Add logging to app, temporarily disable schedule, add todos

.github/workflows/CI.yml

@@ -1,11 +1,11 @@
 name: CI
 
 on:
-  # push:
-  #   branches: 
-  #     - dev
-  schedule: 
-    - cron: "0 20 * * 1"
+  push:
+    branches: 
+      - dev
+  # schedule: 
+  #   - cron: "0 20 * * 1"
 
 jobs:
   build:
@@ -34,31 +34,38 @@ jobs:
       working-directory: ${{runner.workspace}}/test_suite
       run: |
         zip -r report_"`date +"%m_%d_%Y"`" \
-        report_generation/files/logs \
-        report_generation/files/results \
-        report_generation/files/bmdb_models \
-        report.txt
+          report_generation/files/logs \
+          report_generation/files/results \
+          report_generation/files/bmdb_models \
+          report.txt
     
-    - name: Create Release and Upload
-      id: create_release
-      uses: actions/create-release@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.PAT }}
-      with:
-        tag_name: report_${{steps.date.outputs.format}}
-        release_name: report_${{steps.date.outputs.format}}
-        draft: false
-        prerelease: false
-        upload_url_type: application/zip
+    # - name: Create Release and Upload
+    #   id: create_release
+    #   uses: actions/create-release@v1
+    #   env:
+    #     GITHUB_TOKEN: ${{ secrets.PAT }}
+    #   with:
+    #     tag_name: report_${{steps.date.outputs.format}}
+    #     release_name: report_${{steps.date.outputs.format}}
+    #     draft: false
+    #     prerelease: false
+    #     upload_url_type: application/zip
+
+    # - name: Upload Release Asset
+    #   id: upload-release-asset 
+    #   uses: actions/upload-release-asset@v1
+    #   env:
+    #     GITHUB_TOKEN: ${{ secrets.PAT }}
+    #   with:
+    #     upload_url: ${{ steps.create_release.outputs.upload_url }}
+    #     asset_path: ./report_${{steps.date.outputs.format}}.zip
+    #     asset_name: report_${{steps.date.outputs.format}}.zip
+    #     asset_content_type: application/zip
 
-    - name: Upload Release Asset
-      id: upload-release-asset 
-      uses: actions/upload-release-asset@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.PAT }}
+    - name: 'Upload artifacts'
+      uses: actions/upload-artifact@v2
       with:
-        upload_url: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: ./report_${{steps.date.outputs.format}}.zip
-        asset_name: report_${{steps.date.outputs.format}}.zip
-        asset_content_type: application/zip
+        name: comparison_report
+        path: artifact_${{steps.date.outputs.format}}.zip
+        if-no-files-found: warn
 

.gitignore

@@ -149,4 +149,6 @@ report_generation/files/results/vcell/*
 report_generation/files/results/copasi/*
 !report_generation/files/results/copasi/.gitkeep
 
-report.txt
+report.txt
+
+script.sh

report_generation/combine/files_list.py

@@ -1,5 +1,6 @@
 import os
 from report_generation.config import Config
+from logzero import logger
 
 omex_path = Config.OMEX_FILE_PATH
 sedml_doc_path = Config.SEDML_DOC_PATH
@@ -19,9 +20,9 @@ def sbml_file_list(self, path=model_files_path):
                 sbml_file = sbml_file.split('.')[0]
                 sbml_file_list.append(sbml_file)
             elif sbml_file.split('.')[1] != 'xml':
-                print(f"{sbml_file} is not a model file\n")
+                logger.warning(f"{sbml_file} is not a model file\n")
             else:
-                print(
+                logger.error(
                     f"No model files found in the directory {os.path.join(os.path.join(model_files_path))}\n")
         return sbml_file_list
 

report_generation/combine/omex_maker.py

@@ -1,6 +1,7 @@
 from libcombine import *
 from report_generation.combine.files_list import FilesList
 from report_generation.config import Config
+from logzero import logger
 
 omex_path = Config.OMEX_FILE_PATH
 sedml_doc_path = Config.SEDML_DOC_PATH
@@ -57,8 +58,8 @@ def create_omex_archive(sbml_name, sedml_name, simulator):
     out_file = os.path.abspath(os.path.join(
         omex_path, simulator, f"{sbml_name.split('.')[0]}.omex"))
     archive.writeToFile(out_file)
-
-    print('Archive created:', out_file.split('/')[-1])
+    out_file_name = out_file.split('/')[-1]
+    logger.info(f'Archive created: {out_file_name}')
 
 class GenOmex:
     def omex_gen_vcell(self):

report_generation/core.py

@@ -3,23 +3,35 @@
 from report_generation.sedml.sedml_maker import gen_sedml
 from report_generation.comparator.comparator import gen_report
 import subprocess
+from logzero import logger
 
+logger.debug("Download starting...")
 download_sbml()
+logger.debug("Download finished...\n\n")
 
-print("Starting to generate SED-ML")
+logger.debug("Starting to generate SED-ML documents...")
 gen_sedml()
-print("SED-ML generation finished")
+logger.debug("SED-ML generation finished...\n\n")
 
+logger.debug("Creating OMEX archives...")
 omex = GenOmex()
 omex.omex_gen_copasi()
 omex.omex_gen_vcell()
+logger.debug("Archive generation finished...\n\n")
 
 
+logger.debug("Running COPASI simulations...")
 copasi_run = subprocess.run(["./report_generation/run_script/run_copasi_sim.sh"])
-print("The exit code was: %d" % copasi_run.returncode)
+logger.info("The exit code was: %d" % copasi_run.returncode)
+logger.debug("COPASI simulations finished...\n\n")
 
+
+logger.debug("Running VCell simulations...")
 vcell_run = subprocess.run(
     ["./report_generation/run_script/run_vcell_sim.sh"])
-print("The exit code was: %d" % vcell_run.returncode)
+logger.info("The exit code was: %d" % vcell_run.returncode)
+logger.debug("VCell simulations finished...\n\n")
 
+logger.debug("Generating report...")
 gen_report()
+logger.debug("Report generated...")

report_generation/run_script/run_copasi_sim.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-pwd
+
 cd report_generation
 cd files
 cd omex_archives

report_generation/run_script/run_vcell_sim.sh

@@ -1,6 +1,5 @@
 #!/bin/bash
 
-pwd
 cd report_generation
 cd files
 cd omex_archives

report_generation/sbml/sbml_fetcher.py

@@ -3,6 +3,7 @@
 import urllib
 from bs4 import BeautifulSoup
 import requests
+from logzero import logger
 
 model_files_path = Config.MODEL_FILES_PATH
 
@@ -37,13 +38,13 @@ def soup_scraper(model, headers):
     return preview_url
 
 def download_sbml(): 
-    for model in create_model_list(1000, 0, -1):
+    for model in create_model_list(10, 0, -1):
         try: 
             sbml_file_link = Config.BASE_URL + soup_scraper(model, headers=headers)
             urllib.request.urlretrieve(sbml_file_link, os.path.join(
                     model_files_path, f'{model}.xml'))
-            print(f'Downloaded {model}.xml')
+            logger.info(f'Downloaded {model}.xml')
         except IndexError as IE:
-            print(f"{model}.xml is not published yet.")
+            logger.info(f"{model}.xml is not published yet.")
             continue
 

report_generation/sedml/sedml_maker.py

@@ -9,6 +9,7 @@
 from report_generation.config import Config
 import libsbml
 import libsedml
+from logzero import logger
 
 
 model_files_path = Config.MODEL_FILES_PATH
@@ -55,7 +56,8 @@ def create_sedml(filename, simulator,
     elif simulator == 'vcell':
         alg.setKisaoID(f'KISAO:0000019')
     else:
-        print(f"{simulator} is still not supported to generate the SED-ML")
+        logger.warning(
+            f"{simulator} is still not supported to generate the SED-ML")
 
     # create a task that uses the simulation and the model above
     task = doc.createTask()
@@ -118,7 +120,8 @@ def create_sedml(filename, simulator,
 
     # write the document
     libsedml.writeSedML(doc, os.path.join(sedml_doc_path, simulator, f'{filename}.sedml'))
-    print(f"SED-ML Document created for {simulator} with filename {filename}.sedml")
+    logger.info(
+        f"SED-ML Document created for {simulator} with filename {filename}.sedml")
 
 def gen_sedml():
     global model_files
@@ -130,7 +133,8 @@ def gen_sedml():
             create_sedml(model_name, 'vcell')
             create_sedml(model_name, 'copasi')
         elif sbml_model.split('.')[1] != 'xml':
-            print(f"{sbml_model} is not a model file\n")
+            logger.warning(f"{sbml_model} is not a model file\n")
         else:
-            print(f"No SBML files found in the directory {os.path.join(model_files_path)}\n")
+            logger.error(
+                f"No SBML files found in the directory {os.path.join(model_files_path)}\n")
 

report_generation/utils/logging.py

@@ -0,0 +1 @@
+#TODO: Add logger here, replace logzero

requirements.txt

@@ -7,4 +7,5 @@ lxml
 docker
 pkg_utils
 pandas
-docker
+docker
+logzero