Cleanup catalog service

[pcrespov]

What do these changes do?

Cleanup of catalog service before adding more functionality

• upgrade requirements
• upgrade dockerfile and booting scripts from alpine to slim
• app rationale and folder structure
  • api/dependencies: dependencies injected in handlers
  • api/routes: endpoint handlers and routing
  • api/root.py: joins all openapi-specs into a single router
  • models: domain (orm and business logic models) and schema (i/o schemas for openapi) models
  • db: database tables (i.e. sa schemas for tables) and repositories (crud layer between handlers and db calls)
  • core: init application and settings (parses values by args, environs, .env or default, in this order)
  • services: modules/plugins with logic for the app
  • __main__,__version__: main entrypoint and version
• upgrade tests
  • upgrades/downgrades pg fixture
• upgrade makefile
• check docker-compose integration
• upgrade cookie-cutter for fastapi to get this layout

Some extra changes repo-wise

• Frozen all python-bases from ${PYTHON_VERSION}-slim to ${PYTHON_VERSION}-slim-buster
• upgrades pip compatible-version to 20.1.1
• added new fixture in pytest_simcore.postgres_service2 that migrates database on the fly

How to test

Checklist

• Did you change any service's API? Then make sure to bundle document and upgrade version (make openapi-specs, git commit ... and then make version-*)
• Unit tests for the changes exist
• Runs in the swarm
• Documentation reflects the changes
• New module? Add your github username to .github/CODEOWNERS

[codecov]

Codecov Report

Merging #1582 into master will increase coverage by 0.8%.
The diff coverage is 81.4%.

@@           Coverage Diff            @@
##           master   #1582     +/-   ##
========================================
+ Coverage    72.6%   73.4%   +0.8%     
========================================
  Files         271     278      +7     
  Lines       10721   10807     +86     
  Branches     1172    1173      +1     
========================================
+ Hits         7790    7940    +150     
+ Misses       2586    2521     -65     
- Partials      345     346      +1     

Flag	Coverage Δ
#integrationtests	56.7% <ø> (ø)
#unittests	67.1% <81.4%> (-1.2%)	⬇️

Impacted Files	Coverage Δ
...es/catalog/src/simcore_service_catalog/__main__.py	0.0% <0.0%> (ø)
...c/simcore_service_catalog/models/domain/project.py	94.2% <ø> (ø)
...s/catalog/src/simcore_service_catalog/db/events.py	60.0% <60.0%> (ø)
...rc/simcore_service_catalog/db/repositories/dags.py	71.0% <71.0%> (ø)
...c/simcore_service_catalog/services/remote_debug.py	68.7% <71.4%> (ø)
...catalog/src/simcore_service_catalog/core/events.py	78.2% <78.2%> (ø)
...log/src/simcore_service_catalog/api/routes/dags.py	78.0% <78.9%> (ø)
...mcore_service_catalog/api/dependencies/database.py	91.6% <91.6%> (ø)
...talog/src/simcore_service_catalog/core/settings.py	93.7% <93.7%> (ø)
...og/src/simcore_service_catalog/core/application.py	95.4% <95.4%> (ø)
... and 28 more

[sanderegg]

👍

[GitHK]

👍
Is the DAG part of this service used only for parsing the workbench?

[pcrespov]

Is the DAG part of this service used only for parsing the workbench?

@GitHK, a DAG is an "work-in-progress" data structure to define projects with workbench of hierarchical graphs, i.e. graphs can also embed graphs in its nodes. These nodes that "contain" a graph is what some people here call "macro" services