diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 2e58859..e54338d 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -16,3 +16,5 @@ jobs: with: release-type: python package-name: workflow + extra-files: | + workflow/__init__.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 877a345..736d84b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -16,17 +16,17 @@ repos: - --max-complexity=15 id: flake8 repo: https://github.com/pycqa/flake8 - rev: 6.0.0 + rev: 6.1.0 - hooks: - args: - --py36-plus id: pyupgrade repo: https://github.com/asottile/pyupgrade - rev: v3.9.0 + rev: v3.13.0 - hooks: - id: black repo: https://github.com/psf/black - rev: 23.7.0 + rev: 23.9.1 - hooks: - additional_dependencies: - types-attrs @@ -39,7 +39,7 @@ repos: - --no-implicit-optional id: mypy repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.4.1 + rev: v1.5.1 - hooks: - args: - --convention=google @@ -50,7 +50,7 @@ repos: - hooks: - id: blacken-docs repo: https://github.com/asottile/blacken-docs - rev: 1.15.0 + rev: 1.16.0 - hooks: - id: trailing-whitespace - id: end-of-file-fixer @@ -95,4 +95,4 @@ repos: stages: - commit-msg repo: https://github.com/commitizen-tools/commitizen - rev: 3.5.3 + rev: 3.10.0 diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000..7a0ed01 --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,57 @@ +version: "3.8" + +services: + mongo: + image: mongo:latest + command: ["mongod", "--bind_ip_all"] + container_name: mongo + restart: always + ports: + - 27017:27017 + - 27018:27018 + - 27019:27019 + deploy: + mode: replicated + replicas: 1 + + buckets: + image: chimefrb/buckets:latest + command: ["/bin/bash", "-c", "python -m buckets.server"] + container_name: buckets + restart: always + ports: + - 8001:8001 + environment: + - SANIC_HOSTNAME=0.0.0.0 + - SANIC_PORT=8001 + - SANIC_ACCESS_LOG=true + - SANIC_AUTO_RELOAD=true + - SANIC_DEBUG=true + - SANIC_MONGODB_HOSTNAME=mongo + - SANIC_MONGODB_PORT=27017 + deploy: + mode: replicated + replicas: 1 + depends_on: + - mongo + + results: + image: chimefrb/results:latest + command: ["/bin/bash", "-c", "python -m results.server"] + container_name: results + restart: always + ports: + - 8002:8002 + environment: + - SANIC_HOSTNAME=0.0.0.0 + - SANIC_PORT=8002 + - SANIC_ACCESS_LOG=true + - SANIC_AUTO_RELOAD=true + - SANIC_DEBUG=true + - SANIC_MONGODB_HOSTNAME=mongo + - SANIC_MONGODB_PORT=27017 + deploy: + mode: replicated + replicas: 1 + depends_on: + - mongo diff --git a/docs/buckets.md b/docs/buckets.md new file mode 100644 index 0000000..0b6891a --- /dev/null +++ b/docs/buckets.md @@ -0,0 +1,13 @@ +# Workflow Buckets + +::: workflow.http.buckets.Buckets + handler: + python + selection: + docstring_style: google + inherited_members: false + rendering: + show_root_heading: true + show_category_heading: true + show_source: true + heading_level: 4 diff --git a/docs/cli.md b/docs/cli.md new file mode 100644 index 0000000..ab0793a --- /dev/null +++ b/docs/cli.md @@ -0,0 +1,11 @@ +# Workflow CLI + + +## Runners + +```bash +workflow run [PIPELINE] +``` + +!!! Note + If the `work.function` is a Click CLI command, then `workflow run` will inherit the CLI default arguments and then merge them with the `work.parameters` specified in the work object. This allows for a single CLI to be used for both interactive and non-interactive workflows. diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..3749210 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,162 @@ +# What is the Workflow System? + +Workflow is an over-arching framework to manage the lifecycle (execution, state machine chaining, query of results) of any process agnostic of the underlying parameters such as hardware, software, physical constraints etc. + +## Philosophy + +The core tenant of workflow is to provide impeccable bookkeeping. It acts as a singular coordination layer for performing any task through a simple and intuitive interface. At the core of the workflow system is the `Work` object which consists of a generic set of metadata that can be used to describe any action performed by the system. The workflow system manages the entire lifecycle of a single or collection of work objects, from their creation to its completion. The user can then query the workflow framework to get the input parameters or results of the work at any point. + +## Architecture + +The workflow system is designed to be modular and extensible. It is composed of six main components: + +1. User Codebase +2. `Work` object. +3. Buckets Backend. +4. Results Backend. +5. Pipelines Backend. +6. Workflow Web User Interface. + +```mermaid +stateDiagram-v2 + Codebase --> Work: user creates a work object + Work --> Buckets: deposit + Buckets --> Execution: withdraw + Execution --> Buckets: update (success/failure) + Buckets --> Results: automatic transfer of completed work + Buckets --> WebUI: realtime + Results --> WebUI: search and query any work + +``` + +## Usage + +### Define `Work` + +The `Work` object at the core of the workflow system is simply a python dictionary object which contains all parameters that can be used to define a task at the telescope. The `Work` object is defined as follows: + +```python +from chime_frb_api.workflow import Work + +work = Work(pipeline="sample-pipeline", parameters={"a": 1, "b": 2}) +``` + +At a minimum, the `Work` object requires only requires the `pipeline` parameter. Additional lifecycle are automatically added to the `Work` object as it progresses through the workflow system. At any time in its lifecycle, you can see all the parameters in the `Work` object by simply running, + +```python +work.payload +{ + "pipeline": "sample-pipeline", + "parameters": None, + "results": None, + "path": ".", + "event": None, + "tags": None, + "group": None, + "timeout": 3600, + "retries": 2, + "priority": 3, + "products": None, + "plots": None, + "site": "local", + "user": None, + "archive": True, + "precursors": None, + "config": None, + "id": None, + "creation": 1673298165.260349, + "start": None, + "stop": None, + "attempt": 1, + "status": "created", +} +``` + +This dictionary is the exact representation of the `Work` object in the database. + +### Deposit `Work` + +To deposit the `Work` object into the workflow system, simply run, + +```python +work.deposit() +``` + +### Perform Work + +`Work` is usually performed by a user provided python function. This function can be run anywhere, but it is recommended to run it in a container. In future releases of the workflow system, we will provide a container orchestration layer to run the function at any scale or any telescope site and also at Compute Canada sites. + +To perform a unit of work, the user needs to withdraw the work, perform it, update it with the results and finally deposit it back to the workflow system. This can be done manually by the user, or it can also be done automatically by the workflow system using the `workflow run` CLI command. + +### User Provided Function + +Lets say we have the following function, that you wish to run, + +```python +# Function that performs the work. +# We assume that this function is availaible as an import. +def add(a: int, b: int) -> int: + result = a + b + return result +``` + +#### Manual Withdraw and Deposit + +```python +from chime_frb_api.workflow import Work + +work = Work.withdraw(pipeline="sample-pipeline") +result = add(**work.parameters) +work.results = result +work.status = "success" +work.update() +``` + +#### Automatic Withdraw and Deposit + +```bash +workflow run add sample-pipeline +``` + +The simplest and preferred way to run a user function is throught the `workflow run` CLI Command. This command will automatically withdraw the work, perform the work by passing the `parameters` field to the user function, and then deposit the results returned back into the workflow system. + +#### CLI Command: `workflow run` + +```bash +workflow run {pipeline-name} {module.submodule.function} +``` + +where, + +* `pipeline-name`: the name of the pipeline. This defines what work will be withdrawn by the running pipeline. + +* `module.submodule.function`: the full python specficication of the pipeline function that will be ran. + +The pipeline CLI assumes that the pipeline function follows the [CHIME/FRB pipeline interface specification](https://chimefrb.github.io/guidelines/pipeline_interface/). That is, it takes keyword arguments as inputs and outputs a `results` dictionary, a `products` list of paths to output files, and a `plots` lists of paths to output plots. + +Example for header localization persistent container: + +```bash +poetry workflow run header-localization frb_l2l3.utils.header_localization.main +``` + +## Recommended Fields + +It is strongly recommended to use the maximum number of fields in the work object. This will make it easier not only to manage the workflow, but also to manage retrieve the results of the work once completed. + +```python +work.event = [12345, 67890] +work.user = "some-user" +work.tag = ["some-tag", "some-other-tag"] +work.group = ["some-working-group", "some-other-working-group"] +work.site = "chime" +``` + +```python +work.results = {"some-parameter": "some-value"} +work.plots = ["some-plot.png"] +work.products = ["some-product.fits"] +work.status = "success" +``` + +For a full list of parameters that can be set in the Work object see [Work Object](work.md). diff --git a/docs/loki.md b/docs/loki.md new file mode 100644 index 0000000..6dadc3c --- /dev/null +++ b/docs/loki.md @@ -0,0 +1,253 @@ +# Loki logging + +Loki is a log indexing system built around the idea of only indexing the +metadata of the logs. It can also added as a source in Grafana, and so is often +described as "like Prometheus, but for logs". + +## Uploading logs to Loki + +Logs can be uploaded to Loki via two methods: + +- Directly from the [Docker](#logs-from-docker) container's logs. +- As part of the [`workflow run`](#logs-from-workflow-run) CLI command. + +### Logs from Docker + +To upload logs from a Docker container requires configuring the Docker logs to +use the Loki driver. The driver should be installed on all available nodes - if +you believe that this is not the case, please contact a sysadmin. There are two +ways that you might want to configure Docker to use Loki: a stand-alone +container, or service within a compose file. + +1. Stand-alone container: + To use Loki in a stand-alone container, the `--log-driver` flag must be + set to `loki` and the `--log-opt` flag must be used. + + ``` sh + docker run --log-driver=loki \ + --log-opt loki-url="http://frb-vsop:3100/loki/api/v1/push" \ + --log-opt loki-retries=5 \ + --log-opt loki-batch-size=400 \ + --log-opt loki-external-labels="site=chime" \ + grafana/grafana + ``` + +2. Service within a compose file: + To use Loki in a compose file, the `logging` mapping must be defined. + Below is an example which must be placed on the same indentation level as `image`. + + ``` yaml + logging: &loki-logging + driver: loki + options: + loki-url: "http://frb-vsop:3100/loki/api/v1/push" + loki-retries: "5" + loki-batch-size: "102400" # 100 KB + loki-external-labels: "site=chime" + ``` + + Here, the `&loki-logging` tag allows this configuration to be used throughout + the compose file. The tag can be used for another service using: + + ``` yaml + logging: + <<: *loki-logging + ``` + +!!! info "Note: Correct URL for site must be given!" + In the examples above, the URL is correctly given for Chime site. However, this + will change for the other sites. See below for the correct URLs for each site. + + ``` yaml + loki_urls: + aro: "http://localhost:3100/loki/api/v1/push" + canfar: "https://frb.chimenet.ca/loki/loki/api/v1/push" + cedar: "http://localhost:3100/loki/api/v1/push" + chime: "http://frb-vsop:3100/loki/api/v1/push" + gbo: "http://aux:3100/loki/api/v1/push" + hco: "http://aux:3100/loki/api/v1/push" + kko: "http://aux:3100/loki/api/v1/push" + local: "https://frb.chimenet.ca/loki/loki/api/v1/push" + ``` + +### Logs from `workflow run` + +There is no set-up required to upload logs to Loki when using `workflow run`. As +`workflow` always attempts to upload logs by default; it knows which Loki URL to +submit the logs to based on the `--site` flag. However, this can be overridden by +using the `--loki-url` flag. See below for an example of the output from `workflow +run` with the Loki lines highlighted. In this case, it didn't contact the Loki server +as the Loki URL was overridden and set to 'http://not-real-url'. + +``` txt hl_lines="11 20" +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Workflow Run CLI +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Bucket : test +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Function : None +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Command : None +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Mode : Dynamic +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Lifetime : infinite +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Sleep : 1s +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Work Site: local +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Log Level: INFO +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Base URL : https://frb.chimenet.ca/buckets +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Loki URL : http://not-real-url +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Prod URL : + https://frb.chimenet.ca/frb-master/v1/events/query-file?filename= +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Execution Environment +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Operating System: Darwin +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Python Version : 3.11.2 +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Python Compiler : Clang 14.0.0 (clang-1400.0.29.202) +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Virtualization : None +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Configuration Checks +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Loki Logs: ❌ +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Base URL : ✅ +26 Apr 2023 14:18:46 EDT INFO chimefrb.workflow Starting Workflow Lifecycle +``` + +## Querying logs + +Logs submitted to Loki can be queried via Grafana's Explore page. At Chime this is +found at . At the top of this page, to the right +of "Explore" there is a drop down menu, this is where the source is selected. Loki +sources are indicated by orange/yellow 'L'-shaped icon, in the list there should be +one named "CHIME/FRB Logs", select this source if it is not already selected. + +Loki queries are made using LogQL, a PromQL-inspired query language. Here a basic +introduction will be given, if you wish to know more about anything discussed here +please refer to the [LogQL documentation](https://grafana.com/docs/loki/latest/logql/). + +LogQL has two types of queries: + +- Log queries: contents of logs. +- Metric queries: values based on query results. + +### Log queries + +LogQL queries all have a log stream selector. These are placed within curly braces +`{}`. The streams that are available depends on the method that was used the upload +the logs to Loki. + +#### Log streams + +| Streams | Method: Docker | Method: Workflow | +|---------------|------------------|------------------| +| site | :material-check: | :material-check: | +| host | :material-check: | :material-close: | +| pipeline | :material-close: | :material-check: | +| logger | :material-close: | :material-check: | +| severity | :material-check: | :material-check: | +| source | :material-check: | :material-close: | +| swarm_service | :material-check: | :material-close: | +| swarm_stack | :material-check: | :material-close: | + +The stream selector chooses the log streams that will be included in the query. +Eg.: `{site="chime"}` would show all logs from Chime site and +`{swarm_stack="datatrail"}` would show all logs from the Datatrail stack. + +##### Log stream operators + +However, `=` is not the only stream operator that can be used. There are also the +following operators: + +- `=`: Equal. +- `!=`: Not equal. +- `=~`: Regex match. +- `!~`: Not regex match. + +##### Multiple log stream operators + +Additionally, multiple stream operations can be combined together: +`{swarm_stack!="datatrail", site="chime"}`. This would show all logs from Chime, +but not those belonging to the Datatrail stack. + +#### Log pipeline + +Log streams can be followed by a _log pipeline_, which is a set of expressions +that can be linked together and applied to the log stream to filter it. The expressions +are applied in order from left to right. + +##### Line filter expression + +Line filter expressions have a filter operator followed by text or a regex. The operators +are: + +- `|=`: Equal. +- `!=`: Not equal. +- `|~`: Regex match. +- `!~`: Not regex match. + +Examples: + +- `|= "foo"` would show all logs that contain `foo` in the log line. +- `!=bar` would exclude all logs that contain `bar` in the log line. +- ```|~ `error=\w+` ``` would show all logs that contain `error` + followed by one or more words in the log line. + +##### Parser expression and Label filter expressions + +Please refer to the Loki documentation for these. + +- [Label filter expression](https://grafana.com/docs/loki/latest/logql/log_queries/#label-filter-expression) +- [Parser expression](https://grafana.com/docs/loki/latest/logql/log_queries/#parser-expression) + +### Metric queries + +Metric queries apply functions to log query results, in order to create metrics from +logs. Examples of uses of Metrics queries include calculating the rate of error +messages, or finding the top N log sources with the most errors over a specified +time period. + +#### Log range aggregation + +These are queries followed by a duration, the duration can come after either the +log stream or pipeline. Durations are numbers followed by one of the following units: + +- `ms`: milliseconds +- `s`: seconds +- `m`: minutes +- `h`: hours +- `d`: days, assuming a day has always 24h +- `w`: weeks, assuming a week has always 7d +- `y`: years, assuming a year has always 365d + +The functions that are available are: + +- `rate(log-range)`: calculates the number of entries per second. +- `count_over_time(log-range)`: counts the entries for each log stream within the + given range. +- `bytes_rate(log-range)`: calculates the number of bytes per second for each stream. +- `bytes_over_time(log-range)`: counts the amount of bytes used by each log + stream for a given range. +- `absent_over_time(log-range)`: returns an empty vector if the range vector passed + to it has any elements and a 1-element vector with the value 1 if the range vector + passed to it has no elements. (absent_over_time is useful for alerting on when no + time series and logs stream exist for label combination for a certain amount of time.) + +!!! example "Example: Range aggregation query" + ``` + rate({site="chime"}[5m]) + ``` + +There also exist operators that can be used to aggregate the metrics by log streams, resulting +in fewer metrics. The operators are: + +- `sum`: Calculate sum over labels. +- `avg`: Calculate the average over labels. +- `min`: Select minimum over labels. +- `max`: Select maximum over labels. +- `stddev`: Calculate the population standard deviation over labels. +- `stdvar`: Calculate the population standard variance over labels. +- `count`: Count number of elements in the vector. +- `topk`: Select largest k elements by sample value. +- `bottomk`: Select smallest k elements by sample value. +- `sort`: returns vector elements sorted by their sample values, in ascending order. +- `sort_desc`: Same as sort, but sorts in descending order. + +!!! example "Example: Range aggregation query" + ``` + sum(rate({site="chime"}[5m])) + ``` + or + ``` + sum by (host) (rate({site="chime"}[5m])) + ``` diff --git a/docs/notifications.md b/docs/notifications.md new file mode 100644 index 0000000..05ddb4e --- /dev/null +++ b/docs/notifications.md @@ -0,0 +1,99 @@ +# Notification System + +The Work object is now capable of sending Slack notifications to both users and +channels. The notifications can be triggered in two ways: the completion of a Work +object, or a Work submitted to the 'notify' pipeline. In both cases the Work must have a +valid notify configuration. + +## Overview of notify configuration + +``` +Work['notify'] = { + 'slack': { + 'channel_id': None, # Valid Slack config must have a channel_id, + 'member_ids': None, # or at least one member_ids set. + 'message': None, # A written message to be displayed. + 'results': None, # Boolean to display results or omit them. + 'products': None, # Boolean to display list of products or omit them. + 'plots': None,  # Boolean to display list of plots or omit them. + 'blocks': None, # Customise message using Slack Blocks. + 'reply': None, # Sending status of message. + }, +} +``` + +## Usage + +### Define a `Work` + +First define a simple `Work` object with the basic required fields populated. + +```python +from chime_frb_api.workflow import Work + +# Note: When using the notify pipeline, the 'site' must be 'chime'. +work = Work(pipeline="notify", user="tester", site="chime") +``` + +### Configuration for Slack + +Below is an example configuration for sending a Slack message to both a channel and a +member. + +```python +# If both the channel_id and member_ids are defined the message will go to both. However, +# at least one of these MUST be defined. +work.notify.slack.channel_id = "A1B2XY9Z" # Not real +work.notify.slack.member_ids = ["BD31SV4S"] # Not real + +# Tip: If you want to use emojis you can draft your message in Slack then copy/paste it. +work.notify.slack.message = ( + "Hello :wave:, this is a message from the Workflow Slack bot." +) + +# products, plots, and results all behave the same, so here we'll only define one, but +# all of them can be used simulataneously. +work.notify.slack.products = True +# Since the products is currently None lets define that. +work.products = ["test_file.dat"] +``` + +The configuration for `work.notify.slack.blocks` can be quite involved since it uses +Slack's Block Kit. For more info on Block Kit, please visit +. An interactive Block Kit builder is also available to +help you use it without having to learn . + +!!! example "Result of the example above" + + ![example_message](./images/slack_bot_message_eg.png) + +## Finding Slack channel and member ids + +### Channel ID + +1. Navigate to the channel you wish to post to. + +2. Click on the channel's name near the top of the window to get more information about + it. + + ??? info "Image: Obtaining Channel info." + + ![channel_page](./images/channel_page.png) + +3. The channel's id will be shown at the bottom of the pop-up, clicking on it will copy + it the the pasteboard. + + ??? info "Image: Channel info pop-up." + + ![channel_info](./images/channel_info.png) + +### Member ID + +1. Use the Slack search bar navigate to the chat page with the user you wish to +send a message to. + +2. Click on the user's name to bring up their Profile. + +3. Click the button with the three vertical dots. + +4. Select the "Copy member ID" option to copy the ID to the pasteboard. diff --git a/docs/results.md b/docs/results.md new file mode 100644 index 0000000..7a466e8 --- /dev/null +++ b/docs/results.md @@ -0,0 +1,13 @@ +# Workflow Results + +::: workflow.http.results.Results + handler: + python + selection: + docstring_style: google + inherited_members: false + rendering: + show_root_heading: true + show_category_heading: true + show_source: true + heading_level: 4 diff --git a/docs/work.md b/docs/work.md new file mode 100644 index 0000000..db634b9 --- /dev/null +++ b/docs/work.md @@ -0,0 +1,13 @@ +# Work Object + +::: workflow.Work + handler: + python + selection: + docstring_style: google + inherited_members: false + rendering: + show_root_heading: true + show_category_heading: true + show_source: true + heading_level: 4 diff --git a/docs/workflow-pipelines-flow.md b/docs/workflow-pipelines-flow.md new file mode 100644 index 0000000..99d5ec6 --- /dev/null +++ b/docs/workflow-pipelines-flow.md @@ -0,0 +1,70 @@ +# Pipeline configuration flow + +Let's use the following pipeline configuration as an example to explain the current flow it will follow. + +```yaml +version: "1" +name: "demo" +pipeline: + stage-1-a: + stage: 1 + matrix: + job_id: + range: [1, 2] + site: ["aro", "canfar"] + work: + site: ${{ matrix.site }} + parameters: + job_id: ${{ matrix.job_id }} + stage-2-a: + stage: 2 + work: + command: ["ls", "-la"] + site: "local" + event: + - 253483080 + stage-2-b: + stage: 2 + work: + command: ["ls", "-la"] + site: "local" + stage-3-a: + stage: 3 + work: + site: "local" + command: ["ls", "-la"] + tags: + - tag1 + - tag2 + event: + - 253483080 +``` + +There are 4 step definitions on the pipeline configuration, each step contains a `stage` key: + +- On stage 1 there is the step `stage-1-a` with a `matrix` strategy +- On stage 2 there are the steps `stage-2-a` and `stage-2-b` +- On stage 3 there is the step `stage-3-a` + +If there are several steps that have the same `stage` of execution, these will execute concurrently. + +The step `stage-1-a` contains a `matrix` definition, this means that the step will have replicas, following the strategies defined on the `matrix`: + +- `job_id` will have values `[1, 2]` +- `site` will have values `["aro", "canfar"]` + +This means there will be 4 replicas for `stage-1-a` with different values for parameters `job_id` and `site`: + +- `(1, "aro")` +- `(1, "canfar")` +- `(2, "aro")` +- `(2, "canfar")` + +# Execution flow + +```mermaid +flowchart LR + id_1((stage-1))---> stage-1-a_0 & stage-1-a_1 & stage-1-a_2 & stage-1-a_3---> id_2((stage_2)) + id_2((stage-2))--> stage-2-a & stage-2-b --> id_3((stage_3)) + id_3((stage-3))-->stage-3-a +``` diff --git a/docs/workflow-pipelines-intro.md b/docs/workflow-pipelines-intro.md new file mode 100644 index 0000000..48dce89 --- /dev/null +++ b/docs/workflow-pipelines-intro.md @@ -0,0 +1,27 @@ +# `workflow-pipelines` + +A lightweight Python backend using Sanic that allows the creation and monitoring of pipelines configurations by parsing YAML files. + +## Example + +```yaml +version: "1" +name: "test-configuration" +schedule: + cronspec: "*/2 * * * *" + count: 4 +defaults: + user: "chimefrb" + site: "canfar" +pipeline: + test_stage_1: + stage: 1 + work: + command: ["ls", "-la"] + tags: ["tag1", "tag2"] + test_stage_2: + stage: 2 + work: + command: ["ls", "-la"] + tags: ["tag1", "tag2"] +``` diff --git a/docs/workflow-pipelines-yaml-reference.md b/docs/workflow-pipelines-yaml-reference.md new file mode 100644 index 0000000..8b64c49 --- /dev/null +++ b/docs/workflow-pipelines-yaml-reference.md @@ -0,0 +1,226 @@ +# YAML Reference + +Pipeline configuration files use YAML syntax, in a `.yml` or `.yaml` file extension. + +## `version` + +--- + +Version number to be used by the parser, currently only version 1 available. + +## `name` + +--- + +Name for identifying the pipeline configuration. + +## `defaults` + +--- + +Use `defaults` to create a `map` of default settings that will apply to all `Work` objects in the configuration. + +```yaml title="defaults_example.yaml" +version: 1 +name: "defaults_example" +defaults: # (1) + user: "chimefrb" + event: ["123456"] +``` + +1. All Work objects created on this configuration will have `user="chimefrb"` and `event=["123456"]` as default values. + +## `schedule` + +--- + +A map that specifies the schedule for the job. If this is not defined, the pipeline configuration will run only once. + +## `schedule.cronspec` + +--- + +A string that specifies the cron expression for when the job should run. + +#### Example: Creating a pipeline with cronspec + +```yaml title="cronspec_example.yaml" +version: 1 +name: "cronspec_example" +schedule: + cronspec: "30 4 * * 0" # (1) +pipeline: ... +``` + +1. This pipeline configuration will run at 04:30 every Sunday. + +## `schedule.count` + +--- + +An integer that specifies how many times the job should be triggered by the cronspec. Default is 0 (will execute every time the cronspec triggers). + +#### Example: Creating a pipeline with cronspec and count + +```yaml title="cronspec_count_example.yaml" +version: 1 +name: "cronspec_count_example" +schedule: + cronspec: "30 4 * * 0" + count: 2 # (1) +pipeline: ... +``` + +1. Same as the previous example, this will execute at 04:30 every Sunday but only 2 times. Once this limit has been reached, the `Schedule` status will be `expired`. + +## `matrix` + +--- + +Just like in `defaults`, you can use `matrix` on the top level of the configuration to set several default settings for all the `Work` objects with the plus that this will generate several configurations from one file. + +#### Example: Creating a top level matrix + +```yaml title="matrix_example.yaml" +version: 1 +name: "matrix_example" +matrix: + event: ["123456", "456123"] # (1) +pipeline: ... +``` + +1. This matrix will generate 2 pipeline configurations, one for each event listed. + +## `pipeline` + +--- + +The main focus on a workflow pipeline configuration is the `pipeline` which contains all the steps to be executed, these steps can be separated on stages, all the steps inside a stage will execute concurrently. + +## `pipeline.` + +--- + +Use this syntax to give your step a unique identifier on the pipeline. This name will work as a key, which value is a map of the step configuration. The `` must start with a letter and contain only alphanumeric characters or `_`. + +#### Example: Creating steps on a pipeline + +```yaml +version: 1 +name: "pipeline_test" +pipeline: + task_1: # (1) + stage: 1 + work: + ... + task_2: + stage: 1 + work: + ... + task_2_1: + stage: 2 + ... + +``` + +1. Here `task_1` is the name of the step and its value is the map containing the keys `stage` and `work`. + +## `pipeline..stage` + +This represents the order of execution on the pipeline configuration. e.g. In the example `Creating steps on a pipeline` there are 2 steps on the stage 1 and one step on the stages 2; a `Work` object will be created for all of the steps on stage 1 and the stage2 will only be executed if stage1 has completed succesfully. + +## `pipeline..work` + +--- + +All the keys under `.work` will represent the parameters for a `Work` object. For example: + +```yaml + baseband-localization: # (1) + stage: 2 + work: # (2) + parameters: # Work.parameters + path: # Work.path + event: # Work.event + tags: # Work.tags + function: # Work.function + ... +``` + +1. Step name. +2. Fill this as if you were creating a `Work` object on console. + +## `pipeline..matrix` + +Just like in the top level `matrix` you can define a set of values that will be used for the step to generate `Work` objects depending on all the combinations of these values. + +#### Example: Creating a matrix for a step + +```yaml title="inner_matrix_example.yaml" +stage_1_a: + stage: 1 + matrix: # (1) + event: [123456, 645123] + site: ["aro", "canfar"] + work: # (2) + site: ${{ matrix.site }} + command: ["ls", "${{ matrix.event }}"] +``` + +1. This `matrix` will generate 4 `Work` objects, one per each combination: `[123456, "aro"], [123456, "canfar"], [645123, "aro"], [645123, "canfar"]` +2. The values will be replaced where the `matrix.` are specified on the `Work` object. + +Note: You cannot use the same key on a top level `matrix` and on a inner `matrix`. This will raise an error on your pipeline configuration. + +## `pipeline..if` + +Use `.if` when you need to specify conditions for a step to execute. Workflow pipelines keeps a context for all configurations that can be referenced to access several values of the pipeline configuration. + +#### Example: Running a step depending on results of previous steps + +```yaml title="conditionals_example.yaml" +version: 1 +name: "conditionals_tests" +pipeline: + stage_1_step_1: + stage: 1 + work: + ... + stage_1_step_2: + stage: 1 + work: + ... + stage_2_step_1: # (1) + stage: 2 + if: ${{ pipeline.stage_1_step_1.status == 'success' }} + ... +``` + +1. This step will only be executed if `stage_1_step_1` executed successfully. + +#### Example: Running a step using internal functions + +```yaml title="internals_example.yaml" +version: 1 +name: "internals_tests" +pipeline: + stage_1_step_1: + stage: 1 + work: ... + stage_2_step_1: + stage: 2 + work: ... + stage_success: + if: success # (1) + work: ... + stage_failure: + if: failure # (2) + work: ... + stage_always: + if: always # (3) + work: ... +``` + +1. `success` will be true only if the whole pipeline has the status `success`. +2. `failure` will be true only if the whole pipeline has the status `failure`. +3. `always` will always be `True`. diff --git a/docs/workspaces.md b/docs/workspaces.md new file mode 100644 index 0000000..6033e5d --- /dev/null +++ b/docs/workspaces.md @@ -0,0 +1,55 @@ +# Workspaces + +A workspace is `yaml` configuration which defines the behavior of your workflow system. Nominally, a workspace defines any stateful aspects of your workflow system outside the scope of a `Work` Object, e.g. the `baseurls` for connecting to backend services. + +A workspace is, + + - Project-Specific: Each project can have their own workspace, while sharing the same installation. + - YAML-Based: Workspaces are defined in YAML files, which can be version controlled. + - Stored in the client/user's home directory under the path `~/.workflow/workspaces/` + +## How do I activate a workspace? + +Workflow ships with a few workspaces. A `development` workspace that is used for testing and development, and a `chimefrb` workspace that is used by the CHIME/FRB Collaboration. You can list the available workspace by running: + + ```bash + workflow workspace ls + ``` + +Your project administrator should provide you with a workspace configuration file. This file can be hosted as a remote url, a local file or be pushed upstream to be packaged into workflow itself. + +To activate a workspace, + + ```bash + workflow workspace set development + workflow workspace set https://raw.githubusercontent.com/your/repo/development.yaml + workflow workspace set /path/to/development.yaml + ``` + +To remove an active workspace, + + ```bash + workflow workspace rm + ``` +This will only remove the active workspace, i.e. `~/.workflow/workspaces/active.yml`. + +!!! Important + Running workflow without a workspace set will result in an runtime error. + +In order to purge all workspaces, from `~/.workflow/workspaces/` run: + + ```bash + workflow workspace purge + ``` + +### Configuration for container images + +In order to run workflow, pre-configured from container images, it is recommended to set the `workflow set workspace` command during the container build process. For example, in a Dockerfile: + + ```dockerfile + FROM python:3.8-slim-buster + + RUN set -ex \ + pip install workflow && \ + workflow workspace set development + ``` diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..894b592 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,96 @@ +site_name: Workflow +site_author: Shiny Brar +site_description: A pipeline orchestration tool for the scientific community +repo_name: chimefrb/workflow +repo_url: https://github.com/chimefrb/workflow +copyright: Copyright © 2016 - 2021 CHIME/FRB Collaboration + + +theme: + name: material + palette: + scheme: default + primary: indigo + accent: indigo + font: + text: Roboto + code: Roboto Mono + language: en + features: + - navigation.instant + - navigation.tabs + - navigation.tabs.sticky + - search.suggest + - search.highlight + - header.autohide + - content.code.annotate + icon: + repo: fontawesome/brands/github + +plugins: +- search: +- mkdocstrings: + handlers: + python: + paths: [.] # The path to the Python package + +# Extensions +markdown_extensions: + - markdown.extensions.admonition + - markdown.extensions.attr_list + - markdown.extensions.def_list + - markdown.extensions.footnotes + - markdown.extensions.meta + - markdown.extensions.toc: + permalink: true + - pymdownx.arithmatex: + generic: true + - pymdownx.betterem: + smart_enable: all + - pymdownx.caret + - pymdownx.critic + - pymdownx.details + - pymdownx.emoji: + emoji_index: "!!python/name:material.extensions.emoji.twemoji" + emoji_generator: "!!python/name:material.extensions.emoji.to_svg" + - pymdownx.highlight: + use_pygments: true + linenums_style: pymdownx.inline + anchor_linenums: true + line_spans: __span + pygments_lang_class: true + - pymdownx.inlinehilite + - pymdownx.keys + - pymdownx.magiclink: + repo_url_shorthand: true + user: squidfunk + repo: mkdocs-material + - pymdownx.mark + - pymdownx.smartsymbols + - pymdownx.snippets: + check_paths: true + - pymdownx.superfences + - pymdownx.tabbed + - pymdownx.tasklist: + custom_checkbox: true + - pymdownx.tilde + - pymdownx.superfences: + custom_fences: + - name: mermaid + class: mermaid + format: "!!python/name:pymdownx.superfences.fence_code_format" + - tables + +nav: + - Welcome: index.md + - Pipelines: + - Intro: workflow-pipelines-intro.md + - Flow: workflow-pipelines-flow.md + - YAML Reference: workflow-pipelines-yaml-reference.md + - Features: + - Notifications: notifications.md + - Logging: loki.md + - Low Level API: + - Work: work.md + - Buckets: buckets.md + - Results: results.md diff --git a/poetry.lock b/poetry.lock index 5e00bfe..fe4ed28 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,37 +1,45 @@ -# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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index 1b62b8c..020f8e1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ license = "MIT" readme = "README.md" [tool.poetry.dependencies] -python = "^3.8" +python = "^3.9" tenacity = "^8.2" pydantic = "^2.0" requests = "^2.31" @@ -19,14 +19,20 @@ mergedeep = "^1.3" pydantic-settings = "^2.0" [tool.poetry.group.dev.dependencies] -mypy = "^1.4" -pytest = "^7.4" -pytest-cov = "^4.1" -tomli = "^2.0" -pre-commit = "^3.3" -types-requests = "^2.31" -types-toml = "^0.10" -types-setuptools = "^68.0" +mypy = "*" +pytest = "*" +pytest-cov = "*" +tomli = "*" +pre-commit = "*" +types-requests = "*" +types-toml = "*" +types-setuptools = "*" +types-pyyaml = "*" + + +[tool.poetry.group.docs.dependencies] +mkdocs-material = "*" +mkdocstrings-python = "*" [tool.poetry.scripts] workflow = "workflow.cli.main:cli" diff --git a/tests/test_work.py b/tests/test_work.py index 953222a..595d076 100644 --- a/tests/test_work.py +++ b/tests/test_work.py @@ -3,7 +3,13 @@ import pytest from pydantic import ValidationError -from workflow import Work +from workflow.definitions.work import Work + + +def test_good_instantiation(): + """Test that the work object can be instantiated with the correct parameters.""" + work = Work(pipeline="test", site="local", user="test") + assert work.pipeline == "test" def test_bad_instantiation(): diff --git a/workflow/__init__.py b/workflow/__init__.py index d1d9a14..9285363 100644 --- a/workflow/__init__.py +++ b/workflow/__init__.py @@ -1,25 +1,11 @@ """Top-level imports for Tasks API.""" -from logging import getLogger from pathlib import Path -import toml -from pkg_resources import DistributionNotFound, get_distribution - -# Root path to the Skaha Project -BASE_PATH: Path = Path(__file__).absolute().parent.parent -__version__: str = "unknown" - -logger = getLogger(__name__) - -try: - __version__ = get_distribution("workflow").version -except DistributionNotFound as error: # pragma: no cover - logger.warning(error) - pyproject = toml.load(BASE_PATH / "pyproject.toml") - __version__ = pyproject["tool"]["poetry"]["version"] -except Exception as error: # pragma: no cover - logger.warning(error) - logger.warning("unable to find workflow client version") - -from workflow.utils.logger import get_logger # noqa: F401, E402 isort:skip -from workflow.definitions.work import Work # noqa: F401, E402 +# Root path to the Workflow Module +MODULE_PATH: Path = Path(__file__).absolute().parent.parent +# Path to local configurations +CONFIG_PATH: Path = Path.home() / ".workflow" +# Active Workspace Path +DEFAULT_WORKSPACE_PATH: Path = CONFIG_PATH / "workspaces" / "active.yml" +# Workflow Client Version +__version__ = "0.1.0" # {x-release-please-version} diff --git a/workflow/cli/buckets.py b/workflow/cli/buckets.py index 7ba8914..55d2f5f 100644 --- a/workflow/cli/buckets.py +++ b/workflow/cli/buckets.py @@ -2,13 +2,16 @@ from typing import Any, Dict, List, Optional import click -from chime_frb_api.modules.buckets import Buckets from rich import pretty, print from rich.console import Console from rich.table import Table +from workflow.http.context import HTTPContext + pretty.install() console = Console() + + table = Table( title="\nWorkflow Buckets", show_header=True, @@ -26,8 +29,8 @@ def buckets(): @buckets.command("version", help="Show the version.") def version(): """Show the version.""" - buckets = Buckets() - console.print(buckets.version()) + http = HTTPContext() + console.print(http.buckets.info()) @buckets.command("rm", help="Remove a bucket.") @@ -48,18 +51,18 @@ def prune_work(name: str, event: Optional[int] = None, status: Optional[str] = N event (Optional[int], optional): CHIME/FRB Event ID. Defaults to None. status (Optional[str], optional): Status of work[s] to prune. Defaults to None. """ + http = HTTPContext() events: Optional[List[int]] = None if event is not None: events = [event] - buckets = Buckets() - buckets.delete_many(pipeline=name, status=status, events=events) + http.buckets.delete_many(pipeline=name, status=status, events=events) @buckets.command("ls", help="List all active buckets.") def ls(): """List all active buckets.""" - buckets = Buckets() - pipelines = buckets.pipelines() + http = HTTPContext() + pipelines = http.buckets.pipelines() table.add_column("Active Buckets", max_width=50, justify="left") for pipeline in pipelines: table.add_row(pipeline) @@ -76,20 +79,20 @@ def ps(name: Optional[str] = None, all: bool = False): name (Optional[str], optional): Name of the bucket. Defaults to None. all (bool, optional): Whether to show all buckets. Defaults to False. """ - buckets = Buckets() - details = buckets.status(pipeline=None) + http = HTTPContext() + details = http.buckets.status(pipeline=None) table.add_column("name", justify="left") for key in details.keys(): table.add_column(key, justify="right") table.add_row("total", *create_row(details)) if all: - pipelines = buckets.pipelines() + pipelines = http.buckets.pipelines() for pipeline in pipelines: - details = buckets.status(pipeline=pipeline) + details = http.buckets.status(pipeline=pipeline) row = create_row(details) table.add_row(pipeline, *row) elif name: - details = buckets.status(pipeline=name) + details = http.buckets.status(pipeline=name) row = create_row(details) table.add_row(name, *row) console.print(table) @@ -113,8 +116,8 @@ def view(name: str, count: int = 3): name (str): Name of the bucket. count (int, optional): Number of work to show. Defaults to 3. """ - buckets = Buckets() - work = buckets.view(query={"pipeline": name}, projection={}, limit=count) + http = HTTPContext() + work = http.buckets.view(query={"pipeline": name}, projection={}, limit=count) print(work) diff --git a/workflow/cli/main.py b/workflow/cli/main.py index 9500edf..47f7701 100755 --- a/workflow/cli/main.py +++ b/workflow/cli/main.py @@ -1,9 +1,11 @@ """Workflow command line interface.""" import click -from chime_frb_api.workflow.cli.buckets import buckets -from chime_frb_api.workflow.cli.pipelines import pipelines -from chime_frb_api.workflow.cli.run import run + +# from workflow.cli.buckets import buckets +# from workflow.cli.pipelines import pipelines +from workflow.cli.run import run +from workflow.cli.workspace import workspace @click.group() @@ -13,8 +15,9 @@ def cli(): cli.add_command(run) -cli.add_command(buckets) -cli.add_command(pipelines) +# cli.add_command(buckets) +# cli.add_command(pipelines) +cli.add_command(workspace) if __name__ == "__main__": cli() diff --git a/workflow/cli/run.py b/workflow/cli/run.py index 9ff74fb..e7da20e 100644 --- a/workflow/cli/run.py +++ b/workflow/cli/run.py @@ -9,30 +9,43 @@ import click import requests -from chime_frb_api import get_logger -from chime_frb_api.configs import LOKI_URLS, PRODUCTS_URLS, WORKFLOW_URLS -from chime_frb_api.core.logger import set_tag, unset_tag -from chime_frb_api.utils import loki -from chime_frb_api.workflow import Work -from chime_frb_api.workflow.lifecycle import archive, container, execute, validate + +# from chime_frb_api.configs import LOKI_URLS, PRODUCTS_URLS, WORKFLOW_URLS +# from chime_frb_api.utils import loki from rich.console import Console -logger = get_logger("workflow") +from workflow import DEFAULT_WORKSPACE_PATH +from workflow.definitions.work import Work +from workflow.lifecycle import archive, container, execute, validate +from workflow.utils import read as reader +from workflow.utils.logger import get_logger, set_tag, unset_tag + +logger = get_logger("workflow.cli") @click.command("run", short_help="Perform work.") @click.argument("bucket", type=str, required=True) -@click.argument( - "function", +@click.option( + "-f" "--function", + type=str, + required=False, + default=None, + show_default=True, + help="Override work function to execute. e.g `workflow.tasks.example`.", +) +@click.option( + "-c", + "--command", type=str, required=False, default=None, + show_default=True, + help="Override work command to execute. e.g `echo hello world`.", ) @click.option( + "-s", "--site", - type=click.Choice( - ["chime", "allenby", "kko", "gbo", "hco", "aro", "canfar", "cedar", "local"] - ), + type=str, required=True, show_default=True, help="filter work by site.", @@ -54,56 +67,29 @@ required=False, default=None, show_default=True, - help="filter work by parent pipeline.", + help="filter work by parent.", ) @click.option( - "-c", - "--command", - type=str, - required=False, - default=None, - show_default=True, - help="command to perform, e.g. `ls -l`", -) -@click.option( - "-l", - "--lifetime", + "--attempts", type=int, default=-1, show_default=True, - help="works to perform.", + help="number of times to attempt work.", ) @click.option( - "-s", - "--sleep-time", + "--sleep", type=int, default=30, show_default=True, - help="sleep time between working.", -) -@click.option( - "-b", - "--base-url", - type=click.STRING, - default=None, - show_default=True, - help="url for workflow backend.", + help="sleep time between attempts.", ) @click.option( - "--loki-url", - type=click.STRING, - default=None, - required=False, + "-w", + "--workspace", + type=click.Path(exists=True, file_okay=True, dir_okay=False, readable=True), + default=DEFAULT_WORKSPACE_PATH, show_default=True, - help="url for loki logging server.", -) -@click.option( - "--products-url", - type=click.STRING, - default=None, - required=False, - show_default=True, - help="url for products server.", + help="workspace config path.", ) @click.option( "--log-level", @@ -116,26 +102,25 @@ def run( bucket: str, function: str, command: str, - lifetime: int, - sleep_time: int, - base_url: Optional[str], site: str, tag: Tuple[str], parent: Optional[str], - loki_url: Optional[str], - products_url: Optional[str], + lives: int, + sleep: int, + workspace: str, log_level: str, ): """Perform work retrieved from the workflow buckets.""" # Set logging level logger.root.setLevel(log_level) logger.root.handlers[0].setLevel(log_level) - if not base_url: - base_url = str(WORKFLOW_URLS[site]) - if not loki_url: - loki_url = str(LOKI_URLS[site]) - if not products_url: - products_url = str(PRODUCTS_URLS[site]) + config = reader.workspace(workspace) + baseurls = config.get("http", {}).get("baseurls", {}) + + buckets_url = baseurls.get("buckets", None) + loki_url = baseurls.get("loki", None) + products_url = baseurls.get("products", None) + # Reformate tag to be a list of strings tags: List[str] = list(tag) # Setup and connect to the workflow backend @@ -145,10 +130,10 @@ def run( logger.info(f"Command : {command}") logger.info(f"Mode : {'Static' if (function or command) else 'Dynamic'}") # Print inifinity symbol if lifetime is -1, otherwise print lifetime - logger.info(f"Lifetime : {'infinite' if lifetime == -1 else lifetime}") - logger.info(f"Sleep : {sleep_time}s") + logger.info(f"Lives : {'infinite' if lives == -1 else lives}") + logger.info(f"Sleep : {sleep}s") logger.info(f"Log Level: {log_level}") - logger.info(f"Base URL : {base_url}") + logger.info(f"Base URL : {buckets_url}") logger.info(f"Loki URL : {loki_url}") logger.info(f"Prod URL : {products_url}") logger.info( @@ -176,9 +161,9 @@ def run( logger.info(f"Loki Logs: {'✅' if loki_status else '❌'}") try: - requests.get(base_url).headers + requests.get(buckets_url).headers logger.info("Base URL : ✅") - logger.debug(f"base_url: {base_url}") + logger.debug(f"base_url: {buckets_url}") except Exception as error: logger.error(error) raise click.ClickException("unable to connect to workflow backend") @@ -204,9 +189,7 @@ def run( refresh_per_second=1, speed=1 / slowdown, ): - lifecycle( - bucket, function, lifetime, sleep_time, site, tags, parent, base_url - ) + lifecycle(bucket, function, lives, sleep, site, tags, parent, buckets_url) except Exception as error: logger.exception(error) finally: diff --git a/workflow/cli/sample.yaml b/workflow/cli/sample.yaml index 2b65f56..4176892 100644 --- a/workflow/cli/sample.yaml +++ b/workflow/cli/sample.yaml @@ -1,7 +1,21 @@ version: "1" name: "sample" + +# Define a variable called CANFAR + +CANFAR: &canfar + deploy: + reservation: + cpus: 1 + memory: 2GB + limit: + cpus: 2 + memory: 4GB + replicas: 10 + pipeline: alpha: + runs-on: *canfar stage: 1 matrix: job: [1,3,5] @@ -10,6 +24,7 @@ pipeline: - "echo" - "Hello from $(whoami) on $(hostname) doing alpha job ${{ matrix.job }}" beta: + runs-on: *canfar stage: 2 matrix: job: @@ -19,6 +34,7 @@ pipeline: - "echo" - "Hello from $(whoami) on $(hostname) doing beta job ${{ matrix.job }}" gamma: + runs-on: *canfar stage: 3 matrix: denominator: [1,2,3] diff --git a/workflow/cli/workspace.py b/workflow/cli/workspace.py new file mode 100644 index 0000000..01c3921 --- /dev/null +++ b/workflow/cli/workspace.py @@ -0,0 +1,116 @@ +"""Workflow Workspace CLI.""" + +from pathlib import Path +from typing import Any, Dict + +import click +from rich import pretty +from rich.console import Console +from rich.table import Table +from yaml import dump + +from workflow import CONFIG_PATH, MODULE_PATH +from workflow.utils import read as reader + +pretty.install() +console = Console() + +# Local Workflow configurations are kept in ~/.workflow/ +localspaces: Path = CONFIG_PATH / "workspaces" + + +@click.group(name="workspace", help="Manage workflow workspaces.") +def workspace(): + """Manage Workspaces.""" + pass + + +@workspace.command("ls", help="List workspaces.") +def ls(): + """List all workspaces.""" + table = Table( + title="\nWorkflow Workspaces", + show_header=True, + header_style="magenta", + title_style="bold magenta", + ) + table.add_column("Workspace", style="cyan", justify="right") + table.add_column("Source", style="green", justify="left") + table.add_row("", "from workflow package", style="red italic") + for workspace in Path(MODULE_PATH, "workflow", "workspaces").glob("*.y*ml"): + table.add_row(workspace.stem, workspace.as_posix()) + table.add_row("", "from config folder", style="red italic") + for workspace in localspaces.glob("*.y*ml"): + table.add_row(workspace.stem, workspace.as_posix()) + console.print(table) + + +@workspace.command("set", help="Set the active workspace.") +@click.option("--debug", is_flag=True, help="Print debug information.") +@click.argument("workspace", type=str, required=True, nargs=1) +def set(workspace: str, debug: bool = False): + """Set the active workspace. + + Args: + workspace (str): The workspace to set. The workspace + argument can be a url, a local path, or a name of + a local workspace. + debug (bool, optional): Debug Logs. Defaults to False. + """ + console.print(f"Retrieving {workspace}", style="italic blue") + config: Dict[str, Any] = reader.workspace(workspace) + name: str = config["workspace"] + console.print(f"Discovered workspace {name}", style="italic blue") + if debug: + console.print(config, style="green") + # Create the ~/.workflow/workspaces/ + localspaces.mkdir(parents=True, exist_ok=True) + # Copy the workspace to ~/.workflow/workspaces/.yml + console.print(f"Writing {localspaces / f'{name}.yml'}", style="italic green") + with open(localspaces / f"{name}.yml", "w") as filename: + dump(config, filename) + console.print(f"Writing {localspaces / 'active.yml'}", style="italic green") + # Copy the workspace to ~/.workflow/workspaces/active.yml + with open(localspaces / "active.yml", "w") as filename: + dump(config, filename) + console.print(f"Workspace {name} set.", style="bold green") + + +@workspace.command("read", help="Read workspace config.") +@click.option( + "--source", "-s", type=str, required=True, help="Source can be url, path, or name" +) +def read(source: str): + """Read the workspace config. + + Args: + source (str): The source of the workspace config. + """ + try: + if source == "active": + source = (localspaces / "active.yml").as_posix() + config: Dict[str, Any] = reader.workspace(source) + console.print(config, style="green") + except Exception as error: + console.print(error, style="red") + + +@workspace.command("unset", help="Unset active workspace.") +def unset(): + """Unset the active workspace.""" + # Set the default console style. + console.print("Removing the active workspace.", style="italic red") + # If the workspace already exists, warn the user. + (localspaces / "active.yml").unlink(missing_ok=True) + console.print("Workspace Removed.", style="bold red") + + +@workspace.command("purge", help="Purge all local workspaces.") +def purge(): + """Purge all local workspaces.""" + # Remove all files from ~/.workflow/workspaces/ + console.print("Purging all local workspaces", style="italic red") + for workspace in localspaces.glob("*.y*ml"): + console.print(f"Removing {workspace}", style="italic red") + workspace.unlink() + console.print("Done.", style="bold red") diff --git a/workflow/daemons/transfer.py b/workflow/daemons/transfer.py index fae35af..12b0ce9 100644 --- a/workflow/daemons/transfer.py +++ b/workflow/daemons/transfer.py @@ -4,9 +4,9 @@ import click -from workflow import get_logger from workflow.http.buckets import Buckets from workflow.http.results import Results +from workflow.utils.logger import get_logger log = get_logger("workflow.daemons.transfer") diff --git a/workflow/definitions/config.py b/workflow/definitions/config.py index 3697392..b29881c 100644 --- a/workflow/definitions/config.py +++ b/workflow/definitions/config.py @@ -33,7 +33,7 @@ class Archive(BaseSettings): results: bool = Field( default=True, - description="Archive results for the work.", + description="Whether to archive the results of the work.", examples=[True], ) products: str = Field( @@ -99,7 +99,7 @@ class Config(BaseSettings): archive: Archive = Archive() metrics: bool = Field( default=False, - description="Generate metrics from work lifecycle.", + description="Metrics for the workflow lifecycle.", ) parent: Optional[str] = Field( default=None, @@ -108,13 +108,16 @@ class Config(BaseSettings): ) orgs: List[str] = Field( default=["chimefrb"], - description="GitHub organization[s] the work belongs to.", + description=""" + GitHub organization[s] the work belongs to. If authentication is enabled, + this must be a subset of the authenticated user's organizations.""", examples=[["octocat", "chimefrb"]], ) teams: Optional[List[str]] = Field( default=None, description=""" - GitHub Team[s] with access to the work. None implies all org members. + GitHub Team[s] with access to the work. If authentication is enabled, + this must be a subset of the authenticated user's teams. """, examples=[["developers", "admins"]], ) diff --git a/workflow/definitions/work.py b/workflow/definitions/work.py index 5e03f92..0788282 100644 --- a/workflow/definitions/work.py +++ b/workflow/definitions/work.py @@ -1,4 +1,4 @@ -"""Work Object.""" +"""Workflow Work Object.""" from json import loads from time import time @@ -6,84 +6,118 @@ from warnings import warn from pydantic import ( + AliasChoices, Field, + FilePath, SecretStr, - StrictFloat, - StrictInt, - StrictStr, field_validator, model_validator, ) from pydantic_settings import BaseSettings, SettingsConfigDict +from workflow import DEFAULT_WORKSPACE_PATH from workflow.definitions.config import Config from workflow.definitions.notify import Notify from workflow.http.context import HTTPContext +from workflow.utils import read class Work(BaseSettings): - """Work Object. + """Workflow Work Object. + + The work object defines the lifecycle of any action to be performed. Args: BaseSettings (BaseSettings): Pydantic BaseModel with settings. Note: - In the case where default value for a field is specified in multiple places, - the selection priority in descending order is: - 1. Arguments passed to the `Work` Object. - 2. Environment variables defined with the `WORKFLOW_` prefix. - 3. Variables loaded from the secrets directory. - 4. The default values in the constructor. + The selection priority for attributes in descending order is: + + - Arguments passed to the `Work` Object. + - Environment variables with `WORKFLOW_` prefix. + - Variables from /run/secrets secrets directory. + - The default values in the class constructor. Environemnt Prefixes: - - `WORKFLOW_` for all work attributes. - - `WORKFLOW_CONFIG_` for all work config attributes. - - `WORKFLOW_NOTIFY_` for all work notify attributes. - - `WORKFLOW_HTTP_` for all work http attributes. + + - `WORKFLOW_` for all work attributes. + - `WORKFLOW_HTTP_` for all work http attributes. + - `WORKFLOW_CONFIG_` for all work config attributes. + - `WORKFLOW_NOTIFY_` for all work notify attributes. + + The size of the results dictionary is limited to 4MB. If the results + dictionary is larger than 4MB, it is ignored and not mapped to the + work object. Use the `products` attribute to store large data products. Attributes: pipeline (str): Name of the pipeline. (Required) - Automatically reformated to hyphen-case. site (str): Site where the work will be performed. (Required) user (str): User who created the work. (Required) - function (Optional[str]): Name of the function ran as `function(**parameters)`. - command (Optional[List[str]]): Command to run as `subprocess.run(command)`. - parameters (Optional[Dict[str, Any]]): Parameters to pass to the function. - command (Optional[List[str]]): Command to run as `subprocess.run(command)`. - results (Optional[Dict[str, Any]]): Results of the work. - products (Optional[Dict[str, Any]]): Products of the work. - plots (Optional[Dict[str, Any]]): Plots of the work. - tags (Optional[List[str]]): Tags of the work. - timeout (int): Timeout for the work in seconds. Default is 3600 seconds. - retries (int): Number of retries for the work. Default is 2 retries. - priority (int): Priority of the work. Default is 3. - config (WorkConfig): Configuration of the work. - notify (Notify): Notification configuration of the work. - id (str): ID of the work. + + function (str): Python function to run `function(**parameters)`. + parameters (Dict[str, Any]): Parameters to pass to the function. + command (List[str]): Command to run as `subprocess.run(command)`. + results (Dict[str, Any]): Results from the work. + products (List[str]): Data products from work. + plots (List[str]): Visual plots of the work. + tags (List[str]): Searchable tags of the work. + event (List[int]): Unique ID[s] the work was performed against. + + id (str): BSON ID of the work, set by the database. creation (float): Creation time of the work. - start (float): Start time of the work. - stop (float): Stop time of the work. - status (str): Status of the work. + start (float): Start time of the work, set by the backend. + stop (float): Stop time of the work, set by the client. + attempt (int): Attempt number of the work. Defaults to 0. + status (str): Status of the work. Defaults to "created". + timeout (int): Timeout for the work in seconds. Defaults to 3600 seconds. + retries (int): Number of retries for the work. Defaults to 2 retries. + priority (int): Priority of the work. Defaults to 3. + config (Config): Configuration for the lifecycle of the work. + notify (Notify): Notification configuration for the work. + + workspace (FilePath): Path to the active workspace configuration. + Defaults to `~/.workflow/workspaces/active.yml`. (Excluded from payload) + token (SecretStr): Workflow Access Token. (Excluded from payload) + http (HTTPContext): HTTP Context for backend connections. (Excluded from payload) + Raises: - ValueError: If the work is not valid. + ValueError: When work is invalid. Returns: - Work: Work object. + Object (Work): Work object. Example: - ```python - from workflow import Work + ```bash + # Set the environment variables to override the defaults. + export WORKFLOW_PRIORITY=4 + ``` - work = Work(pipeline="test-pipeline", site="chime", user="shinybrar") + ```python + from workflow.definitions.work import Work + + work = Work(pipeline="test", site="local", user="shinybrar") + work.dump_model() + { + "config": {...}, + "notify": {"slack": {}}, + "pipeline": "test-pipeline", + "site": "local", + "user": "shinybrar", + "timeout": 3600, + "retries": 2, + "priority": 4, # Overridden by the environment variable. + "attempt": 0, + "status": "created", + } work.deposit(return_ids=True) ``` """ + # * Configuration for the Pydantic Model. model_config = SettingsConfigDict( title="Workflow Work Object", - validate_default=True, validate_assignment=True, validate_return=True, revalidate_instances="always", @@ -91,44 +125,73 @@ class Work(BaseSettings): secrets_dir="/run/secrets", extra="ignore", ) - - pipeline: StrictStr = Field( + # * Runtime configurations for the Work Object, these are not part of the payload. + # * and describe the behavior of the work object in the current instantiation. + workspace: FilePath = Field( + default=DEFAULT_WORKSPACE_PATH, + validate_default=True, + description="Default workspace configuration filepath.", + examples=["/home/user/.workflow/active.yml"], + exclude=True, + ) + token: SecretStr | None = Field( + default=None, + validation_alias=AliasChoices( + "WORKFLOW_HTTP_TOKEN", + "WORKFLOW_TOKEN", + "GITHUB_TOKEN", + "GITHUB_PAT", + ), + exclude=True, + description="Workflow Access Token.", + examples=["ghp_1234567890abcdefg"], + ) + http: HTTPContext = Field( + default=None, + validate_default=False, + description="HTTP Context for backend connections.", + exclude=True, + repr=False, + ) + # * Required attributes, must be provided by the user. + pipeline: str = Field( ..., min_length=1, + max_length=128, description="Name of the pipeline (required). Reformated to hyphen-case.", examples=["sample-pipeline"], ) site: str = Field( ..., - description="Site where the work will be performed (required).", + description=""" + Site where the work will be performed (required). + Valid sites are defined in the workspace configuration. + """, examples=["chime"], ) - user: StrictStr = Field( + user: str = Field( ..., description="User ID who created the work (required).", examples=["shinybrar"], ) - ########################################################################### - # Optional attributes, might be provided by the user. - ########################################################################### - function: Optional[str] = Field( + # * Optional attributes, can be provided by the user. + function: str | None = Field( default=None, description=""" - Name of the function to run as `function(**parameters)`. + Name of the Python function to run as `function(**parameters)`, Only either `function` or `command` can be provided. """, examples=["workflow.example.mean"], ) - parameters: Optional[Dict[str, Any]] = Field( + parameters: Dict[str, Any] | None = Field( default=None, description=""" Parameters to pass the pipeline function. Equivalent to - running `function(**parameters)`. Note, only either - `function` or `command` can be provided. + running `function(**parameters)`. Ignored if `command` is set. """, examples=[{"a": 1, "b": 2}], ) - command: Optional[List[str]] = Field( + command: List[str] | None = Field( default=None, description=""" Command to run as `subprocess.run(command)`. @@ -136,38 +199,60 @@ class Work(BaseSettings): """, examples=[["python", "example.py", "--example", "example"]], ) - results: Optional[Dict[str, Any]] = Field( + results: Dict[str, Any] | None = Field( default=None, description="Results of the work performed.", examples=[{"dm": 100.0, "snr": 10.0}], ) - products: Optional[List[StrictStr]] = Field( + products: List[str] | None = Field( default=None, description=""" Name of the non-human-readable data products generated by the pipeline. """, examples=[["spectra.h5", "dm_vs_time.png"]], ) - plots: Optional[List[StrictStr]] = Field( + plots: List[str] | None = Field( default=None, + validate_default=False, description=""" Name of visual data products generated by the pipeline. """, examples=[["waterfall.png", "/arc/projects/chimefrb/9385707/9385707.png"]], ) - tags: Optional[List[str]] = Field( + tags: List[str] | None = Field( default=None, description=""" Searchable tags for the work. Merged with values from env WORKFLOW_TAGS. """, examples=[["tag", "tagged", "tagteam"]], ) - event: Optional[List[int]] = Field( + event: List[int] | None = Field( default=None, description="Unique ID[s] the work was performed against.", examples=[[9385707, 9385708]], ) - timeout: StrictInt = Field( + # * State Machine Attributes, set by the backend or optionally by the user. + # * These attributed describe the lifecycle of the work object, irrespective + # * of the current instantiation. + id: str | None = Field(default=None, description="Work ID created by the database.") + creation: float | None = Field( + default=None, description="Unix timestamp of when the work was created." + ) + start: float | None = Field( + default=None, + description="Unix timestamp when the work was started, reset at each attempt.", + ) + stop: float | None = Field( + default=None, + description="Unix timestamp when the work was stopped, reset at each attempt.", + ) + attempt: int = Field( + default=0, ge=0, description="Attempt number at performing the work." + ) + status: Literal["created", "queued", "running", "success", "failure"] = Field( + default="created", description="Status of the work." + ) + timeout: int = Field( default=3600, ge=1, le=86400, @@ -191,56 +276,25 @@ class Work(BaseSettings): le=5, description=""" Priority of the work. Higher priority works are performed first. - i.e. priority 5 > priority 1. Defaults to 3.""", + i.e. 5 > 1 in priority. Defaults to 3.""", examples=[1], ) - ########################################################################### - # Automaticaly set attributes - ########################################################################### - id: Optional[str] = Field( - default=None, description="Work ID created by the database." - ) - creation: Optional[StrictFloat] = Field( - default=None, description="Unix timestamp of when the work was created." - ) - start: Optional[StrictFloat] = Field( - default=None, - description="Unix timestamp when the work was started, reset at each attempt.", - ) - stop: Optional[StrictFloat] = Field( - default=None, - description="Unix timestamp when the work was stopped, reset at each attempt.", - ) - attempt: int = Field( - default=0, ge=0, description="Attempt number at performing the work." - ) - status: Literal["created", "queued", "running", "success", "failure"] = Field( - default="created", description="Status of the work." - ) - http: HTTPContext = Field( - default=None, - validate_default=False, - description="HTTP Context for doing work.", - exclude=True, - repr=False, - ) - ########################################################################### - # Configuration attributes - ########################################################################### + # Config defines the flow of state before and after the work. config: Config = Field( default=Config(), - description="Configuration of the work.", + description="Configuration of the work lifecycle.", examples=[Config()], ) + # Notify defines the notification settings for the work. notify: Notify = Field( default=Notify(), - description="Notification configuration of the work.", + description="Notifications for work.", examples=[Notify()], ) + ########################################################################### - # Default Validators + # Validation Methods for Work Attributes ########################################################################### - @field_validator("pipeline", mode="after", check_fields=True) def validate_pipeline(cls, pipeline: str) -> str: """Validate the pipeline name. @@ -261,59 +315,34 @@ def validate_pipeline(cls, pipeline: str) -> str: for char in pipeline: if not char.isalnum() and char not in ["-"]: raise ValueError( - "pipeline name can only contain letters, numbers & dashes" + "pipeline name can only contain letters, numbers & hyphens." ) if original != pipeline: warn( - SyntaxWarning(f"pipeline reformatted {original}->{pipeline}"), + SyntaxWarning( + f"pipeline reformatted {original}->{pipeline} to hyphen-case." + ), stacklevel=2, ) return pipeline - @field_validator("site", mode="after", check_fields=True) - def validate_site(cls, site: str) -> str: - """Validate the site name. - - Args: - site (str): Name of the site. - - Raises: - ValueError: If the site name is not in the list of valid sites. - - Returns: - str: Validated site name. - """ - valid: List[str] = [ - "local", - "chime", - "kko", - "gbo", - "hco", - "canfar", - "cedar", - "calcul-quebec", - ] - if site not in valid: - raise ValueError(f"site must be one of {valid}") - return site - - @field_validator("creation", mode="after", check_fields=True) - def validate_creation(cls, creation: Optional[StrictFloat]) -> float: + @field_validator("creation") + def validate_creation(cls, creation: float | None) -> float: """Validate and set the creation time. Args: - creation (Optional[StrictFloat]): Creation time in unix timestamp. + creation (Optional[float]): Creation time in unix timestamp. Returns: - StrictFloat: Creation time in unix timestamp. + float: Creation time in unix timestamp. """ if creation is None: return time() return creation @model_validator(mode="before") - def validate_model(cls, data: Any) -> Any: - """Validate the work model. + def pre_validation(cls, data: Any) -> Any: + """Validate the work model before creating the object. Args: data (Any): Work data to validate. @@ -325,11 +354,32 @@ def validate_model(cls, data: Any) -> Any: Any: Validated work data. """ if data.get("function") and data.get("command"): - raise ValueError("command and function cannot be set together.") + raise ValueError("Only either function or command can be provided.") return data + @model_validator(mode="after") + def post_model_validation(self) -> "Work": + """Validate the work model after creating the object. + + Raises: + ValueError: Raised if, + the site provided is not allowed in the workspace. + + Returns: + Work: The current work object. + """ + # Validate if the site provided is allowed in the workspace. + config: Dict[str, Any] = read.workspace(self.workspace.as_posix()) + sites: List[str] = config.get("sites", []) + if self.site not in sites: + error = ( + f"site: {self.site} not in workspace: {self.workspace} sites: {sites}." + ) + raise ValueError(error) + return self + ########################################################################### - # Default Work Class Methods + # Work Class Methods ########################################################################### @property def payload(self) -> Dict[str, Any]: @@ -379,28 +429,45 @@ def withdraw( user: Optional[str] = None, tags: Optional[List[str]] = None, parent: Optional[str] = None, - baseurl: str = "http://localhost:8004", timeout: float = 15.0, token: Optional[SecretStr] = None, + http: Optional[HTTPContext] = None, ) -> Any: """Withdraw work from the buckets backend. Args: - pipeline (str): Name of the pipeline to withdraw work from. - event (Optional[List[int]]): List of event ids to withdraw work for. + pipeline (str):Pipeline to withdraw work from. (Required) + event (Optional[List[int]]): Unique event ids to withdraw work for. site (Optional[str]): Name of the site to withdraw work for. priority (Optional[int]): Priority of the work to withdraw. user (Optional[str]): Name of the user to withdraw work for. tags (Optional[List[str]]): List of tags to withdraw work from. - parent (Optional[str]): Parent id of the work to withdraw. - httpargs (Optional[Dict[str, Any]]): Additional args for http client. + parent (Optional[str]): Parent Pipeline ID of the work to withdraw. + timeout (float, optional): HTTP timeout in seconds. Defaults to 15.0. + token (Optional[SecretStr], optional): Workflow Access Token. + http (Optional[HTTPContext], optional): HTTP Context for connecting to + workflow servers. + + Note: + `token` and `timeout` arguments can also be provided via the environment, + + - "WORKFLOW_HTTP_TOKEN" + - "WORKFLOW_TOKEN" + - "GITHUB_TOKEN" + - "GITHUB_PAT" + - "WORKFLOW_HTTP_TIMEOUT" + + The `http` argument can be provided, to avoid creating a new HTTPContext + object each time the work object interacts with a backend. This is useful + when doing bulk withdraws from the same backend. Returns: Optional[Work]: The withdrawn work if successful, None otherwise. """ # Context is used to source environtment variables, which are overwriten # by the arguments passed to the function. - http = HTTPContext(baseurl=baseurl, token=token, timeout=timeout) + if not http: + http = HTTPContext(timeout=timeout, token=token) payload = http.buckets.withdraw( pipeline=pipeline, event=event, @@ -419,21 +486,29 @@ def withdraw( def deposit( self, return_ids: bool = False, - baseurl: str = "http://localhost:8004", timeout: float = 15.0, token: Optional[SecretStr] = None, + http: Optional[HTTPContext] = None, ) -> Union[bool, List[str]]: """Deposit work to the buckets backend. Args: - return_ids (bool, optional): Whether to return database ids. - Defaults to False. + return_ids (bool, optional): Return Database ID. Defaults to False. + timeout (float, optional): HTTP request timeout in seconds. + token (Optional[SecretStr], optional): Workflow Access Token. + http (Optional[HTTPContext], optional): HTTP Context for backend. + + Note: + Both token and http can be either provided as arguments to the function + or also inherited from the work object itself. Returns: Union[bool, List[str]]: True if successful, False otherwise. """ + if not token and self.token: + token = self.token if not self.http: - self.http = HTTPContext(baseurl=baseurl, token=token, timeout=timeout) + self.http = HTTPContext(timeout=timeout, token=token) return self.http.buckets.deposit(works=[self.payload], return_ids=return_ids) def update(self) -> bool: diff --git a/workflow/http/buckets.py b/workflow/http/buckets.py index 495aa1b..de1a984 100644 --- a/workflow/http/buckets.py +++ b/workflow/http/buckets.py @@ -9,9 +9,9 @@ from tenacity.stop import stop_after_delay from tenacity.wait import wait_random -from workflow import get_logger from workflow.http.client import Client from workflow.utils.decorators import try_request +from workflow.utils.logger import get_logger logger = get_logger("workflow.http.buckets") diff --git a/workflow/http/client.py b/workflow/http/client.py index d847791..eb11936 100644 --- a/workflow/http/client.py +++ b/workflow/http/client.py @@ -17,8 +17,8 @@ from requests.exceptions import RequestException from requests.models import Response -from workflow import __version__ as version -from workflow import get_logger +from workflow import __version__ +from workflow.utils.logger import get_logger logger = get_logger("workflow.http.client") @@ -60,7 +60,7 @@ class Client(BaseSettings): description="Authentication token", ) session: Session = Field( - default=Session(), description="Requests session", exclude=True + default=Session(), description="Requests Session", exclude=True ) @model_validator(mode="after") @@ -75,7 +75,7 @@ def configure_session(self) -> "Client": self.session.headers.update({"Accept": "*/*"}) self.session.headers.update({"User-Agent": "workflow-client"}) self.session.headers.update({"Date": asctime(gmtime())}) - self.session.headers.update({"X-Workflow-Core-Version": version}) + self.session.headers.update({"X-Workflow-Core-Version": __version__}) self.session.headers.update( {"X-Workflow-Client-Python-Version": python_version()} ) @@ -108,12 +108,10 @@ def validate_baseurl(cls, baseurl: str) -> str: AnyHttpUrl(baseurl) response: Response = head(f"{baseurl}/version", timeout=5) response.raise_for_status() - except AttributeError as error: - logger.exception(error) - logger.error(f"Invalid baseurl: {baseurl}") - raise error except RequestException as error: - logger.exception(error) + logger.warning(f"Unable to connect to the {baseurl}.") + except Exception as error: + logger.warning("Unknown error.") raise error return baseurl diff --git a/workflow/http/context.py b/workflow/http/context.py index ad0b7a2..881e17c 100644 --- a/workflow/http/context.py +++ b/workflow/http/context.py @@ -1,11 +1,15 @@ """HTTP client for interacting with the Workflow Servers.""" -from typing import Optional +from typing import Any, Dict, Optional -from pydantic import AliasChoices, Field, SecretStr, model_validator +from pydantic import AliasChoices, Field, FilePath, SecretStr, model_validator from pydantic_settings import BaseSettings, SettingsConfigDict -from workflow import get_logger +from workflow import DEFAULT_WORKSPACE_PATH from workflow.http.buckets import Buckets +from workflow.http.pipelines import Pipelines +from workflow.http.results import Results +from workflow.utils import read +from workflow.utils.logger import get_logger logger = get_logger("workflow.http.context") @@ -20,7 +24,6 @@ class HTTPContext(BaseSettings): baseurl (str): HTTP baseurl of the buckets backend. timeout (float): HTTP Request timeout in seconds. token (Optional[SecretStr]): Workflow Access Token. - buckets (Buckets): Buckets Backend API Client. Returns: HTTPContext: The current HTTPContext object. @@ -34,14 +37,15 @@ class HTTPContext(BaseSettings): validate_assignment=True, extra="ignore", ) - baseurl: str = Field( - default="http://localhost:8004", - description="HTTP baseurl of the buckets backend.", - examples=["http://localhost:8004"], + workspace: FilePath = Field( + default=DEFAULT_WORKSPACE_PATH, + frozen=True, + description="Path to the active workspace configuration.", + examples=["/home/user/.workflow/workspaces/active.yml"], ) timeout: float = Field( default=15.0, - ge=1.0, + ge=0.5, le=60.0, description="HTTP Request timeout in seconds", examples=[15.0], @@ -64,19 +68,47 @@ class HTTPContext(BaseSettings): exclude=True, ) + results: Results = Field( + default=None, + validate_default=False, + description="Results Backend API Client.", + exclude=True, + ) + + pipelines: Pipelines = Field( + default=None, + validate_default=False, + description="Pipelines Backend API Client.", + exclude=True, + ) + @model_validator(mode="after") - def create_buckets_client(self) -> "HTTPContext": - """Create the buckets client. + def create_clients(self) -> "HTTPContext": + """Create the HTTP Clients for the Workflow Servers. Returns: HTTPContext: The current HTTPContext object. """ - if not self.buckets: - try: - self.buckets = Buckets( - baseurl=self.baseurl, token=self.token, timeout=self.timeout - ) - except Exception as error: - logger.error("unable to create buckets client") - raise error + clients: Dict[str, Any] = { + "buckets": Buckets, + "results": Results, + "pipelines": Pipelines, + } + logger.debug(f"creating http clients for {list(clients.keys())}") + config: Dict[str, Any] = read.workspace(self.workspace.as_posix()) + baseurls = config.get("http", {}).get("baseurls", {}) + logger.debug(f"baseurls: {baseurls}") + for _name, _class in clients.items(): + baseurl = baseurls.get(_name, None) + client = getattr(self, _name) + if baseurl and not client: + try: + setattr( + self, + _name, + _class(baseurl=baseurl, token=self.token, timeout=self.timeout), + ) + except Exception as error: + logger.exception(f"failed to create {_name} client.") + raise error return self diff --git a/workflow/http/pipelines.py b/workflow/http/pipelines.py index 827d450..d980dbe 100644 --- a/workflow/http/pipelines.py +++ b/workflow/http/pipelines.py @@ -1 +1,16 @@ """Workflow Pipelines API.""" + +from workflow.http.client import Client + + +class Pipelines(Client): + """HTTP Client for interacting with the Pipelines backend. + + Args: + Client (workflow.http.client): The base class for interacting with the backend. + + Returns: + Results: A client for interacting with the Pipelines backend. + """ + + pass diff --git a/workflow/lifecycle/archive.py b/workflow/lifecycle/archive.py index e689bff..721b849 100644 --- a/workflow/lifecycle/archive.py +++ b/workflow/lifecycle/archive.py @@ -4,12 +4,10 @@ import subprocess from datetime import datetime from pathlib import Path -from typing import List, Optional +from typing import Any, Dict, List, Optional -from chime_frb_api.configs import MOUNTS, TEST_MOUNTS -from chime_frb_api.workflow import Work - -from workflow import get_logger +from workflow.definitions.work import Work +from workflow.utils.logger import get_logger logger = get_logger("workflow") @@ -19,24 +17,26 @@ def copy(path: Path, payload: Optional[List[str]]) -> bool: Args: path (Path): Destination path. - payload (List[str]): List of products to copy. - site (str): Site name. + payload (List[str]): List of files to copy. """ - status: bool = False try: path.mkdir(parents=True, exist_ok=True) - if path.exists() and path.is_dir() and os.access(path, os.W_OK) and payload: - for index, item in enumerate(payload): - shutil.copy(item, path.as_posix()) - payload[index] = (path / item.split("/")[-1]).as_posix() - elif not payload: + if not path.exists() or not path.is_dir() or not os.access(path, os.W_OK): + logger.error("Destination path is invalid or not writable.") + return False + if not payload: logger.info("No files in payload.") - status = True + return True + for index, item in enumerate(payload): + if not os.path.exists(item): + logger.warning(f"File {item} does not exist.") + continue + shutil.copy(item, path.as_posix()) + payload[index] = (path / item.split("/")[-1]).as_posix() + return True except Exception as error: logger.exception(error) - status = False - finally: - return status + return False def move(path: Path, payload: Optional[List[str]]) -> bool: @@ -63,29 +63,25 @@ def move(path: Path, payload: Optional[List[str]]) -> bool: return status -def delete(path: Path, payload: Optional[List[str]]) -> bool: +def delete(path: Path, payload: None | List[str]) -> bool: """Delete the work products from the archive. Args: path (Path): Destination path. payload (List[str]): List of products to delete. """ + status: bool = False try: if payload: - to_remove = [] - for index, item in enumerate(payload): + for item in payload: os.remove(item) - to_remove.append(item) + payload.remove(item) else: - logger.info("No files in payload.") + logger.info("no files to delete.") status = True except Exception as error: logger.exception(error) - status = False finally: - if payload: - for item in to_remove: - payload.remove(item) return status @@ -99,44 +95,45 @@ def upload(path: Path, payload: Optional[List[str]]) -> bool: Returns: bool: True if the upload was successful, False otherwise. """ - logger.warning("upload not implemented") - return True + logger.warning("upload currently not implemented") + raise NotImplementedError def permissions(path: Path, site: str) -> bool: """Set the permissions for the work products in the archive.""" + status: bool = False try: if site == "canfar": subprocess.run(f"setfacl -R -m g:chime-frb-ro:r {path.as_posix()}") subprocess.run(f"setfacl -R -m g:chime-frb-rw:rw {path.as_posix()}") status = True except FileNotFoundError as error: - logger.exception(error) + logger.warning(error) logger.debug( - "Linux dependency 'acl' not installed. Trying to use chgrp and chmod instead." # noqa: E501 + "Linux tool 'acl' not installed, trying chgrp and chmod instead." # noqa: E501 ) try: subprocess.run(f"chgrp -R chime-frb-rw {path.as_posix()}") subprocess.run(f"chmod g+w {path.as_posix()}") status = True except Exception as error: - logger.exception(error) + logger.warning(error) status = False finally: return status -def run(work: Work, test_mode: bool = False): +def run(work: Work, workspace: Dict[str, Any]): """Run the archive lifecycle for a work object. - Parameters - ---------- - work : Work - The work object to run the archive lifecycle for. - test_mode: bool - If being run in tests. + Args: + work (Work): The work object to run the archive lifecycle for. + workspace (Dict[str, Any]): The workspace configuration. """ try: + # workspace: Dict[str, Any] = read.workspace(DEFAULT_WORKSPACE_PATH.as_posix()) + mounts: Dict[str, Any] = workspace.get("archive", {}).get("mounts", {}) + changes: bool = False actions = { "copy": copy, "move": move, @@ -144,24 +141,16 @@ def run(work: Work, test_mode: bool = False): "upload": upload, } date = datetime.fromtimestamp(work.creation).strftime("%Y%m%d") # type: ignore - if not test_mode: - path = Path( - f"{MOUNTS.get(work.site)}/workflow/{date}/{work.pipeline}/{work.id}" - ) - else: - path = Path( - f"{TEST_MOUNTS.get(work.site)}/workflow/{date}/{work.pipeline}/{work.id}" - ) - if work.config.archive.products != "pass": - if work.products: - actions[work.config.archive.products](path, work.products) - if work.config.archive.plots != "pass": - if work.plots: - actions[work.config.archive.plots](path, work.plots) - if ( - work.config.archive.products != "pass" - or work.config.archive.plots != "pass" - ): + path: Path = Path( + f"{mounts.get(work.site)}/workflow/{date}/{work.pipeline}/{work.id}" + ) + if work.config.archive.products != "pass" and work.products: + actions[work.config.archive.products](path, work.products) + changes = True + if work.config.archive.plots != "pass" and work.plots: + actions[work.config.archive.plots](path, work.plots) + changes = True + if changes: permissions(path, work.site) except Exception as error: - logger.exception(error) + logger.warning(error) diff --git a/workflow/lifecycle/execute.py b/workflow/lifecycle/execute.py index 9c7ba0f..8f79e76 100644 --- a/workflow/lifecycle/execute.py +++ b/workflow/lifecycle/execute.py @@ -2,36 +2,60 @@ import ast import subprocess import time -from typing import Any, Callable, Dict, List, Optional, Tuple +from sys import getsizeof +from typing import Any, Callable, Dict, List, Tuple import click from mergedeep import merge # type: ignore -from workflow import Work, get_logger +from workflow.definitions.work import Work +from workflow.utils.logger import get_logger -logger = get_logger("workflow") +logger = get_logger("workflow.lifecycle.execute") def function(func: Callable[..., Any], work: Work) -> Work: - """Execute the user function. + """Execute a Python function. Args: - user_func (FUNC_TYPE): Callable function - work (Work): Work object + func (Callable[..., Any]): Python function + work (Work): The work object Returns: - Work: Work object + Work: The work object """ # Execute the function - logger.debug(f"executing user_func: {func}") + logger.debug(f"executing func: {func}") func, parameters = gather(func, work) + logger.info(f"executing: {func.__name__}(**{parameters})") start = time.time() + outcome: None | Dict[str, Any] | Tuple[Dict[str, Any], List[str], List[str]] = None + results: None | Dict[str, Any] = None + products: None | List[str] = None + plots: None | List[str] = None try: - results, products, plots = func(**parameters) - logger.debug(f"results : {results}") + outcome = func(**parameters) + # * If the outcome is a dict, assume it is results + if isinstance(outcome, dict): + results = outcome + # * If the outcome is tuple of len 3, assume it is results, products, plots + elif isinstance(outcome, tuple) and len(outcome) == 3: + results, products, plots = outcome + else: + logger.warning(f"could not parse work outcome: {outcome}") + logger.error(f"outcome ignored for work: {work.id}") + logger.debug(f"results: {results}") logger.debug(f"products: {products}") - logger.debug(f"plots : {plots}") + logger.debug(f"plots: {plots}") + # * Merge function output with work object if results: + # * Check if results are less than 4MB + if getsizeof(results) > 4_000_000: + logger.error( + f"results size {getsizeof(results)/1000000:.2f}MB exceeds 4MB" + ) + logger.error("results not mapped to work object") + results = None work.results = merge(work.results or {}, results) # type: ignore if products: work.products = (work.products or []) + products @@ -54,7 +78,7 @@ def gather( """Gather the parameters for the user function. Args: - user_func (Callable[..., Any]): User function + func (Callable[..., Any]): User function work (Work): Work object Returns: @@ -63,14 +87,13 @@ def gather( """ defaults: Dict[Any, Any] = {} if isinstance(func, click.Command): - logger.debug("click cli: ✅") # Get default options from the click command known: List[Any] = list(work.parameters.keys()) if work.parameters else [] for parameter in func.params: if parameter.name not in known: # type: ignore defaults[parameter.name] = parameter.default if defaults: - logger.debug(f"cli defaults: {defaults}") + logger.debug(f"click cli defaults: {defaults}") func = func.callback # type: ignore # If work.parameters is empty, merge an empty dict with the defaults # Otherwise, merge the work.parameters with the defaults @@ -79,12 +102,11 @@ def gather( parameters = {**work.parameters, **defaults} else: parameters = defaults - logger.info(f"executing: {func.__name__}(**{parameters})") return func, parameters def command(command: List[str], work: Work) -> Work: - """Execute the command. + """Execute a command. Args: command (List[str]): Command to execute @@ -110,7 +132,7 @@ def command(command: List[str], work: Work) -> Work: stdout = process.stdout.decode("utf-8").splitlines() stderr = process.stderr.decode("utf-8").splitlines() # Convert last line of stdout to a Tuple - response: Optional[Any] = None + response: None | Any = None try: response = ast.literal_eval(stdout[-1]) except SyntaxError as error: @@ -133,6 +155,12 @@ def command(command: List[str], work: Work) -> Work: "stderr": stderr, "returncode": process.returncode, } + # * Check if results are less than 4MB + size: int = getsizeof(work.results) # type: ignore + if size > 4_000_000: + logger.error(f"results size {size:.2f}MB exceeds 4MB") + logger.error("results not mapped to work object") + work.results = None work.status = "success" except Exception as error: work.status = "failure" diff --git a/workflow/lifecycle/validate.py b/workflow/lifecycle/validate.py index e7cd2b7..9326bc6 100644 --- a/workflow/lifecycle/validate.py +++ b/workflow/lifecycle/validate.py @@ -3,7 +3,7 @@ from importlib import import_module from typing import Any, Callable -from chime_frb_api import get_logger +from workflow.utils.logger import get_logger logger = get_logger("workflow") diff --git a/workflow/settings/__init__.py b/workflow/settings/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/workflow/settings/example.py b/workflow/settings/example.py deleted file mode 100644 index 4849293..0000000 --- a/workflow/settings/example.py +++ /dev/null @@ -1,78 +0,0 @@ -"""Example Workflow Settings.""" -from typing import Optional - -from pydantic import AliasChoices, Field, SecretStr -from pydantic_settings import BaseSettings, SettingsConfigDict -from rich import print - - -class ExampleSettings(BaseSettings): - """Example Workflow Settings. - - Args: - BaseSettings (BaseSettings): Pydantic BaseSettings. - - Note: - In case a value is specified in multiple places, the priority is: - 1. Arguments passed to the `Settings` constructor. - 2. Environment variables. - 3. Variables loaded from the secrets directory. - 4. The default values in the Settings class. - - Returns: - Settings: Workflow settings. - """ - - model_config = SettingsConfigDict( - title="Example Workflow Settings", - env_prefix="WORKFLOW_", - secrets_dir="/run/secrets", - validate_assignment=True, - extra="ignore", - ) - - token: Optional[SecretStr] = Field( - default=None, - validation_alias=AliasChoices( - "WORKFLOW_TOKEN", - "WORKFLOW_ACCESS_TOKEN", - "GITHUB_TOKEN", - "GITHUB_ACCESS_TOKEN", - "GITHUB_PAT", - "GITHUB_PERSONAL_ACCESS_TOKEN", - "GITHUB_OAUTH_TOKEN", - "GITHUB_OAUTH_ACCESS_TOKEN", - ), - ) - - buckets_baseurl: Optional[str] = Field( - default="http://localhost:8004", - validation_alias=AliasChoices( - "WORKFLOW_BUCKETS_BASEURL", - ), - ) - - results_baseurl: Optional[str] = Field( - default="http://localhost:8005", - validation_alias=AliasChoices( - "WORKFLOW_RESULTS_BASEURL", - ), - ) - - pipelines_baseurl: Optional[str] = Field( - default="http://localhost:8006", - validation_alias=AliasChoices( - "WORKFLOW_PIPELINES_BASEURL", - ), - ) - - loki_baseurl: Optional[str] = Field( - default="http://localhost:8007", - validation_alias=AliasChoices( - "WORKFLOW_LOKI_BASEURL", - ), - ) - - -if __name__ == "__main__": - print(ExampleSettings().model_dump()) # type: ignore diff --git a/workflow/utils/decorators.py b/workflow/utils/decorators.py index d4d58d9..1656c30 100644 --- a/workflow/utils/decorators.py +++ b/workflow/utils/decorators.py @@ -1,7 +1,7 @@ """Workflow decorators.""" from typing import Any, Callable -from workflow import get_logger +from workflow.utils.logger import get_logger logger = get_logger("workflow.utils.decorators") diff --git a/workflow/utils/read.py b/workflow/utils/read.py new file mode 100644 index 0000000..367a917 --- /dev/null +++ b/workflow/utils/read.py @@ -0,0 +1,77 @@ +"""Read various workflow configurations.""" + +from pathlib import Path +from typing import Any + +from requests import get +from requests.exceptions import RequestException +from yaml import safe_load + +from workflow import MODULE_PATH +from workflow.utils.logger import get_logger + +logger = get_logger("workflow.utils.read") + + +def workspace(source: str) -> Any: + """Read a namespace YAML file. + + Args: + source (str): Source of the namespace. + Can be a URL, a file path, or a namespace name. + + Returns: + Any: The namespace contents. + """ + # Check if the source provided is a URL + if source.startswith("http") or source.startswith("https"): + logger.debug(f"source url: {source}") + return url(source) + + # Check if the source provided is a valid file path + if Path(source).exists(): + logger.debug(f"source path: {source}") + return filename(source) + + for workspace in Path(MODULE_PATH, "workflow", "workspaces").glob("*.y*ml"): + if workspace.stem == source: + logger.debug(f"source path: {workspace.as_posix()}") + return filename(workspace.as_posix()) + + logger.error(f"workspace: {source} does not exist.") + raise ValueError(f"workspace {source} does not exist.") + + +def url(source: str) -> Any: + """Read a URL. + + Args: + source (str): The URL to read. + + Returns: + Any: The URL JSON response. + """ + try: + response = get(source) + response.raise_for_status() + return response.json() + except RequestException as error: + logger.exception(error) + raise error + + +def filename(source: str) -> Any: + """Read a source filename. + + Args: + source (str): The filename to read. + + Returns: + Any: The source contents. + """ + try: + with open(source) as stream: + return safe_load(stream) + except Exception as error: + logger.exception(error) + raise error diff --git a/workflow/resources/__init__.py b/workflow/workspaces/__init__.py similarity index 100% rename from workflow/resources/__init__.py rename to workflow/workspaces/__init__.py diff --git a/workflow/workspaces/chimefrb.yml b/workflow/workspaces/chimefrb.yml new file mode 100644 index 0000000..58c4096 --- /dev/null +++ b/workflow/workspaces/chimefrb.yml @@ -0,0 +1,32 @@ +workspace: chimefrb + +sites: + - local + - chime + - kko + - gbo + - hco + - aro + - canfar + - cedar + - calcul-quebec + +http: + baseurls: + buckets: "https://frb.chimenet.ca/buckets" + results: "https://frb.chimenet.ca/results" + pipelines: "https://frb.chimenet.ca/pipelines" + loki: "https://frb.chimenet.ca/loki/loki/api/v1/push" + products: "https://frb.chimenet.ca/frb-master/v1/events/query-file?filename=" + +archive: + posix: + base: "/data/frb-archiver" + buckets: "/data/frb-archiver/buckets" + results: "/data/frb-archiver/results" + pipelines: "/data/frb-archiver/pipelines" + loki: "/data/frb-archiver/loki" + products: "/data/frb-archiver/products" + s3: + minion: + url: "https://s3.us-west-2.amazonaws.com/frb-archiver" diff --git a/workflow/workspaces/development.yml b/workflow/workspaces/development.yml new file mode 100644 index 0000000..8c523f3 --- /dev/null +++ b/workflow/workspaces/development.yml @@ -0,0 +1,32 @@ +workspace: development + +# List the valid sites for this workspace +sites: + - local + +# Show archiving locations +archive: + mounts: + allenby: "/" + aro: "/" + chime: "/data/chime/baseband/processed" + canfar: "/arc/projects/chime_frb/data/canfar/processed" + gbo: "/" + kko: "/" + hco: "/" + +http: + baseurls: + buckets: http://localhost:8001 + results: http://localhost:8002 + pipelines: http://localhost:8003 + products: http://localhost:8004 + minio: http://localhost:8005 + loki: http://localhost:8005/loki/api/v1/push + +config: + archive: + results: "move" # Can also be copy or delete + plots: "move" # Can also be copy or delete + products: "move" # Can also be copy or delete + slack: