Remove alchy and use SQLAlchemy instead

[northwestwitch]

This PR adds | fixes:

• This PR is testing also the interaction with this chanjo PR when it comes to creating a report
• Fix Completely replace alchy with sqlservice #57

How to prepare for test:

• pip install -e .
• Start a local demo database --> chanjo init --auto demodata
• Load the transcripts --> chanjo --config demodata/chanjo.yaml link demodata/hgnc.grch37p13.exons.bed

Load 3 samples (coverage files are located in chanjo, not chanjo2)

• chanjo --config demodata/chanjo.yaml load --sample sample1 --name sample1 --group-name test_group -g test_group <PATH_TO_CHANJO>/chanjo/init/demo-files/sample1.coverage.bed
• chanjo --config demodata/chanjo.yaml load --sample sample2 --name sample2 --group-name test_group -g test_group <PATH_TO_CHANJO>/chanjo/init/demo-files/sample2.coverage.bed
• chanjo --config demodata/chanjo.yaml load --sample sample3 --name sample3 --group-name test_group -g test_group <PATH_TO_CHANJO>/chanjo/init/demo-files/sample3.coverage.bed

How to test:

• Run the server --> chanjo --config demodata/chanjo.yaml report --render html
• Check the report in a brower at this address --> http://localhost:5000/report?sample_id=sample1&sample_id=sample2&sample_id=sample3
• Check the genes overview at http://localhost:5000/genes?level=10&sample_id=sample1&sample_id=sample2&sample_id=sample3
• Check the endpoint used by scout to create the MT coverage on the MT report:

curl --header "Content-Type: application/json" \
  --request POST \
  --data '{"chrom":"1","sample_ids":"sample1,sample2,sample3"}' \
http://localhost:5000/json_chrom_coverage

Expected outcome:

• The report shoud be shown without errors

Review:

• Code approved by DN
• Tests executed by CR

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[northwestwitch]

This won't work in PyPI, so we have to create a chanjo release first

[northwestwitch]

@dnil I've created a PR that works in a combo with a chanjo one

[dnil]

😸

[northwestwitch]

I gets installed by chanjo, so it's not that the lib isn't going to be there..

[dnil]

If you actually import something from it, or use it directly, it should certainly be here. If you don't... 😜
It's all good as it is now with this PR as well. Just saying. 😉

[dnil]

This looks good to me, but we should test carefully with some real life cases in an integrated env (stage) before releasing!

[dnil]

If you actually import something from it, or use it directly, it should certainly be here. If you don't... 😜
It's all good as it is now with this PR as well. Just saying. 😉

[northwestwitch]

This looks good to me, but we should test carefully with some real life cases in an integrated env (stage) before releasing!

I agree!

[northwestwitch]

This is tested again after changing the requirements to use the new chanjo v4.7. Works fine so I'm merging!