ENH: setup logging and reporting for serverside execution

Summary

• crawler_run_model.yml contains a model for Records that contain informaiton on crawler jobs
• the new logging module sets up logging for serverside jobs
• crawl.py was refactored and now use the above additions

Focus

Point the reviewer to the core of the code change. Where should they start reading? What should they focus on (e.g. security, performance, maintainability, user-friendliness, compliance with the specs, finding more corner cases, concrete questions)?

Test Environment

I suggest local-testing setup of dpz.

• set pylib to package: "git+https://gitlab.indiscale.com/caosdb/src/caosdb-pylib.git@f-validate-caoscrawler"
• set caoscrawler to package: "git+https://gitlab.indiscale.com/caosdb/src/caosdb-crawler.git@f-email-notify"
• add the data model crawler_run_model.yml
• call python runcrawler.py
• check the email folder in docker /tmp/mail/somemail
• check the CrawlerRun Record in LinkAhead

Check List for the Author

Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab comments for the reviewer. They should guide the reviewer through the changes, explain your changes and also point out open questions. For further good practices have a look at our review guidelines

• All automated tests pass
• Reference related issues
• Up-to-date CHANGELOG.md (or not necessary)
• Up-to-date JSON schema (or not necessary)
• Appropriate user and developer documentation (or not necessary)
  • How do I use the software? Assume "stupid" users.
  • How do I develop or debug the software? Assume novice developers.
• Annotations in code (Gitlab comments)
  • Intent of new code
  • Problems with old code
  • Why this implementation?

Check List for the Reviewer

• I understand the intent of this MR
• All automated tests pass
• Up-to-date CHANGELOG.md (or not necessary)
• Appropriate user and developer documentation (or not necessary)
• The test environment setup works and the intended behavior is reproducible in the test environment
• In-code documentation and comments are up-to-date.
• Check: Are there specifications? Are they satisfied?

For further good practices have a look at our review guidelines.

src/caoscrawler/crawl.py

@@ -1035,7 +1035,7 @@ def _treat_deprecated_prefix(prefix, remove_prefix):
     return remove_prefix
 
 
-def _fix_file_paths(crawled_data):
+def _fix_file_paths(crawled_data, remove_prefix):
     for elem in crawled_data:
         if isinstance(elem, db.File):
             # correct the file path:
@@ -1148,7 +1148,7 @@ def crawler_main(crawled_directory_path: str,
         debug_tree = DebugTree()
         crawled_data = scan_directory(
             crawled_directory_path, cfood_file_name, restricted_path, debug_tree=debug_tree)
-        _fix_file_paths(crawled_data)
+        _fix_file_paths(crawled_data, remove_prefix)
         _check_record_types(crawled_data)
 
         if provenance_file is not None and debug: