/{commit_id}" + r = requests.get(url, headers=gitlab_headers) + r.raise_for_status() + return r.json() + +def ci_commit_statuses(commit_id, **kwargs): + check_gitlab_token() + url = f"{gitlab_api}/projects/{gitlab_project_id}/repository/commits/{commit_id}/statuses" + r = requests.get(url, headers=gitlab_headers, params=kwargs) + r.raise_for_status() + return r.json() + + + +def update_gitlab_status(state, name, target_url, description, commit_id=commit_id): + check_gitlab_token() + url = f"{gitlab_api}/projects/{gitlab_project_id}/statuses/{commit_id}" + params = { + "state": state, + "name": name, + "target_url": target_url, + "description": description, + # "ref": commit_branch, + } + try: + r = requests.post(url, headers=gitlab_headers, params=params) + r.raise_for_status() + # print(r.json()) + except Exception as e: + print(r) + print(url) + print(e) + pass + + + + + +def lastest_successful_ci_commit(commit_id: str, max_parents_depth=config.get('bit_accuracy', {}).get('max_parents_depth', 5)): + if not gitlab_token: + return commit_id + + from .git import git_parents + if max_parents_depth < 0: + click.secho(f'Could not find a commit that passed CI', fg='red', bold=True, err=True) + exit(1) + + failed_ci_job_name = config.get('bit_accuracy', {}).get('failed_ci_job_name') + if failed_ci_job_name and subproject: + failed_ci_job_name = f"{failed_ci_job_name} {subproject.name}", + + + wait_time = 15 # seconds + while True: + statuses = ci_commit_statuses(commit_id, ref=commit_branch, name=failed_ci_job_name) + # print(statuses) + + if statuses is None: + click.secho(f'WARNING: Could not get the CI status. You may need a different GITLAB_ACCESS_TOKEN.', fg='yellow', err=True) + return commit_id + + if failed_ci_job_name: + # print('filtering') + statuses = [s for s in statuses if s['name'] == f"{subproject.name} {failed_ci_job_name}"] + # print(statuses) + + commit_failed = any(s['status'] in ['failed', 'canceled'] and not s.get('allow_failure', False) for s in statuses) + if commit_failed: + click.secho(f"WARNING: {commit_id[:8]} failed the CI pipeline. (statuses: {set(s['status'] for s in statuses)})", fg='yellow', bold=True, err=True) + if config.get('bit_accuracy', {}).get('on_reference_failed_ci') == 'compare-first-parent': + click.secho(f"We now try to compare against its first parent.", fg='yellow', err=True) + return lastest_successful_ci_commit(git_parents(commit_id)[0], max_parents_depth=1) + else: + return commit_id + + commit_success = all(s['status'] == 'success' or s.get('allow_failure', False) for s in statuses) + if commit_success: + return commit_id + + click.secho(f"The CI pipeline for {commit_id[:8]} is not over yet (statuses: {set(s['status'] for s in statuses)}). Retrying in {wait_time}s", fg='yellow', dim=True, err=True) + # click.secho(str(statuses), fg='yellow', dim=True, err=True) + import time + time.sleep(wait_time) diff --git a/qaboard/iterators.py b/qaboard/iterators.py index 7b0d0bc1..dd8aee02 100755 --- a/qaboard/iterators.py +++ b/qaboard/iterators.py @@ -8,7 +8,7 @@ import numbers import fnmatch import traceback -from copy import copy +from copy import deepcopy from pathlib import Path from itertools import chain from dataclasses import replace @@ -32,6 +32,8 @@ def flatten(lst: Union[str, List, Tuple]) -> Iterator[Union[str, List, Tuple]]: def resolve_aliases(names : Union[str, List[str], Tuple[str, ...]], aliases: Dict[str, List[str]], depth=10) -> Iterator[Union[str, List[str], Tuple[str, ...]]]: # TODO: Expose an API that -> Iterator[str], after all the recursive calls. + if names is None: + return [] if not depth: yield from chain.from_iterable(names) if isinstance(names, tuple) or isinstance(names, list): @@ -82,6 +84,9 @@ def iter_inputs_at_path(path, database, globs, use_parent_folder, qatools_config raise ValueError else: click.secho(f'WARNING: No inputs found for the batch "{path}"', fg='yellow', err=True) + if 'QABOARD_TUNING' in os.environ and not database.is_absolute(): + click.secho(' You look for your input inside the project directory, but we cannot find them...', fg='red', err=True) + click.secho(' Make sure that (1) your inputs are declared as artifacts, and (2) you called `qa save-artifacts`.', fg='red', err=True) return if not globs: @@ -135,6 +140,8 @@ def _iter_inputs(path, database, inputs_settings, qatools_config, only=None, exc database_str, *path_parts = Path(path).parts path = Path(*path_parts) database = Path(database_str) + if database.is_absolute(): # normalization to avoid common issues where users ask for "//some/path" instead of "/some/path" + database = database.resolve() entrypoint_module_ = entrypoint_module(qatools_config) if hasattr(entrypoint_module_, 'iter_inputs'): try: @@ -192,7 +199,7 @@ def iter_inputs(batches: List[str], batches_files: List[os.PathLike], default_da if not default_inputs_settings: inputs_settings = get_settings(qatools_config.get('inputs', {}).get('types', {}).get('default', 'default'), qatools_config) else: - inputs_settings = copy(default_inputs_settings) + inputs_settings = deepcopy(default_inputs_settings) run_context = RunContext( input_path=Path(), database=default_database, @@ -235,7 +242,7 @@ def iter_batch(batch: Dict, default_run_context: RunContext, qatools_config, def if batch is None: return - run_context = copy(default_run_context) + run_context = deepcopy(default_run_context) run_context.configurations = batch.get('configs', batch.get('configurations', batch.get('configuration', run_context.configurations))) run_context.configurations = list(flatten(run_context.configurations)) if 'platform' in batch: @@ -250,7 +257,7 @@ def iter_batch(batch: Dict, default_run_context: RunContext, qatools_config, def from .config import get_default_database run_context.database = get_default_database(inputs_settings) else: - inputs_settings = copy(default_inputs_settings) + inputs_settings = deepcopy(default_inputs_settings) inputs_settings.update(batch) batch_database = location_from_spec(batch.get('database', run_context.database)) @@ -259,19 +266,25 @@ def iter_batch(batch: Dict, default_run_context: RunContext, qatools_config, def if batch.get('matrix'): from sklearn.model_selection import ParameterGrid for matrix in ParameterGrid(batch['matrix']): - batch_ = copy(batch) + batch_ = deepcopy(batch) for key in ['matrix', 'configuration', 'configurations', 'configs', 'platform']: if key in batch: del batch_[key] - matrix_run_context = copy(run_context) + matrix_run_context = deepcopy(run_context) if 'platform' in matrix: matrix_run_context.platform = matrix['platform'] - if 'configuration' in matrix: - matrix_run_context.configurations = matrix['configuration'] - if 'configurations' in matrix: - matrix_run_context.configurations = matrix['configurations'] - if 'configs' in matrix: - matrix_run_context.configurations = matrix['configs'] + matrix_config = None + for k in ['configuration', 'configurations', 'configs']: + if k in matrix: + matrix_config = matrix[k] + if matrix_config: + # if no config is specified in the batch, but the matrix defined some + # them we want to replace the default config, not append to it + run_context_uses_default_config = not any([k in batch for k in ['configs', 'configurations', 'configuration']]) + if matrix_run_context.configurations and not run_context_uses_default_config: + matrix_run_context.configurations.append(matrix_config) + else: + matrix_run_context.configurations = matrix_config for param, value in matrix.items(): if param in ['configuration', 'configurations', 'configs', 'platform']: continue @@ -286,18 +299,25 @@ def iter_batch(batch: Dict, default_run_context: RunContext, qatools_config, def return # We also allow each input to have its settings... - if isinstance(locations, list): - locations_as_dict: Dict = {} + if isinstance(locations, dict): # {inputA: config, inputB: config} + locations_and_configs = [(location, config) for location, config in locations.items()] + if isinstance(locations, list): # [inputA, inputA] or [(inputA, configA), (inputB, configB)] or [{inputA: configA, inputB: configB}] + locations_and_configs = [] for l in locations: - if l in locations: - if not isinstance(l, dict): - locations_as_dict[l] = None - else: - locations_as_dict.update(l) - locations = locations_as_dict + if isinstance(l, str): + locations_and_configs.append((l, None)) + elif isinstance(l, list): + location, *location_configurations = l + locations_and_configs.append((location, location_configurations)) + elif isinstance(l, dict): + for location, location_configurations in l.items(): + locations_and_configs.append((location, location_configurations)) + else: + click.secho(f'ERROR: Could not understand the inputs in the batch ({locations_and_configs}).', fg='red', err=True) + raise ValueError - for location, location_configurations in locations.items(): - location_run_context = copy(run_context) + for location, location_configurations in locations_and_configs: + location_run_context = deepcopy(run_context) location_inputs_settings = inputs_settings if location_configurations: if isinstance(location_configurations, dict): @@ -309,7 +329,7 @@ def iter_batch(batch: Dict, default_run_context: RunContext, qatools_config, def location_run_context.database = location_database if 'platform' in batch: location_run_context.platform = location_configurations['platform'] - location_inputs_settings = copy(inputs_settings) + location_inputs_settings = deepcopy(inputs_settings) if 'type' in location_configurations: location_run_context.type = location_configurations['type'] location_inputs_settings = get_settings(location_run_context.type, qatools_config) diff --git a/qaboard/optimize.py b/qaboard/optimize.py index 671285ff..d512c542 100755 --- a/qaboard/optimize.py +++ b/qaboard/optimize.py @@ -1,14 +1,12 @@ -import subprocess -from functools import lru_cache import yaml import json +import subprocess -import requests import click -import numpy as np +from joblib import Parallel, delayed -from .api import NumpyEncoder, batch_info, notify_qa_database -from .config import subproject, commit_id, outputs_commit, available_metrics, default_batches_files, default_platform +from .api import NumpyEncoder, batch_info, notify_qa_database, print_url +from .config import project, subproject, commit_id, outputs_commit, available_metrics, default_batches_files, default_platform from .conventions import batch_dir from .utils import PathType @@ -21,102 +19,126 @@ @click.option('--batch', '-b', 'batches', required=True, multiple=True, help="Use the inputs+configs+database in those batches") @click.option('--batches-file', 'batches_files', default=default_batches_files, multiple=True, help="YAML file listing batches of inputs+config+database selected from the database.") @click.option('--config-file', required=True, type=PathType(), help="YAML search space configuration file.") +@click.option('--parallel-param-sampling', type=int, help="Parallel paramater sampling.") @click.argument('forwarded_args', nargs=-1, type=click.UNPROCESSED) @click.pass_context -def optimize(ctx, batches, batches_files, config_file, forwarded_args): - ctx.obj['batch_dir'].mkdir(parents=True, exist_ok=True) +def optimize(ctx, batches, batches_files, config_file, parallel_param_sampling, forwarded_args): + batch_dir_for = lambda label: batch_dir(outputs_commit, label, save_with_ci=True) + optim_dir = batch_dir_for(ctx.obj['batch_label']) + optim_dir.mkdir(parents=True, exist_ok=True) + ctx.obj['batches'] = batches ctx.obj['batches_files'] = batches_files ctx.obj['forwarded_args'] = forwarded_args + print_url(ctx) from shutil import rmtree from .api import aggregated_metrics objective, optimizer, optim_config, dim_mapping = init_optimization(config_file, ctx) + if not parallel_param_sampling: + parallel_param_sampling = optim_config.get('parallel_sampling', 1) # TODO: warm-start # load and "tell" existing results (if there are any) # (or use a checkpoint?) - for iteration in range(optim_config['evaluations']): click.secho(f"Starting iteration {iteration}", fg='blue') - suggested = optimizer.ask() + if parallel_param_sampling == 1: + suggested = optimizer.ask() + else: + click.secho(f" {parallel_param_sampling} parallel samples", fg='blue') + suggested = optimizer.ask(n_points=parallel_param_sampling) + # print("suggested", suggested) click.secho(f"Computing objective", fg='blue') - y = objective([*suggested, iteration]) + if parallel_param_sampling == 1: + y = objective([*suggested, iteration]) + else: + y = Parallel(n_jobs=parallel_param_sampling)(delayed(objective)([*s, iteration+idx]) for idx, s in enumerate(suggested)) + # print(f"y={y}", suggested) click.secho(f"Updating optimizer", fg='blue') results = optimizer.tell(suggested, y) + click.secho(f"Updating QA-Board", fg='blue') + if parallel_param_sampling == 1: + suggested = [suggested] + y = [y] + for idx, y_iter in enumerate(y): + iteration_batch_label = f"{ctx.obj['batch_label']}|iter{iteration+idx+1}" + iteration_batch_dir = batch_dir_for(iteration_batch_label) + aggregated_metrics_ = aggregated_metrics(iteration_batch_label) + notify_qa_database(**{ + **ctx.obj, + **{ + "extra_parameters": dim_mapping(suggested[idx]), + # TODO: we really should to tuning/platform in make_batch_conf_dir + # 1. make change, 2. rename existing folders) + "output_directory": iteration_batch_dir, + 'input_path': '|'.join(batches), + # we want to show in the summary tab the best results for the tuning experiment + # but in the exploration see the results per iteration.... + "input_type": 'optim_iteration', # or... single ? don't show them in the UI + "is_pending": False, + "is_failed": False, + "metrics": { + "iteration": iteration+idx+1, + "objective": y_iter, + **aggregated_metrics_, + }, + }, + }) - iteration_batch_label = f"{ctx.obj['batch_label']}|iter{iteration+1}" - iteration_batch_dir = batch_dir(outputs_commit, iteration_batch_label) - notify_qa_database(**{ - **ctx.obj, - **{ - "extra_parameters": dim_mapping(suggested), - # TODO: we really should to tuning/platform in make_batch_conf_dir - # 1. make change, 2. rename existing folders) - "output_directory": iteration_batch_dir, - 'input_path': '|'.join(batches), - # we want to show in the summary tab the best results for the tuning experiment - # but in the exploration see the results per iteration.... - "input_type": 'optim_iteration', # or... single ? don't show them in the UI - "is_pending": False, - "is_failed": False, - "metrics": { - "iteration": iteration+1, - "objective": y, - **aggregated_metrics(iteration_batch_label), + # results + # .x [float]: location of the minimum. + # .fun [float]: function value at the minimum. + # .models: surrogate models used for each iteration. + # .x_iters [array]: location of function evaluation for each iteration. + # .func_vals [array]: function value for each iteration. + # .space [Space]: the optimization space. + # .specs [dict]: parameters passed to the function. + is_best = results.func_vals[iteration+idx] <= results.fun or iteration+idx==0 + if is_best: + click.secho(f'New best @iteration{iteration+idx+1}: {y} at iteration {iteration+idx+1}', fg='green') + + is_best_data = { + "is_best_iter": True, + "best_params": dim_mapping(suggested[idx]), + "best_metrics": { + "objective": y_iter, + **aggregated_metrics_, }, - }, - }) - - notify_qa_database(object_type='batch', **{ - **ctx.obj, - **{ - "data": { - "optimization": True, - "iterations": iteration+1, - "last_iteration_label": iteration_batch_label, - }, - }, - }) - - # results - # .x [float]: location of the minimum. - # .fun [float]: function value at the minimum. - # .models: surrogate models used for each iteration. - # .x_iters [array]: location of function evaluation for each iteration. - # .func_vals [array]: function value for each iteration. - # .space [Space]: the optimization space. - # .specs [dict]: parameters passed to the function. - is_best = results.func_vals[iteration] <= results.fun - if iteration==0 or is_best: - click.secho(f'New best @iteration{iteration+1}: {y} at iteration {iteration+1}', fg='green') + } if is_best else {} + notify_qa_database(object_type='batch', **{ **ctx.obj, **{ "data": { - "best_params": dim_mapping(suggested), - "best_iter": iteration+1, - "best_metrics": aggregated_metrics(iteration_batch_label), + "optimization": True, + "iteration": iteration+idx+1, + "iteration_label": iteration_batch_label, + **is_best_data, }, }, }) - try: - click.secho(f'Creating plots', fg='blue') - make_plots(results, batch_dir(outputs_commit, ctx.obj['batch_label'])) - except: - pass - else: - # TODO: do it using an API call...? 1. get the batch ID 2. DELETE /api/v1/batch// - # We remove the results to make sure we don't waste disk space - rmtree(iteration_batch_dir, ignore_errors=True) + + if is_best: + try: + click.secho(f'Creating plots', fg='blue') + make_plots(results, optim_dir) + except: + pass + else: + # We remove the results to make sure we don't waste disk space + # It is also be done server-side... + print(f"RM {iteration_batch_dir}") + rmtree(iteration_batch_dir, ignore_errors=True) + exit(0) print(results) if not results.models: # needs at least n_initial_points(=5) evaluations! return # tuning plots are saved in the label directory - make_plots(results, batch_dir(outputs_commit, ctx.obj['batch_label'])) + make_plots(results, optim_dir) @@ -163,7 +185,7 @@ def objective(**opt_params): # From the UI we will want to see the iteration as a metric del params["iteration"] - batch_label = f"{ctx.obj['batch_label']}|iter{opt_params['iteration']+1}" + batch_label = f"{ctx.obj['raw_batch_label']}|iter{opt_params['iteration']+1}" command = ' '.join([ 'qa', f"--label '{batch_label}'", @@ -195,7 +217,8 @@ def objective(**opt_params): # Now that we finished computing all the results, we will download the results and # compute the objective function: - return batch_objective(commit_id, batch_label, optim_config['objective']) + shared_batch_label = f"{ctx.obj['batch_label']}|iter{opt_params['iteration']+1}" + return batch_objective(project, commit_id, shared_batch_label, optim_config['objective']) # For the full list of options, refer to: # https://scikit-optimize.github.io/stable/modules/generated/skopt.optimizer.Optimizer.html#skopt.optimizer.Optimizer @@ -279,8 +302,8 @@ def match_key(output): -def batch_objective(commit_id, batch_label, config_objective): - this_batch_info = batch_info(reference=commit_id, is_branch=False, batch=batch_label) +def batch_objective(project, commit_id, batch_label, config_objective): + this_batch_info = batch_info(reference=commit_id, is_branch=False, batch=batch_label, project=project) # We can compare to KPI quality target defined if 'target' in config_objective and config_objective['target']: target = config_objective['target'] @@ -291,6 +314,8 @@ def batch_objective(commit_id, batch_label, config_objective): target.get('id', target.get('branch', target.get('tag', ''))), batch=target.get('batch', 'default'), is_branch='branch' in target, # for tag we need special care... + # the working directory changed... + project=project, ) else: use_default_targets = True @@ -332,6 +357,7 @@ def batch_objective(commit_id, batch_label, config_objective): def make_plots(results, dir): + # click.secho(str(dir), dim=True) import matplotlib import matplotlib.pyplot as plt # https://matplotlib.org/faq/usage_faq.html#non-interactive-example @@ -383,16 +409,6 @@ def make_plots(results, dir): # plot.legend(loc="best", prop={'size': 6}, numpoints=1); -# parallel optimization -# in the yaml: -# parallel: X (if you have a small dataset.self.) -# https://github.com/scikit-optimize/scikit-optimize/blob/master/examples/parallel-optimization.ipynb -# from sklearn.externals.joblib import Parallel, delayed -# x = optimizer.ask(n_points=4) # x is a list of n_points points -# y = Parallel()(delayed(branin)(v) for v in x) # evaluate points in parallel -# optimizer.tell(x, y) - - # checkpoints? # https://github.com/scikit-optimize/scikit-optimize/blob/master/examples/interruptible-optimization.ipynb # https://github.com/scikit-optimize/scikit-optimize/blob/master/examples/store-and-load-results.ipynb diff --git a/qaboard/qa.py b/qaboard/qa.py index ba73a352..32f43f49 100755 --- a/qaboard/qa.py +++ b/qaboard/qa.py @@ -3,22 +3,22 @@ CLI tool to runs various tasks related to QA. """ import os -import time -from pathlib import Path +import re import sys -import traceback import json -import yaml +import time import uuid +import yaml import datetime +import traceback +from pathlib import Path import click from .run import RunContext -from .runners import runners, Job, JobGroup -from .runners.lsf import LsfPriority +from .runners import Job, JobGroup -from .conventions import batch_dir, batch_dir, make_batch_dir, make_batch_conf_dir, make_hash +from .conventions import make_batch_dir, make_batch_conf_dir from .conventions import serialize_config, deserialize_config, get_settings from .utils import PathType, entrypoint_module, load_tuning_search from .utils import save_outputs_manifest, total_storage @@ -32,7 +32,7 @@ from .config import project, project_root, subproject, config from .config import default_batches_files, get_default_database, default_batch_label, default_platform from .config import get_default_configuration, default_input_type -from .config import commit_id, outputs_commit, artifacts_commit, root_qatools, artifacts_commit_root, outputs_commit_root +from .config import commit_id, outputs_commit, artifacts_commit, root_qatools, artifacts_commit_root from .config import user, is_ci, on_windows @@ -86,7 +86,7 @@ def qa(ctx, platform, configurations, label, tuning, tuning_filepath, dryrun, sh # Note: to support multiple databases per project, # either use / as database, or somehow we need to hash the db in the output path. ctx.obj['raw_batch_label'] = label - ctx.obj['batch_label'] = label if not share else f"@{user}| {label}" + ctx.obj['batch_label'] = label if (not share or is_ci) else f"@{user}| {label}" ctx.obj['platform'] = platform ctx.obj['input_type'] = input_type @@ -176,12 +176,14 @@ def run(ctx, input_path, output_path, keep_previous, no_postprocess, forwarded_a """ run_context = RunContext.from_click_run_context(ctx, config) - # Usually we want to remove any files already present in the output directory. - # It avoids issues with remaining state... This said, - # In some cases users want to debug long, multi-stepped runs, for which they have their own caching - if not keep_previous: - import shutil - shutil.rmtree(run_context.output_dir, ignore_errors=True) + if run_context.output_dir.exists(): + # Usually we want to remove any files already present in the output directory. + # It avoids issues with remaining state... This said, + # In some cases users want to debug long, multi-stepped runs, for which they have their own caching + if not (keep_previous or 'QABOARD_RUN_KEEP' in os.environ): + # TODO: check in the database the status of the run? + import shutil + shutil.rmtree(run_context.output_dir, ignore_errors=True) run_context.output_dir.mkdir(parents=True, exist_ok=True) with (run_context.output_dir / 'run.json').open('w') as f: @@ -286,24 +288,26 @@ def postprocess_(runtime_metrics, run_context, skip=False, save_manifests_in_dat } with (run_context.output_dir / 'metrics.json').open('w') as f: json.dump(metrics, f, sort_keys=True, indent=2, separators=(',', ': ')) - # To help identify if input files change, we compute and save some metadata. - if is_ci or save_manifests_in_database: - manifest_inputs = run_context.obj.get('manifest-inputs', [run_context.input_path]) - input_files = {} - for manifest_input in manifest_inputs: - manifest_input = Path(manifest_input) - if manifest_input.is_dir(): - for idx, path in enumerate(manifest_input.rglob('*')): - if idx >= 200: - break - if not path.is_file(): - continue - input_files[path.as_posix()] = file_info(path, config=config) - elif manifest_input.is_file(): - input_files.update({manifest_input.as_posix(): file_info(manifest_input, config=config)}) - with (run_context.output_dir / 'manifest.inputs.json').open('w') as f: - json.dump(input_files, f, indent=2) + manifest_inputs = run_context.obj.get('manifest-inputs', [run_context.input_path]) + input_files = {} + for manifest_input in manifest_inputs: + manifest_input = Path(manifest_input) + if manifest_input.is_dir(): + for idx, path in enumerate(manifest_input.rglob('*')): + if idx >= 200: + break + if not path.is_file(): + continue + input_files[path.as_posix()] = file_info(path, config=config) + elif manifest_input.is_file(): + input_files.update({manifest_input.as_posix(): file_info(manifest_input, config=config)}) + try: + with (run_context.output_dir / 'manifest.inputs.json').open('w') as f: + json.dump(input_files, f, indent=2) + except Exception as e: + click.secho(f'WARNING: When writing the input manifest:', fg="yellow", bold=True, err=True) + click.secho(str(e), fg="yellow", err=True) outputs_manifest = save_outputs_manifest(run_context.output_dir, config=config) output_data = { @@ -322,6 +326,10 @@ def postprocess_(runtime_metrics, run_context, skip=False, save_manifests_in_dat if not run_context.obj.get('offline') and not run_context.obj.get('dryrun'): notify_qa_database(**run_context.obj, metrics=metrics, data=output_data, is_pending=False, is_running=False) + if os.name == "nt" and not run_context.obj.get('dryrun') and (run_context.obj.get('share') or is_ci): + from qaboard.compat import fix_linux_permissions + fix_linux_permissions(run_context.output_dir) + return metrics @@ -407,7 +415,7 @@ def wait(ctx, output_id): @click.option('--runner', default=default_runner, help="Run runs locally or using a task queue like Celery, LSF...") @click.option('--local-concurrency', default=os.environ.get('QA_BATCH_CONCURRENCY', local_config.get('concurrency')), type=int, help="joblib's n_jobs: 0=unlimited, 2=2 at a time, -1=#cpu-1") @click.option('--lsf-threads', default=lsf_config.get('threads', 0), type=int, help="restrict number of lsf threads to use. 0=no restriction") -@click.option('--lsf-memory', default=lsf_config.get('memory', 0), help="restrict memory (MB) to use. 0=no restriction") +@click.option('--lsf-max-memory', default=lsf_config.get('max_memory', lsf_config.get('memory', 0)), help="restrict memory (MB) to use. 0=no restriction") @click.option('--lsf-queue', default=lsf_config.get('queue'), help="LSF queue (-q)") @click.option('--lsf-fast-queue', default=lsf_config.get('fast_queue', lsf_config.get('queue')), help="Fast LSF queue, for interactive jobs") @click.option('--lsf-resources', default=lsf_config.get('resources', None), help="LSF resources restrictions (-R)") @@ -417,7 +425,7 @@ def wait(ctx, output_id): @click.option('--prefix-outputs-path', type=PathType(), default=None, help='Custom prefix for the outputs; they will be at $prefix/$output_path') @click.argument('forwarded_args', nargs=-1, type=click.UNPROCESSED) @click.pass_context -def batch(ctx, batches, batches_files, tuning_search_dict, tuning_search_file, no_wait, list_contexts, list_output_dirs, list_inputs, runner, local_concurrency, lsf_threads, lsf_memory, lsf_queue, lsf_fast_queue, lsf_resources, lsf_priority, action_on_existing, action_on_pending, prefix_outputs_path, forwarded_args): +def batch(ctx, batches, batches_files, tuning_search_dict, tuning_search_file, no_wait, list_contexts, list_output_dirs, list_inputs, runner, local_concurrency, lsf_threads, lsf_max_memory, lsf_queue, lsf_fast_queue, lsf_resources, lsf_priority, action_on_existing, action_on_pending, prefix_outputs_path, forwarded_args): """Run on all the inputs/tests/recordings in a given batch using the LSF cluster.""" if not batches_files: click.secho(f'WARNING: Could not find how to identify input tests.', fg='red', err=True, bold=True) @@ -467,7 +475,7 @@ def batch(ctx, batches, batches_files, tuning_search_dict, tuning_search_file, n default_runner_options.update({ "project": lsf_config.get('project', str(project) if project else "qaboard"), "max_threads": lsf_threads, - "max_memory": lsf_memory, + "max_memory": lsf_max_memory, 'resources': lsf_resources, "queue": lsf_queue, "fast_queue": lsf_fast_queue, @@ -499,8 +507,8 @@ def batch(ctx, batches, batches_files, tuning_search_dict, tuning_search_file, n batch_conf_dir = batch_conf_dir / Path(tuning_file).stem from qaboard.conventions import slugify_hash input_dir = run_context.rel_input_path.with_suffix('') - if len(input_dir.as_posix()) > 90: - input_dir = Path(slugify_hash(input_dir.as_posix(), maxlength=90)) + if len(input_dir.as_posix()) > 70: + input_dir = Path(slugify_hash(input_dir.as_posix(), maxlength=70)) run_context.output_dir = batch_conf_dir / input_dir if forwarded_args: run_forwarded_args = [a for a in forwarded_args if not a in ("--keep-previous", "--no-postprocess", "--save-manifests-in-database")] @@ -556,7 +564,7 @@ def batch(ctx, batches, batches_files, tuning_search_dict, tuning_search_file, n f'--share' if ctx.obj["share"] else None, f'--offline' if ctx.obj['offline'] else None, f'--label "{ctx.obj["raw_batch_label"]}"' if ctx.obj["raw_batch_label"] != default_batch_label else None, - f'--platform "{run_context.platform}"' if run_context.platform != default_platform else None, # TODO: make it customizable in batches + f'--platform "{run_context.platform}"' if run_context.platform != default_platform else None, f'--type "{run_context.type}"' if run_context.type != default_input_type else None, f'--database "{run_context.database.as_posix()}"' if run_context.database != get_default_database(ctx.obj['inputs_settings']) else None, configuration_cli, @@ -569,7 +577,6 @@ def batch(ctx, batches, batches_files, tuning_search_dict, tuning_search_file, n command = ' '.join([arg for arg in args if arg is not None]) click.secho(command, fg='cyan', err=True) click.secho(f" {run_context.output_dir if run_context.output_dir.is_absolute else run_context.output_dir.relative_to(subproject)}", fg='blue', err=True) - import re if 'QA_TESTING' in os.environ: # we want to make sure we test the current code command = re.sub('^qa', 'python -m qaboard', command) @@ -586,6 +593,9 @@ def batch(ctx, batches, batches_files, tuning_search_dict, tuning_search_file, n **ctx.obj, **run_context.obj, # for now we don't want to worry about backward compatibility, and input_path being abs vs relative... "is_pending": True, + "data": { + "job_options": run_context.job_options, + } }) if db_output: # Note: the ID is already in the matching job above job.id = db_output["id"] @@ -611,8 +621,20 @@ def batch(ctx, batches, batches_files, tuning_search_dict, tuning_search_file, n ) from .gitlab import gitlab_token, update_gitlab_status + from .api import qaboard_url if gitlab_token and jobs and is_ci and 'QABOARD_TUNING' not in os.environ: - update_gitlab_status(commit_id, 'failed' if is_failed else 'success', ctx.obj["batch_label"], f"{len(jobs)} results") + name = f"QA {subproject.name}" if subproject else 'QA' + target_url = f"{qaboard_url}/{config['project']['name']}/commit/{commit_id}" + label = ctx.obj["batch_label"] + if label != "default": + name += f" | {label}" + target_url += f"?batch={label}" + update_gitlab_status( + state='failed' if is_failed else 'success', + name=name, + target_url=target_url, + description=f"{len(jobs)} results", + ) if is_failed and not no_wait: del os.environ['QA_BATCH'] # restore verbosity @@ -636,7 +658,7 @@ def save_artifacts(ctx, files, excluded_groups, artifacts_path, groups): from .utils import copy, file_info from .compat import cased_path - click.secho(f"Saving artifacts in: {artifacts_commit}", bold=True, underline=True) + click.secho(f"Saving artifacts in: {artifacts_commit if not artifacts_path else artifacts_path}", bold=True, underline=True) artifacts = {} @@ -671,7 +693,12 @@ def save_artifacts(ctx, files, excluded_groups, artifacts_path, groups): for artifact_name, artifact_config in artifacts.items(): click.secho(f'Saving artifacts: {artifact_name}', bold=True) manifest_path = artifacts_commit / 'manifests' / f'{artifact_name}.json' - manifest_path.parent.mkdir(parents=True, exist_ok=True) + try: + manifest_path.parent.mkdir(parents=True, exist_ok=True) + except Exception as e: + click.secho(f"ERROR: {e}", fg='red') + click.secho(f"We could not create one the folders required to save the artifacts..", fg='red', dim=True) + exit(1) if manifest_path.exists(): with manifest_path.open() as f: try: @@ -682,7 +709,7 @@ def save_artifacts(ctx, files, excluded_groups, artifacts_path, groups): manifest = {} nb_files = 0 - globs = artifact_config.get('glob') + globs = artifact_config.get('globs', artifact_config.get('glob', [])) if not isinstance(globs, list): globs = [globs] @@ -716,151 +743,21 @@ def save_artifacts(ctx, files, excluded_groups, artifacts_path, groups): click.secho(f"{nb_files} files copied") if os.name == "nt" and not ctx.obj['dryrun']: - # [Samsung-SIRC specific] - print("... Fixing linux file permissions") - try: - # Windows does not set file permissions correctly on the shared storage, - # it does not respect umask 0: files are not world-writable. - # Trying to each_file.chmod(0o777) does not work either - # The only option is to make the call from linux. - # We could save a list of paths and chmod them with their parent directories... - # but to make things faster to code, we just "ssh linux chmod everything" - # from qaboard.compat import windows_to_linux_path - # # We can assume SSH to be present on Windows10 - # ssh = f"ssh -i \\\\networkdrive\\home\\{user}\\.ssh\\id_rsa -oStrictHostKeyChecking=no" - # chmod = f'{ssh} {user}@{user}-srv \'chmod -R 777 "{windows_to_linux_path(artifacts_commit).as_posix()}"\'' - # print(chmod) - # os.system(chmod) - pass - except Exception as e: - print(f'WARNING: {e}') + from qaboard.compat import fix_linux_permissions + fix_linux_permissions(artifacts_commit) # if the commit was deleted, this notification will mark it as good again notify_qa_database(object_type='commit', **ctx.obj) -@qa.command() -@click.pass_context -@click.option('--batch', '-b', 'batches', required=True, multiple=True, help="Only check bit-accuracy for this batch of inputs+configs+database.") -@click.option('--batches-file', 'batches_files', type=PathType(), default=default_batches_files, multiple=True, help="YAML file listing batches of inputs+config+database selected from the database.") -def check_bit_accuracy_manifest(ctx, batches, batches_files): - """ - Checks the bit accuracy of the results in the current ouput directory - versus the latest commit on origin/develop. - """ - from .bit_accuracy import is_bit_accurate - - commit_dir = outputs_commit if is_ci else Path() - all_bit_accurate = True - nb_compared = 0 - for run_context in iter_inputs(batches, batches_files, ctx.obj['database'], ctx.obj['configurations'], default_platform, {}, config, ctx.obj['inputs_settings']): - nb_compared += 1 - if run_context.input_path.is_file(): - click.secho('ERROR: check_bit_accuracy_manifest only works for inputs that are folders', fg='red', err=True) - # otherwise the manifest is at - # * input_path.parent / 'manifest.json' in the database - # * input_path.with_suffix('') / 'manifest.json' in the results - # # reference_output_directory = run_context.input_path if run_context.input_path.is_folder() else run_context.input_path.parent - exit(1) - - batch_conf_dir = make_batch_conf_dir(Path(), ctx.obj['batch_label'], ctx.obj["platform"], run_context.configurations, ctx.obj['extra_parameters'], ctx.obj['share']) - input_is_bit_accurate = is_bit_accurate(commit_dir / batch_conf_dir, run_context.database, [run_context.rel_input_path]) - all_bit_accurate = all_bit_accurate and input_is_bit_accurate - - if not all_bit_accurate: - click.secho("\nError: you are not bit-accurate versus the manifest.", fg='red', underline=True, bold=True) - click.secho("Reminder: the manifest lists the expected inputs/outputs for each test. It acts as an explicit gatekeeper against changes", fg='red', dim=True) - if not run_context.database.is_absolute(): - click.secho("If that's what you wanted, update and commit all manifests.", fg='red') - # click.secho("If that's what you wanted, update all manifests using:", fg='red') - # click.secho("$ qa batch * --save-manifests-in-database", fg='red') - # click.secho("$ git add # your changes", fg='red') - # click.secho("$ git commit # now retry your CI", fg='red') - else: - click.secho("To update the manifests for all tests, run:", fg='red') - click.secho("$ qa batch --save-manifests --batch *", fg='red') - exit(1) - - if not nb_compared: - click.secho("\nWARNING: Nothing was compared! It's not likely to be what you expected...", fg='yellow', underline=True, bold=True) - - - -@qa.command() -@click.pass_context -@click.option( - "--reference", - default=config.get('project', {}).get('reference_branch', 'master'), - help="Branch, tag or commit used as reference." -) -@click.option('--batch', '-b', 'batches', multiple=True, help="Only check bit-accuracy for those batches of inputs+configs+database.") -@click.option('--batches-file', 'batches_files', type=PathType(), default=default_batches_files, multiple=True, help="YAML file listing batches of inputs+config+database selected from the database.") -@click.option('--reference-platform', help="Compare against a difference platform.") -def check_bit_accuracy(ctx, reference, batches, batches_files, reference_platform): - """ - Checks the bit accuracy of the results in the current ouput directory - versus the latest commit on origin/develop. - """ - from .config import is_in_git_repo, commit_branch, is_ci, outputs_project_root, repo_root - from .bit_accuracy import is_bit_accurate - from .gitlab import lastest_successful_ci_commit - from .conventions import get_commit_dirs - from .git import latest_commit, git_show, git_parents - - if not is_in_git_repo: - click.secho("You are not in a git repository, maybe in an artifacts folder. `check_bit_accuracy` is unavailable.", fg='yellow', dim=True) - exit(1) - - - if is_ci and commit_branch == reference: - click.secho(f'We are on branch {reference}', fg='cyan', bold=True, err=True) - click.secho(f"Comparing bit-accuracy against this commit's ({commit_id[:8]}) parents.", fg='cyan', bold=True, err=True) - # It will work until we try to rebase merge requests. - # We really should use Gitlab' API (or our database) to ask about previous pipelines on the branch - reference_commits = git_parents(commit_id) - else: - click.secho(f'Comparing bit-accuracy versus the latest remote commit of {reference}', fg='cyan', bold=True, err=True) - reference_commits = [latest_commit(reference)] - - click.secho(f"{commit_id[:8]} versus {reference_commits}.", fg='cyan', err=True) - - # This where the new results are located - commit_dir = outputs_commit_root if is_ci else Path() +from .bit_accuracy import check_bit_accuracy, check_bit_accuracy_manifest +qa.add_command(check_bit_accuracy) +qa.add_command(check_bit_accuracy_manifest) - if not batches: - output_directories = list(p.parent.relative_to(commit_dir) for p in (commit_dir / subproject / 'output').rglob('manifest.outputs.json')) - else: - output_directories = [] - for run_context in iter_inputs(batches, batches_files, ctx.obj['database'], ctx.obj['configurations'], default_platform, {}, config, ctx.obj['inputs_settings']): - batch_conf_dir = make_batch_conf_dir(subproject, ctx.obj['batch_label'], ctx.obj["platform"], run_context.configurations, ctx.obj["extra_parameters"], ctx.obj['share']) - input_path = run_context.input_path.relative_to(run_context.database) - output_directory = batch_conf_dir / input_path.with_suffix('') - output_directories.append(output_directory) - - for reference_commit in reference_commits: - # if the reference commit is pending or failed, we wait or maybe pick a parent - reference_commit = lastest_successful_ci_commit(reference_commit) - click.secho(f'Current directory : {commit_dir}', fg='cyan', bold=True, err=True) - reference_rootproject_ci_dir = outputs_project_root / get_commit_dirs(reference_commit, repo_root) - click.secho(f"Reference directory: {reference_rootproject_ci_dir}", fg='cyan', bold=True, err=True) - all_bit_accurate = True - for o in output_directories: - all_bit_accurate = is_bit_accurate(commit_dir, reference_rootproject_ci_dir, [o], reference_platform) and all_bit_accurate - if not all_bit_accurate: - click.secho(f"\nERROR: results are not bit-accurate to {reference_commits}.", bg='red', bold=True) - if is_ci: - click.secho(f"\nTo investigate, go to", fg='red', underline=True) - for reference_commit in reference_commits: - click.secho(f"https://qa/{project.as_posix()}/commit/{commit_id}?reference={reference_commit}&selected_views=bit_accuracy", fg='red') - exit(1) from .optimize import optimize qa.add_command(optimize) -# TODO: split more... -# from .bit_accuracy import check_bit_accuracy, check_bit_accuracy_manifest -# qa.add_command(check_bit_accuracy) -# qa.add_command(check_bit_accuracy_manifest) @qa.command() @click.pass_context diff --git a/qaboard/run.py b/qaboard/run.py index 2c0f98bd..06f73394 100755 --- a/qaboard/run.py +++ b/qaboard/run.py @@ -74,11 +74,14 @@ def is_failed(self, verbose=False): with metrics_path.open() as f: is_failed = json.load(f).get('is_failed', True) if verbose and is_failed: - click.secho(f"ERROR: Failed run! More info at: {self.output_directory}/log.txt", fg='red', err=True) + click.secho(f"[ERROR] Failed run! More info at: {self.output_directory}/log.txt", fg='red', err=True) return is_failed else: if verbose: - click.secho(f'ERROR: Failed run! Could not find {metrics_path}', fg='red', err=True) + if not self.output_dir.exists(): + click.secho(f'[ERROR] Failed run! The ouput directory does not exist. It usually implies that your disk/quota is full. ({self.output_dir})', fg='red', err=True) + else: + click.secho(f'[ERROR] Failed run! Could not find {metrics_path}', fg='red', err=True) return True @staticmethod @@ -107,8 +110,8 @@ def from_click_run_context(ctx, config): if not ctx.params.get('output_path'): assert input_path_absolute.relative_to(database) input_dir = input_path.with_suffix('') - if len(input_dir.as_posix()) > 90: - input_dir = Path(slugify_hash(input_dir.as_posix(), maxlength=90)) + if len(input_dir.as_posix()) > 70: + input_dir = Path(slugify_hash(input_dir.as_posix(), maxlength=70)) output_dir = ctx.obj['batch_conf_dir'] / input_dir # we don't want people using ../ in the input causing issues assert output_dir.resolve().relative_to(ctx.obj['batch_conf_dir'].resolve()) diff --git a/qaboard/runners/job.py b/qaboard/runners/job.py index c8aa7c53..8285aaaa 100755 --- a/qaboard/runners/job.py +++ b/qaboard/runners/job.py @@ -95,26 +95,29 @@ def start(self, blocking=True, qa_context: Optional[Dict[str, Any]] = None) -> b # it happens often when users use a lot of memory and some task queue manager gets angry jobs_with_pending_outputs = [] for job in self.jobs: - # we still fallback to the server-less check, in case it was down during part of the runs... + # we still fallback to the server-less check, in case the server was down during part of the runs... if job.run_context.output_dir not in outputdir_to_qaboard_output: is_failed = is_failed or job.run_context.is_failed(verbose=True) else: job.qaboard_output = outputdir_to_qaboard_output[job.run_context.output_dir] assert job.qaboard_output - is_failed = is_failed or job.qaboard_output["is_failed"] + is_failed = is_failed or job.qaboard_output["is_failed"] if job.qaboard_output['is_pending']: jobs_with_pending_outputs.append(job) - for j in jobs_with_pending_outputs: + for job in jobs_with_pending_outputs: + job_is_failed = job.run_context.is_failed(verbose=True) + if not job_is_failed: + print("[INFO] Job status was 'pending':", job.run_context, job.qaboard_output) + is_failed = is_failed or job_is_failed notify_qa_database(**{ **(qa_context if qa_context else {}), - **j.run_context.obj, # for now we don't want to worry about backward compatibility, and input_path being abs vs relative... + **job.run_context.obj, # for now we don't want to worry about backward compatibility, and input_path being abs vs relative... "is_pending": False, - "is_failed": True, # we know something went wrong + "is_failed": job_is_failed, }) return is_failed - # Currently called onlt by the backend when it tries to stop a `qa batch` command # Sadly it only knows about the command_id, not jobs.... # TODO: make it stop_command to make usage clearer.. diff --git a/qaboard/runners/lsf.py b/qaboard/runners/lsf.py index 41c0378d..b236e5f0 100755 --- a/qaboard/runners/lsf.py +++ b/qaboard/runners/lsf.py @@ -9,6 +9,7 @@ Note: - Windows compatibility is not garanteed since we rely on shell features (heredocs) and """ +import re import os import subprocess from pathlib import Path @@ -83,7 +84,7 @@ def name(self): # We want a unique job name, with the same prefix as other related jobs # so that's it's easy to list/kill them together job_prefix = f"{self.run_context.job_options['command_id'][:8]}/" - output_dir_slug = f"{self.output_dir}".replace(" ", "-").replace('"','') if self.output_dir else '' + output_dir_slug = re.sub(r"[^A-Za-z0-9/_]", "-", str(self.output_dir)) if self.output_dir else '' return f"{job_prefix}{output_dir_slug}" diff --git a/qaboard/utils.py b/qaboard/utils.py index f4737bd9..841ee4d5 100755 --- a/qaboard/utils.py +++ b/qaboard/utils.py @@ -269,20 +269,22 @@ def md5_hex(path): - -def save_outputs_manifest(output_directory: Path, config=None, compute_hashes=True) -> Dict: - """Save a manifest of all the files from the directory. It helps QA-Board list them quickly.""" +def outputs_manifest(output_directory: Path, config=None, compute_hashes=True) -> Dict: def should_be_in_manifest(path): # avoid logs with timestamps and temporary NFS files return path.is_file() and path.name != 'log.txt' and not path.name.startswith('.nfs00000') - output_files = { + return { path.relative_to(output_directory).as_posix(): file_info(path, config=config, compute_hashes=compute_hashes) for path in output_directory.rglob('*') if should_be_in_manifest(path) } + +def save_outputs_manifest(output_directory: Path, config=None, compute_hashes=True) -> Dict: + """Save a manifest of all the files from the directory. It helps QA-Board list them quickly.""" + manifest = outputs_manifest(output_directory, config, compute_hashes) with (output_directory / 'manifest.outputs.json').open('w') as f: - json.dump(output_files, f, indent=2) - return output_files + json.dump(manifest, f, indent=2) + return manifest def total_storage(manifest): diff --git a/services/db/backup b/services/db/backup index ba819f27..148d28bb 100755 --- a/services/db/backup +++ b/services/db/backup @@ -12,8 +12,8 @@ if [ -z ${AS_USER_NAME+x} ]; then pg_dump -Fc > "/backups/$backup" else # we should use gosu but it's nice to use the official image as-is - addgroup -S $AS_USER_GROUP group -g $AS_USER_GID || true - adduser $AS_USER_NAME -u $AS_USER_UID -G $AS_USER_GROUP || true + addgroup -S $AS_USER_GROUP -g $AS_USER_GID group || true + adduser --disabled-password $AS_USER_NAME -u $AS_USER_UID -G $AS_USER_GROUP || true su $AS_USER_NAME -c "pg_dump -Fc > '/backups/$backup'" fi diff --git a/services/nginx/conf.d/qaboard.conf b/services/nginx/conf.d/qaboard.conf index 2fefb8c5..311c117f 100644 --- a/services/nginx/conf.d/qaboard.conf +++ b/services/nginx/conf.d/qaboard.conf @@ -13,6 +13,9 @@ server { listen 80; listen [::]:80 ipv6only=on; + # otherwise accessing qa/s/folder will redirect to qa:whatever/s/folder/ + # https://serverfault.com/questions/905657/nginx-redirects-to-http-after-port-in-redirect-off/905740 + absolute_redirect off; location /docs { alias /docs/; @@ -59,6 +62,13 @@ server { autoindex on; access_log off; include cors; + # let users save precompressed $file.gz + # using "gzip $file" or https://github.com/google/zopfli + gzip_static on; + # https://stackoverflow.com/questions/33375304/what-are-the-options-for-the-gzip-proxied-directive-for + # gzip_proxied expired no-cache no-store private auth; + # for clients that don't support gzip if only that version is available + gunzip on; } # IIIF Cantaloupe Server diff --git a/services/nginx/cors b/services/nginx/cors index 8a3c19ed..f580af2f 100644 --- a/services/nginx/cors +++ b/services/nginx/cors @@ -1,5 +1,6 @@ + # http://nginx.org/en/docs/http/ngx_http_headers_module.html#add_header if ($request_method ~* "(GET|POST|PUT|DELETE)") { - add_header "Access-Control-Allow-Origin" *; + add_header "Access-Control-Allow-Origin" * always; } # Preflighted requests if ($request_method = OPTIONS ) { diff --git a/setup.py b/setup.py index 10b50e0e..ed3a0e2e 100755 --- a/setup.py +++ b/setup.py @@ -50,10 +50,8 @@ 'simplejson', 'pyyaml', # YAML reader 'joblib', # Parallelism for dummies - # Used only for parameter sampling. Depends on numpy/scipy. - # TODO: To make installation faster, especially on windows - # we should remove this dependency and implement what we need ourselves. 'sklearn', + 'scikit-optimize', ], extras_require={ @@ -63,9 +61,6 @@ 'mypy', # type hint checks # 'black' # TODO: formatter ], - # Optional needed only for `qa optimize` - `pip install qaboard[optimize]` - # Since its CLI usage is not straightforward, it's best kept at an optionnal dependency - 'optimize': ["scikit-optimize>=0.7.2"], # we need https://github.com/scikit-optimize/scikit-optimize/pull/806 }, entry_points={ diff --git a/tests/test_iterators.py b/tests/test_iterators.py index c5055d7f..e895ff53 100755 --- a/tests/test_iterators.py +++ b/tests/test_iterators.py @@ -111,12 +111,20 @@ def get_batch(batch): self.assertEqual(batches[0].configurations, ['base']) self.assertEqual(batches[1].configurations, ['base', 'low-light', {"cde": ["-DD"]}]) + batches = get_batch('each-input-can-have-its-own-configuration-and-appear-twice') + self.assertEqual(batches[0].configurations, ['base', {"crop": "A"}]) + self.assertEqual(batches[1].configurations, ['base', {"crop": "B"}]) + self.assertEqual(batches[2].configurations, ['base', {"crop": "C"}]) + batches = get_batch('you-can-override-globs') self.assertEqual(len(batches), 1) batches = get_batch('my-alias') self.assertEqual(len(batches), 2) + batches = get_batch('expand-lists-to-work-well-with-aliases') + self.assertEqual(batches[0].configurations, ['base', 'delta1', 'delta2']) + # batches-can-be-paths batches = get_batch('../cli_tests/dir') self.assertEqual(len(batches), 1) @@ -131,6 +139,11 @@ def get_batch(batch): self.assertEqual(len(batches), 1) self.assertEqual(batches[0].configurations, ['base', 'calibration']) + batches = get_batch('matrix-configurations-and-per-input-with-base') + self.assertEqual(len(batches), 2) + self.assertEqual(batches[0].configurations, ['basebase', 'base']) + self.assertEqual(batches[1].configurations, ['basebase', 'base', 'delta']) + batches = get_batch('matrix-many') self.assertEqual(len(batches), 8) @@ -206,6 +219,25 @@ def get_batch(batch): - "-DD" #=> configurations == ["base", "low-light", {"cde": ["-DD"]}] +each-input-can-have-its-own-configuration-and-appear-twice: + configurations: + - base + inputs: + - a.txt: {crop: A} + #=> configurations == ["base", {"crop": ["A"]}] + - a.txt: {crop: B} + #=> configurations == ["base", {"crop": ["B"]}] + - [a.txt, {crop: C}] + #=> configurations == ["base", {"crop": ["C"]}] + + +expand-lists-to-work-well-with-aliases: + configurations: + - base + - [delta1, delta2] + inputs: + - a.txt: + aliases: my-alias: - my-batch @@ -227,6 +259,20 @@ def get_batch(batch): matrix: configurations: [[base]] +matrix-configurations-and-per-input-with-base: + configs: + - basebase + inputs: + - a.txt + matrix: + configurations: + - + - base + - + - base + - delta + + matrix-many: inputs: - a.txt diff --git a/webapp/Dockerfile b/webapp/Dockerfile index 60c18647..c7cd1e93 100644 --- a/webapp/Dockerfile +++ b/webapp/Dockerfile @@ -1,13 +1,12 @@ -FROM node:lts +FROM node:latest WORKDIR /webapp - RUN apt update -qq && apt-get install -y --no-install-recommends rsync ENV PATH /app/node_modules/.bin:$PATH -COPY package.json npm-shrinkwrap.json ./ +COPY package.json package-lock.json ./ # In the past we had ulimit issues and "ulimit -n 2000 &&" RUN npm ci diff --git a/webapp/npm-shrinkwrap.json b/webapp/package-lock.json similarity index 65% rename from webapp/npm-shrinkwrap.json rename to webapp/package-lock.json index dd117829..c0091c34 100644 --- a/webapp/npm-shrinkwrap.json +++ b/webapp/package-lock.json @@ -15,17 +15,17 @@ } }, "@babel/code-frame": { - "version": "7.0.0", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.0.0.tgz", - "integrity": "sha512-OfC2uemaknXr87bdLUkWog7nYuliM9Ij5HUcajsVcMCpQrcLmtxRbVFTIqmcSkSeYRBFBRxs2FiUqFJDLdiebA==", + "version": "7.12.13", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.12.13.tgz", + "integrity": "sha512-HV1Cm0Q3ZrpCR93tkWOYiuYIgLxZXZFVG2VgK+MBWjUqZTundupbfx2aXarXuw5Ko5aMcjtJgbSs4vUGBS5v6g==", "requires": { - 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"8.1.0", "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-8.1.0.tgz", @@ -22795,11 +18738,6 @@ "graceful-fs": "^4.1.6" } }, - "regenerator-runtime": { - "version": "0.13.7", - "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.13.7.tgz", - "integrity": "sha512-a54FxoJDIr27pgf7IgeQGxmqUNYrcV338lf/6gH456HZ/PhX+5BcwHXG9ajESmwe6WRO0tAzRUrRmNONWgkrew==" - }, "source-map": { "version": "0.7.3", "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.7.3.tgz", @@ -22910,21 +18848,6 @@ "upath": "^1.1.2", "webpack-sources": "^1.3.0", "workbox-build": "^5.1.4" - }, - "dependencies": { - "@babel/runtime": { - "version": "7.12.1", - "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.12.1.tgz", - "integrity": "sha512-J5AIf3vPj3UwXaAzb5j1xM4WAQDX3EMgemF8rjCP3SoW09LfRKAXQKt6CoVYl230P6iWdRcBbnLDDdnqWxZSCA==", - "requires": { - "regenerator-runtime": "^0.13.4" - } - }, - "regenerator-runtime": { - "version": "0.13.7", - "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.13.7.tgz", - "integrity": "sha512-a54FxoJDIr27pgf7IgeQGxmqUNYrcV338lf/6gH456HZ/PhX+5BcwHXG9ajESmwe6WRO0tAzRUrRmNONWgkrew==" - } } }, "workbox-window": { @@ -22967,44 +18890,6 @@ "ansi-styles": "^4.0.0", "string-width": "^4.1.0", "strip-ansi": "^6.0.0" - }, - "dependencies": { - "ansi-styles": { - "version": "4.3.0", - "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz", - "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==", - "requires": { - "color-convert": "^2.0.1" - } - }, - "color-convert": { - "version": "2.0.1", - "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz", - "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==", - "requires": { - "color-name": "~1.1.4" - } - }, - "emoji-regex": { - "version": "8.0.0", - "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", - "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==" - }, - "is-fullwidth-code-point": { - "version": "3.0.0", - "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-3.0.0.tgz", - "integrity": "sha512-zymm5+u+sCsSWyD9qNaejV3DFvhCKclKdizYaJUuHA83RLjb7nSuGnddCHGv0hk+KY7BMAlsWeK4Ueg6EV6XQg==" - }, - "string-width": { - "version": "4.2.0", - "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.0.tgz", - "integrity": "sha512-zUz5JD+tgqtuDjMhwIg5uFVV3dtqZ9yQJlZVfq4I01/K5Paj5UHj7VyrQOJvzawSVlKpObApbfD0Ed6yJc+1eg==", - "requires": { - "emoji-regex": "^8.0.0", - "is-fullwidth-code-point": "^3.0.0", - "strip-ansi": "^6.0.0" - } - } } }, "wrappy": { @@ -23012,14 +18897,6 @@ "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=" }, - "write": { - "version": "1.0.3", - "resolved": "https://registry.npmjs.org/write/-/write-1.0.3.tgz", - "integrity": "sha512-/lg70HAjtkUgWPVZhZcm+T4hkL8Zbtp1nFNOn3lRrxnlv50SRBv7cR7RqR+GMsd3hUXy9hWBo4CHTbFTcOYwig==", - "requires": { - "mkdirp": "^0.5.1" - } - }, "write-file-atomic": { "version": "3.0.3", "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-3.0.3.tgz", @@ -23032,9 +18909,9 @@ } }, "ws": { - "version": "7.3.1", - "resolved": "https://registry.npmjs.org/ws/-/ws-7.3.1.tgz", - "integrity": "sha512-D3RuNkynyHmEJIpD2qrgVkc9DQ23OrN/moAwZX4L8DfvszsJxpjQuUq3LMx6HoYji9fbIOBY18XWBsAux1ZZUA==" + "version": "7.4.5", + "resolved": "https://registry.npmjs.org/ws/-/ws-7.4.5.tgz", + "integrity": "sha512-xzyu3hFvomRfXKH8vOFMU3OguG6oOvhXMo3xsGy3xWExqaM2dxBbVxuD99O7m3ZUFMvvscsZDqxfgMaRr/Nr1g==" }, "xml-name-validator": { "version": "3.0.0", @@ -23047,14 +18924,14 @@ "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==" }, "xtend": { - "version": "4.0.1", - "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.1.tgz", - "integrity": "sha1-pcbVMr5lbiPbgg77lDofBJmNY68=" + "version": "4.0.2", + "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", + "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==" }, "y18n": { - "version": "4.0.0", - "resolved": "https://registry.npmjs.org/y18n/-/y18n-4.0.0.tgz", - "integrity": "sha512-r9S/ZyXu/Xu9q1tYlpsLIsa3EeLXXk0VwlxqTcFRfg9EhMW+17kbt9G0NrgCmhGb5vT2hyhJZLfDGx+7+5Uj/w==" + "version": "4.0.3", + "resolved": "https://registry.npmjs.org/y18n/-/y18n-4.0.3.tgz", + "integrity": "sha512-JKhqTOwSrqNA1NY5lSztJ1GrBiUodLMmIZuLiDaMRJ+itFd+ABVE8XBjOvIWL+rSqNDC74LCSFmlb/U4UZ4hJQ==" }, "yallist": { "version": "4.0.0", @@ -23062,9 +18939,9 @@ "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==" }, "yaml": { - "version": "1.10.0", - "resolved": "https://registry.npmjs.org/yaml/-/yaml-1.10.0.tgz", - "integrity": "sha512-yr2icI4glYaNG+KWONODapy2/jDdMSDnrONSjblABjD9B4Z5LgiircSt8m8sRZFNi08kG9Sm0uSHtEmP3zaEGg==" + "version": "1.10.2", + "resolved": "https://registry.npmjs.org/yaml/-/yaml-1.10.2.tgz", + "integrity": "sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg==" }, "yargs": { "version": "15.4.1", @@ -23082,28 +18959,6 @@ "which-module": "^2.0.0", "y18n": "^4.0.0", "yargs-parser": "^18.1.2" - }, - "dependencies": { - "emoji-regex": { - "version": "8.0.0", - "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", - "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==" - }, - "is-fullwidth-code-point": { - "version": "3.0.0", - "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-3.0.0.tgz", - "integrity": "sha512-zymm5+u+sCsSWyD9qNaejV3DFvhCKclKdizYaJUuHA83RLjb7nSuGnddCHGv0hk+KY7BMAlsWeK4Ueg6EV6XQg==" - }, - "string-width": { - "version": "4.2.0", - "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.0.tgz", - "integrity": "sha512-zUz5JD+tgqtuDjMhwIg5uFVV3dtqZ9yQJlZVfq4I01/K5Paj5UHj7VyrQOJvzawSVlKpObApbfD0Ed6yJc+1eg==", - "requires": { - "emoji-regex": "^8.0.0", - "is-fullwidth-code-point": "^3.0.0", - "strip-ansi": "^6.0.0" - } - } } }, "yargs-parser": { @@ -23122,6 +18977,11 @@ } } }, + "yocto-queue": { + "version": "0.1.0", + "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", + "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==" + }, "zero-crossings": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/zero-crossings/-/zero-crossings-1.0.1.tgz", diff --git a/webapp/package.json b/webapp/package.json old mode 100755 new mode 100644 index ddcce9e9..a3285731 --- a/webapp/package.json +++ b/webapp/package.json @@ -16,7 +16,7 @@ "@types/styled-components": "^4.4.3", "acorn": "^8.0.4", "ansi-to-html": "^0.6.14", - "axios": "^0.21.0", + "axios": "^0.21.3", "ci": "^1.0.0", "d3-color": "^2.0.0", "d3-dsv": "^2.0.0", @@ -30,8 +30,8 @@ "js-md5": "^0.7.3", "localforage": "^1.9.0", "lodash": "^4.17.20", + "luxon": "^1.26.0", "mathjs": "^7.5.1", - "moment": "^2.29.1", "monaco-editor": "^0.20.0", "monaco-editor-webpack-plugin": "^1.9.1", "openseadragon": "^2.4.2", @@ -46,7 +46,6 @@ "react-full-screen": "^0.3.1", "react-intersection-observer": "^8.29.1", "react-loadable": "^5.5.0", - "react-moment": "^0.9.7", "react-monaco-editor": "^0.36.0", "react-plotly.js": "^2.5.0", "react-redux": "^7.2.2", @@ -59,7 +58,7 @@ "reselect": "^4.0.0", "sanitize-html": "^2.1.1", "styled-components": "^4.4.1", - "three": "^0.106.2", + "three": "^0.128.0", "typescript": "^4.0.5" }, "scripts": { diff --git a/webapp/src/AppNavbar.js b/webapp/src/AppNavbar.js index ceac7e2e..ac13cd1e 100755 --- a/webapp/src/AppNavbar.js +++ b/webapp/src/AppNavbar.js @@ -152,7 +152,7 @@ class AppNavbar extends Component { { const { dispatch, project } = this.props; - dispatch(updateSelected(project, {branch: null, committer: null})) + dispatch(updateSelected(project, {branch: null, committer: null})) } - render() { + render() { const { project, project_data={} } = this.props; - const git = (project_data.data || {}).git || {}; + const git = project_data.data?.git || {}; let project_name = project.split('/').slice(-1)[0]; const is_subproject = git.path_with_namespace !== project; - const has_custom_avatar = !!(((project_data.data || {}).qatools_config || {}).project || {}).avatar_url + const has_custom_avatar = !!project_data.data?.qatools_config?.project?.avatar_url const should_tweak_image = is_subproject && !has_custom_avatar; const avatar_style = should_tweak_image ? project_avatar_style(project) : null; - const gitlab_host = (git.web_url || 'https://gitlab.com/').split('/').slice(0,3).join('/') - const avatar_url = !!git.avatar_url ? (git.avatar_url.startsWith('http') ? git.avatar_url : `${gitlab_host}${git.avatar_url}`) : null + + const project_git_hostname = git_hostname(project_data?.data?.qatools_config) ?? default_git_hostname + git.web_url = git.web_url ?? `${project_git_hostname}/${git.path_with_namespace}` + const gitlab_host = git.web_url.split('/').slice(0,3).join('/') + let avatar_url = git.avatar_url + if (!!avatar_url && avatar_url.startsWith(gitlab_host)) { + avatar_url = encodeURI(`/api/v1/gitlab/proxy?url=${avatar_url}`) + } return <> + /> {project_name} - } + } } class ProjectSideCommitList extends React.Component { @@ -101,11 +107,12 @@ class ProjectSideCommitList extends React.Component { selectMilestone = milestone => { const { project, dispatch } = this.props; - dispatch(fetchCommit({project, id: milestone.commit})); + dispatch(fetchCommit({project: milestone.project ?? project, id: milestone.commit})); dispatch(updateSelected(project, { - 'new_commit_id': milestone.commit, - 'selected_batch_new': milestone.batch, - 'filter_batch_new': milestone.filter, + new_project: milestone.project ?? project, + new_commit_id: milestone.commit, + selected_batch_new: milestone.batch, + filter_batch_new: milestone.filter, })) }; @@ -131,8 +138,11 @@ class ProjectSideCommitList extends React.Component { } let project_repo = git.path_with_namespace || ''; let subproject = project.slice(project_repo.length + 1); + + const project_git_hostname = git_hostname(project_data?.data?.qatools_config) ?? default_git_hostname + git.web_url = git.web_url ?? `${project_git_hostname}/${git.path_with_namespace}` let code_url = subproject.length > 0 ? `${git.web_url}/tree/${is_branch ? match.params.name : reference_branch}/${subproject}` : git.web_url; - return <> + return <> {is_project_home ?
this.updateBranch(reference_branch)}/>
: } @@ -152,17 +162,17 @@ class ProjectSideCommitList extends React.Component { transitionDuration: 800, }} > - + {qatools_milestones.length === 0 && Define project.milestones [array] in your qaboard.yaml configuration.} - - + + } - } + } } // {false && } - // {false && } + // {false && } class ProjectSideResults extends React.Component { @@ -170,21 +180,22 @@ class ProjectSideResults extends React.Component { this.props.dispatch(updateSelected(this.props.project, { [attribute]: value })) } - render() { + render() { const { project, project_data={}, commit, batch } = this.props; const git = project_data.data?.git || {}; let project_repo = git.path_with_namespace || ''; let subproject = project.slice(project_repo.length + 1); let commit_code_sufffix = !!commit ? (subproject.length > 0 ? `blob/${commit.id}/${subproject}` : `commit/${commit.id}`) : '' - let code_url = `${git.web_url || ''}/${commit_code_sufffix}` + + const project_git_hostname = git_hostname(project_data?.data?.qatools_config) ?? default_git_hostname + git.web_url = git.web_url ?? `${project_git_hostname}/${git.path_with_namespace}` + let code_url = `${git.web_url}/${commit_code_sufffix}` // we can only do tuning for projects whose database is outside the repo // otherwise we would need to checkout the repo and manage access... const commit_qatools_config = ((commit || {}).data || {}).qatools_config || {}; const project_qatools_config = (project_data.data || {}).qatools_config || {}; const qatools_config = commit_qatools_config || project_qatools_config || {}; - const disable_tuning = !!qatools_config.inputs && !!qatools_config.inputs.database && !!qatools_config.inputs.database.linux && - !qatools_config.inputs.database.linux.startsWith('/'); const has_optim = batch.data?.optimization === true; const active = view => this.props.selected_views.includes(view); @@ -207,12 +218,12 @@ class ProjectSideResults extends React.Component { - + - } + } } @@ -222,13 +233,15 @@ class AppSider extends React.Component { render() { return
    - - + + QA-Board Click to see the docs! - + + + {!window.location.pathname.includes('/commit/') && !window.location.pathname.includes('/history/') && } diff --git a/webapp/src/CiCommitList.js b/webapp/src/CiCommitList.js index 9067b1a5..0e68cef2 100755 --- a/webapp/src/CiCommitList.js +++ b/webapp/src/CiCommitList.js @@ -3,7 +3,8 @@ import { connect } from 'react-redux' import { withRouter } from "react-router"; import styled from "styled-components"; -import Moment from "react-moment"; +import { DateTime } from 'luxon'; + import { Classes, @@ -115,12 +116,14 @@ class CiCommitList extends React.Component { {error && } {is_loading && !some_commits_loaded && } />} {is_loaded && !is_loading && !error && !some_commits_loaded && - Searched {" "} - from + from {DateTime.fromJSDate(date_range[0]).toRelativeCalendar({unit: "days"})} {" "}to{" "} - {date_range[1] > new Date() ? "today" : } + {date_range[1] > new Date() ? "today" : + {DateTime.fromJSDate(date_range[1]).toRelativeCalendar({unit: "days"})} + } } icon="search" />} @@ -131,12 +134,13 @@ class CiCommitList extends React.Component { <> {Object.keys(commits_by_day).map(day => ( -

    - {(!!day && day !== "undefined") ? <>{" "} - — {commits_by_day[day].length} commits : `${commits_by_day[day].length} commits`} +

    + {(!!day && day !== "undefined") ? <> + {DateTime.fromISO(day).toRelativeCalendar({unit: "days"})} + {" "} + — {commits_by_day[day].length} commits + + : `${commits_by_day[day].length} commits`}

    diff --git a/webapp/src/CiCommitResults.js b/webapp/src/CiCommitResults.js index 086e6445..49f54835 100755 --- a/webapp/src/CiCommitResults.js +++ b/webapp/src/CiCommitResults.js @@ -44,6 +44,7 @@ import { batchSelector, } from './selectors/projects' +import PrivateContent from "./components/authentication/RequireAuth" @@ -125,9 +126,9 @@ class CiCommitResults extends Component { }; fetchCommits() { - const { project, new_commit_id, ref_commit_id, dispatch } = this.props; - dispatch(fetchCommit({project, id: new_commit_id, update_selected: "new_commit_id"})); - dispatch(fetchCommit({project, id: ref_commit_id, update_selected: "ref_commit_id"})); + const { project, new_project, ref_project, new_commit_id, ref_commit_id, dispatch } = this.props + dispatch(fetchCommit({project: new_project, id: new_commit_id, update_with_id: {project, commit: "new_commit_id"}})) + dispatch(fetchCommit({project: ref_project, id: ref_commit_id, update_with_id: {project, commit: "ref_commit_id"}})) } componentDidMount() { @@ -144,8 +145,8 @@ class CiCommitResults extends Component { // } const config_curr = this.props.config; const config_prev = prevProps.config; - const new_outputs = (config_curr || {}).outputs; - const old_outputs = (config_prev || {}).outputs; + const new_outputs = config_curr?.outputs; + const old_outputs = config_prev?.outputs; if (new_outputs !== old_outputs ) { let controls = controls_defaults(config_curr) @@ -178,7 +179,7 @@ class CiCommitResults extends Component { } = this.props; var warning_messages = ; @@ -189,7 +190,9 @@ class CiCommitResults extends Component { ) : null; let metricTableSelect = ( new_batch.used_metrics.has(key)) + .map(([k, m]) => m)} itemPredicate={this.filterMetric} itemRenderer={this.renderMetric} onItemSelect={this.handleMetricSelect} @@ -245,6 +248,8 @@ class CiCommitResults extends Component { // flex-wrap: wrap; // justify-content: space-between; // align-items: baseline; + const tuned_params = new_batch.sorted_extra_parameters.filter(p => new_batch.extra_parameters[p].size > 1) + const has_tuning = tuned_params.length > 0 const all_controls = <>
    {show_viewer_controls && controls} @@ -257,12 +262,15 @@ class CiCommitResults extends Component { > - {new_batch.sorted_extra_parameters.map( + {has_tuning && } + {tuned_params + .map( param => + )} + {Object.values(available_metrics).map( m => (

    Files & Bit Accuracy

    Auto-Tuning Analysis

    @@ -478,10 +492,7 @@ const mapStateToProps = (state, ownProps) => { let project = projectSelector(state) let selected = selectedSelector(state) - let new_commit_id = selected.new_commit_id - let ref_commit_id = selected.ref_commit_id - let filter_batch_new = selected.filter_batch_new - let filter_batch_ref = selected.filter_batch_ref + const { new_commit_id, ref_commit_id, filter_batch_new, filter_batch_ref, new_project, ref_project } = selected let { new_commit, ref_commit } = commitSelector(state) @@ -504,12 +515,15 @@ const mapStateToProps = (state, ownProps) => { return { params, project, + selected, config, metrics, git, available_metrics, selected_metrics, // selected commit + new_project, + ref_project, new_commit_id, ref_commit_id, new_commit, diff --git a/webapp/src/Dashboard.js b/webapp/src/Dashboard.js index 64156ef6..b77ff156 100755 --- a/webapp/src/Dashboard.js +++ b/webapp/src/Dashboard.js @@ -147,7 +147,9 @@ class Dashboard extends React.Component { let clearButton = selected_metrics.length > 0 ? ); - - + // onmount ref + // this.log_ref.current.scrollTop = offsetTop const header_prefix = <> - {show_button} {output.output_type !== "batch" && } + {show_button}{button_text==="Hide" && } {output.output_type !== "batch" && } return (
    @@ -152,6 +173,8 @@ class OutputLog extends React.Component { /> : 
                 {!!command.job_url && }
-          	
-              {command.command_created_at_datetime}
-              {command.command_created_at_datetime}
-            
+            {DateTime.fromISO(command.command_created_at_datetime).toRelative()}
             {!!command.user && ` as ${command.user}`}{!!command.HOST && ` @${command.HOST}`}
           }>
           {command.argv.join(" ")}
diff --git a/webapp/src/components/CommitNavbar.js b/webapp/src/components/CommitNavbar.js
index 8c20fdc3..44861c0f 100755
--- a/webapp/src/components/CommitNavbar.js
+++ b/webapp/src/components/CommitNavbar.js
@@ -14,6 +14,7 @@ import {
   Button,
   FormGroup,
   InputGroup,
+  ControlGroup,
   NavbarGroup,
   Dialog,
   Tooltip,
@@ -104,29 +105,53 @@ class CommitNavbar extends React.Component {
     this.state = {
       waiting: false,
       show_rename_dialog: false,
-      renamed_batch_label: '',
+      show_move_dialog: false,
+      dst_batch_label: '',
+      project_input: null,
     };
   }
 
   renameBatch = () => {
     const { batch } = this.props;
-    const { renamed_batch_label: label } = this.state;
+    const { dst_batch_label: label } = this.state;
     this.setState({waiting: true, show_rename_dialog: false})
-    toaster.show({message: "Redo requested."});
+    toaster.show({message: "Rename requested."});
     axios.post(`/api/v1/batch/rename/`, {id: batch.id, label})
-      .then(response => {
+      .then(() => {
         this.setState({waiting: false})
         toaster.show({message: `Renamed ${batch.label} to ${label}.`, intent: Intent.PRIMARY});
         this.refresh()    
       })
       .catch(error => {
         this.setState({waiting: false });
-        toaster.show({message: JSON.stringify(error), intent: Intent.DANGER});
+        toaster.show({message: error.response?.data?.error ?? JSON.stringify(error), intent: Intent.DANGER});
+      });
+  }
+
+  moveBatch = () => {
+    const { batch, selected, type } = this.props;
+    const { dst_batch_label: label } = this.state;
+    const filter = selected[`filter_batch_${type}`]
+    this.setState({waiting: true, show_rename_dialog: false})
+    toaster.show({message: "Move requested."});
+    axios.post(`/api/v1/batch/move/`, {id: batch.id, label, filter})
+      .then(() => {
+        this.setState({waiting: false})
+        toaster.show({message: `Moved to ${label}.`, intent: Intent.PRIMARY});
+        this.refresh()
+      })
+      .catch(error => {
+        this.setState({waiting: false });
+        toaster.show({message: error.response?.data?.error ?? JSON.stringify(error), intent: Intent.DANGER});
       });
   }
 
   render() {
-    const { project, project_data, commits, commit, batch, selected, type, dispatch, update } = this.props;
+    const { project, project_data, commit, batch, selected, type, dispatch, update } = this.props;
+    const { project_input } = this.state;
+    const project_attr = `${type}_project`
+    const filter = selected[`filter_batch_${type}`]
+
     const qatools_config = project_data?.data?.qatools_config
     const reference_branch = qatools_config?.project?.reference_branch || 'master';
 
@@ -137,16 +162,30 @@ class CommitNavbar extends React.Component {
     const private_milestones = project_data.milestones || {}
 
     const milestones_menu = 
+      
+      
+         this.setState({project_input: e.target.value})}
+          onBlur={e => {
+            this.setState({project_input: e.target.value}, () => this.selectCommit(commit.id))
+          }}
+          fill
+        />
+        
+      
       
       
       
        this.removeSelection()} />
       
        this.selectBranch(reference_branch)} />
-      
+      
       {qatools_milestones.length === 0 && Define project.milestones [array] in your qaboard.yaml configuration.}
-      
-      
+      
+      
     
 
     let has_selected_batch = !!commit && !!commit.batches && !!batch && Object.keys(commit.batches).includes(batch.label)
@@ -169,6 +208,7 @@ class CommitNavbar extends React.Component {
 
             
             
             
+            {!!selected[project_attr] && project !== selected[project_attr] && {selected[project_attr]}}
             
 
             {" "}
@@ -229,33 +270,37 @@ class CommitNavbar extends React.Component {
           onChange={update(`selected_batch_${type}`)}
           hide_counts
         />
-        {!!commit && !!commits[commit.id] && <>
+        {!!commit && <>
    + this.setState({dst_batch_label: batch.label})} + onClose={() => this.setState({show_move_dialog: false})} + title={filter.length > 0 ? "Move runs to another batch" : "Move selection to another batch" } + icon="send-to-graph" + > +
    + this.setState({dst_batch_label: event.target.value})} + className={Classes.INPUT} + style={{marginBottom: '15px'}} + /> +

    The destination batch will be created if needed.

    +
    +
    +
    + + +
    +
    +     + 0 ? "Move runs to another batch" : "Move selection to another batch"} + minimal + disabled={this.state.waiting} + shouldDismissPopover={false} + onClick={() => this.setState({show_move_dialog: true})} + > + 0 ? "Rename whole batch" : "Rename batch"} minimal disabled={this.state.waiting} shouldDismissPopover={false} @@ -297,6 +374,27 @@ class CommitNavbar extends React.Component { }); }} />} + {batch.failed_outputs > 0 && { + this.setState({waiting: true}) + toaster.show({message: "Redo of failed outputs requested."}); + axios.post(`/api/v1/batch/redo/`, {id: batch.id, only_failed: true}) + .then(response => { + this.setState({waiting: false}) + toaster.show({message: `Redo ${batch.label}.`, intent: Intent.PRIMARY}); + this.refresh() + }) + .catch(error => { + this.setState({waiting: false }); + toaster.show({message: JSON.stringify(error), intent: Intent.DANGER}); + }); + }} + />} { - const { project, commit, dispatch } = this.props; - dispatch(fetchCommit({project, id: commit.id})) + const { project, type, selected, commit, dispatch } = this.props; + dispatch(fetchCommit({project: selected[`${type}_project`] ?? project, id: commit.id})) } selectCommit = e => { - const { project, type, selected, dispatch } = this.props; - const id = e.target.value; - const attribute = `${type}_commit_id` - const commit_id = selected[attribute] - if (commit_id === undefined || commit_id === null || !commit_id.startsWith(id)) { - dispatch(fetchCommit({project, id, update_selected: attribute})); - dispatch(updateSelected(project, { [attribute]: id })) + const { type, selected, dispatch } = this.props; + const { project_input } = this.state; + const project = project_input ?? this.props.project + const id = e.target?.value ?? e; + + const commit_attr = `${type}_commit_id` + const project_attr = `${type}_project` + const commit_id = selected[commit_attr] + if (commit_id === undefined || commit_id === null || !commit_id.startsWith(id) || selected[project_attr] !== project) { + dispatch(fetchCommit({project, id, update_with_id: {project: this.props.project, commit: commit_attr}})); + let selected_update = {[commit_attr]: id} + if (project_input) { + selected_update[project_attr] = project + } + dispatch(updateSelected(this.props.project, selected_update)) } }; @@ -398,16 +504,17 @@ class CommitNavbar extends React.Component { } selectBranch = branch => { - const { project, type, dispatch } = this.props; - dispatch(fetchCommit({project, branch, update_selected: `${type}_commit_id`})); + const { project, type, dispatch, selected } = this.props; + dispatch(fetchCommit({project: selected[`${type}_project`], branch, update_with_id: {project, commit: `${type}_commit_id`}})); }; selectMilestone = milestone => { const { project, type, dispatch } = this.props; - dispatch(fetchCommit({project, id: milestone.commit})); + dispatch(fetchCommit({project: milestone.project ?? project, id: milestone.commit})); dispatch(updateSelected(project, { [`${type}_commit_id`]: milestone.commit, [`selected_batch_${type}`]: milestone.batch, [`filter_batch_${type}`]: milestone.filter, + [`${type}_project`]: milestone.project ?? project, })) }; @@ -419,6 +526,7 @@ class CommitNavbar extends React.Component { [`${other_type}_commit_id`]: selected[`${type}_commit_id`], [`selected_batch_${other_type}`]: selected[`selected_batch_${type}`], [`filter_batch_${other_type}`]: selected[`filter_batch_${type}`], + [`${other_type}_project`]: selected[`${type}_project`], })) } @@ -426,6 +534,8 @@ class CommitNavbar extends React.Component { switchSelection = () => { const { project, selected, dispatch } = this.props; dispatch(updateSelected(project, { + new_project: selected.ref_project, + ref_project: selected.new_project, new_commit_id: selected.ref_commit_id, ref_commit_id: selected.new_commit_id, selected_batch_new: selected.selected_batch_ref, diff --git a/webapp/src/components/CommitRow.js b/webapp/src/components/CommitRow.js index 6caddc5d..1bd871b5 100755 --- a/webapp/src/components/CommitRow.js +++ b/webapp/src/components/CommitRow.js @@ -27,6 +27,7 @@ import { Avatar } from "./avatars"; import { DoneAtTag } from "./DoneAtTag"; import { CopyToClipboard } from "react-copy-to-clipboard"; import { shortId, pretty_label, linux_to_windows } from "../utils"; +import { git_hostname, default_git_hostname } from "../utils" const CommitDetails = styled.div` display: flex; @@ -72,6 +73,8 @@ class CommitResults extends React.Component { return const git = project_data.data?.git || {}; + const project_git_hostname = git_hostname(project_data.data?.qatools_config) ?? default_git_hostname + git.web_url = git.web_url ?? `${project_git_hostname}/${git.path_with_namespace}` const gitlab_commit_url = `${git.web_url}/commit/${commit.id}`; let batches_with_results = Object.entries(commit.batches) .filter( ([label, batch]) => has_outputs_in_batch(label)(commit) ) @@ -257,18 +260,22 @@ class CommitRow extends React.Component { render() { const { commit, project, project_data={}, className, tag, toaster, dispatch } = this.props; - console.log(project_data) const git = project_data.data?.git || {}; + const project_git_hostname = git_hostname(project_data?.data?.qatools_config) ?? default_git_hostname + git.web_url = git.web_url ?? `${project_git_hostname}/${git.path_with_namespace}` const is_subproject = git.path_with_namespace !== project; - console.log(git) const commit_url = `${git.web_url}/commit/${commit.id}` - console.log(commit_url) const has_data = !!commit?.authored_datetime let maybe_skeletton = has_data ? null : Classes.SKELETON; + let avatar_url = commit?.committer_avatar_url + const gitlab_host = git.web_url.split('/').slice(0,3).join('/') + if (!!avatar_url && avatar_url.startsWith(gitlab_host)) { + avatar_url = encodeURI(`/api/v1/gitlab/proxy?url=${avatar_url}`) + } return ( dispatch(updateSelected(project, {branch: null, committer: commit.committer_name}))} alt={commit.committer_name || commit.id || '?'} diff --git a/webapp/src/components/DoneAtTag.js b/webapp/src/components/DoneAtTag.js index 0da523a2..db0225c8 100644 --- a/webapp/src/components/DoneAtTag.js +++ b/webapp/src/components/DoneAtTag.js @@ -2,8 +2,8 @@ import React from "react"; import { Link } from "react-router-dom"; import styled from "styled-components"; -import Moment from "react-moment"; -import { Tooltip, Classes } from "@blueprintjs/core"; +import { DateTime } from 'luxon'; +import { Classes } from "@blueprintjs/core"; import { updateSelected } from "../actions/selected"; @@ -17,20 +17,19 @@ class DoneAtTagUnstyled extends React.Component { render() { const { project, commit, className, style, dispatch } = this.props; const has_data = !!commit?.authored_datetime - let maybe_skeletton = has_data ? null : Classes.SKELETON; + const maybe_skeletton = has_data ? null : Classes.SKELETON; return ( - - - {commit?.authored_datetime} - {" "} + + {DateTime.fromISO(commit?.authored_datetime ?? defaults.date).toRelative()} + {" "} dispatch(updateSelected(project, {branch: null, committer: commit.committer_name}))} > - by {has_data ? commit.committer_name : defaults.committer_name} + by {commit?.committer_name ?? defaults.committer_name} ); diff --git a/webapp/src/components/authentication/Auth.js b/webapp/src/components/authentication/Auth.js new file mode 100644 index 00000000..4505ffae --- /dev/null +++ b/webapp/src/components/authentication/Auth.js @@ -0,0 +1,230 @@ +import React from "react"; +import { post, get } from "axios"; +import { connect } from 'react-redux' +import { + Classes, + Intent, + MenuItem, + Icon, + Tooltip, + InputGroup, + Button, + Dialog, + Toaster, +} from "@blueprintjs/core"; +import { login, logout } from '../../actions/users' + +// TODO: +// - sign-up ? +// - move login/logout to the action + +const toaster = Toaster.create(); + +class AuthButton extends React.Component { + constructor(props) { + super(props); + this.state = { + is_loading: false, + }; + } + + checkAuth = () => { + get("/api/v1/user/me/") + .then(response => { + const { is_authenticated, user_id, user_name, full_name, email, is_ldap } = response.data; + this.setState({ + is_loading: false, + }); + if (is_authenticated) { + this.props.dispatch(login({user_name, email, is_ldap, full_name, user_id})) + } else { + this.props.dispatch(logout()) + } + }) + .catch(error => { + toaster.show({ message: `${error}`, intent: Intent.DANGER, timeout: 3000 }) + console.log(error.response) + }) + } + + // componentDidMount() { + // if (!this.props.user.is_logged) + // this.checkAuth() + // } + + logout = () => { + const { user_name, full_name } = this.props.user; + const display_name = full_name ?? user_name + this.props.dispatch(logout()) + post("/api/v1/user/logout/") + .then(response => { + if(response.status == 200){ + // this.props.getAuth() + toaster.show({ message: `Goodbye, ${display_name}`, intent: Intent.WARNING, timeout: 3000 }); + } + }) + .catch(error => { + toaster.show({ message: `${error}`, intent: Intent.DANGER, timeout: 3000 }) + console.log(error.response) + }) + } + + render() { + if (this.state.loading) + return +
    + +
    +
    +
    +
    + + + + } + + handleOpen = () => this.setState({ isOpen: true , error: null, is_loading: false}); + handleClose = () => this.setState({ isOpen: false }); +} + + +const mapStateToProps = state => { + return { + user: state.user || null, + } +} +export default connect(mapStateToProps)(AuthButton); diff --git a/webapp/src/components/authentication/RequireAuth.js b/webapp/src/components/authentication/RequireAuth.js new file mode 100644 index 00000000..ad7907ef --- /dev/null +++ b/webapp/src/components/authentication/RequireAuth.js @@ -0,0 +1,45 @@ +import React from "react"; +import { connect } from 'react-redux' +import { + Classes, + Intent, + Callout, +} from "@blueprintjs/core"; +import AuthButton from "./Auth" + + + +class PrivateContent extends React.Component { + constructor(props) { + super(props); + } + + render() { + const is_logged = this.props.user ? this.props.user.is_logged : undefined; + return <> + {is_logged ? + this.props.children : + +

    The content is available for logged-in users only.

    + +     + } + + } +} + + +// export const require_authentication_button = ( on_click_func, user_state ) => { +// // const user_state = store ? store.getState().user : undefined +// const is_auth = user_state ? user_state.is_logged : undefined +// return is_auth ? on_click_func : undefined +// } + + +const mapStateToProps = state => { + return { + user: state.user || null, + } +} + +export default connect(mapStateToProps)(PrivateContent); \ No newline at end of file diff --git a/webapp/src/components/avatars.js b/webapp/src/components/avatars.js index 5514e986..8a1fde96 100644 --- a/webapp/src/components/avatars.js +++ b/webapp/src/components/avatars.js @@ -67,10 +67,11 @@ class CommitAvatar extends React.PureComponent { render() { const { commit, size } = this.props; let maybe_skeleton = (!commit || !commit.committer_name) ? Classes.SKELETON : null; + let avatar_url = !!commit?.committer_avatar_url ? encodeURI(`/api/v1/gitlab/proxy?url=${commit?.committer_avatar_url}`) : null return if (badge) { var right_label = integration.icon && @@ -454,7 +457,7 @@ const default_gitlab_integrations = [ { href: "${git.web_url}/commits/${branch}", alt: "Build status", - src: "${git.web_url}/badges/${branch}/build.svg", + src: "${git.web_url}/badges/${branch}/pipeline.svg", only: "${branch}" // won't be displayed in per-commit pages }, { diff --git a/webapp/src/components/messages.js b/webapp/src/components/messages.js index 19b17adf..1eb4602f 100755 --- a/webapp/src/components/messages.js +++ b/webapp/src/components/messages.js @@ -40,9 +40,6 @@ class CommitWarningMessages extends React.Component { this.setState({waiting: false}) toaster.show({message: `Restore artifacts.`, intent: Intent.PRIMARY}); this.refresh() - setTimeout(this.refresh, 1*1000) - setTimeout(this.refresh, 5*1000) - setTimeout(this.refresh, 10*1000) }) .catch(error => { this.setState({waiting: false }); @@ -121,13 +118,14 @@ class BatchStatusMessages extends React.Component { }); } - refresh = () => { + refresh = (refresh_again=true) => { const { project, commit, dispatch } = this.props; dispatch(fetchCommit({project, id: commit.id})) - this.refresh() - setTimeout(this.refresh, 1*1000) - setTimeout(this.refresh, 5*1000) - setTimeout(this.refresh, 10*1000) + if (refresh_again) { + setTimeout(() => this.refresh(false), 1*1000) + setTimeout(() => this.refresh(false), 5*1000) + setTimeout(() => this.refresh(false), 10*1000) + } } redo_batch(batch) { @@ -139,13 +137,10 @@ class BatchStatusMessages extends React.Component { this.setState({waiting_redo: false}) toaster.show({message: `Redo ${batch.label}.`, intent: Intent.PRIMARY}); this.refresh() - setTimeout(this.refresh, 1*1000) - setTimeout(this.refresh, 5*1000) - setTimeout(this.refresh, 10*1000) -}) + }) .catch(error => { this.setState({waiting_redo: false }); - toaster.show({message: JSON.stringify(error), intent: Intent.DANGER}); + toaster.show({message: JSON.stringify(error.response ?? error), intent: Intent.DANGER}); this.refresh() }); } diff --git a/webapp/src/components/milestones.js b/webapp/src/components/milestones.js index 663bec7e..52c84e51 100755 --- a/webapp/src/components/milestones.js +++ b/webapp/src/components/milestones.js @@ -1,5 +1,5 @@ -import React from "react"; -import Moment from "react-moment"; +import React, { useState } from "react"; +import { DateTime } from 'luxon'; import { post } from "axios"; import { @@ -17,6 +17,8 @@ import { Switch, FormGroup, InputGroup, + ControlGroup, + HTMLSelect, Tooltip, Popover, Alert, @@ -24,27 +26,58 @@ import { } from "@blueprintjs/core"; import { updateMilestones, fetchProjects } from "../actions/projects"; +import { match_query } from "../utils"; const toaster = Toaster.create(); +// FIXME: Right now we can only have 1 filter per commit/batch, because it's not in the key... +// The design is really bad. Instead we could use uuids, or just have a list of milestones +// that we filter for match on project+commit+batch+filter +// It requires a migration, so let's leave it for later... +const MilestonesMenu = ({project, milestones, title, icon, onSelect, type}) => { + const [filter, setFilter] = useState(''); + const [orderBy, setOrderBy] = useState("date ↓"); -const MilestonesMenu = ({milestones, title, icon, onSelect, type}) => { - const has_milestones = Object.keys(milestones).length > 0; + const has_milestones = Object.keys(milestones).length > 0; + const matcher = match_query(filter) + const sortWeight = orderBy.includes("↓") ? -1 : 1 const milestones_menu_items = has_milestones ? (Object.values(milestones) - .sort( (m0, m1) => new Date(m1.date) - new Date(m0.date)) + .filter(m => matcher(`${m.project} ${m.commit} ${m.batch} ${m.filter} ${m.label} ${m.notes}`)) + .sort( (m0, m1) => sortWeight * (new Date(m0.date) - new Date(m1.date))) || []) - .map( (m, idx) => ) + .map( (m, idx) => ) : <> return <> {(!!title && has_milestones) &&
  • {title}
    • } + {Object.keys(milestones).length > 1 && + + { + setFilter(e.target.value) + }} + fill + /> + { + setOrderBy(e.currentTarget.value) + }} + options={["date ↓", "date ↑"]} + value={orderBy} + /> + + } {milestones_menu_items} } -const MilestoneMenu = ({ milestone, onSelect, icon }) => { +const MilestoneMenu = ({ project, milestone, onSelect, icon }) => { const { commit: commit_id, batch, filter, label, notes, date } = milestone; const has_filter = !!filter && filter.length > 0; const has_label = !!label && label.length > 0; @@ -53,16 +86,19 @@ const MilestoneMenu = ({ milestone, onSelect, icon }) => { return {has_label && <>{label}
    } - {!!date && set } + {!!date && + set {DateTime.fromJSDate(new Date(date)).toRelative()} + } } icon={} label={<> - {has_batch && {batch}} - {has_filter && {filter}} - {!!milestone.branch && {milestone.branch}} - {!!commit_id && {commit_id.slice(0, 8)}} + {(!!milestone.project && milestone.project !== project) && {milestone.project}} + {has_batch && {batch}} + {has_filter && {filter}} + {!!milestone.branch && {milestone.branch}} + {!!commit_id && {commit_id.slice(0, 8)}} {has_notes && - + 
    {notes}
    } } @@ -85,7 +121,7 @@ class CommitMilestoneEditor extends React.Component { // TODO: how exactly do we use current/previous? // FIXME: we should keep proper "milesone" objects for the current milestone // do we even need the previous milestone? - date: new Date().toLocaleString(), + date: new Date(), notes: '', label: '', // we ask for confirmation when users delete/overwrite a milestone @@ -145,9 +181,13 @@ class CommitMilestoneEditor extends React.Component { isOpen={show_alert_remove} onCancel={() => this.setState({ show_alert_remove: false })} onConfirm={this.deleteMilestone} - style={{width: '1200px'}} + style={{width: '1200px', maxWidth: "fit-content"}} > -

    Are you sure you want to delete

    ?

    +

    Are you sure you want to delete this milestone? +

    + + +

    }