Extract datamodel to json and excel

[JosePizarro3]

Added CLI features to extract the datamodel objects and print them to json in a subfolder bam_data_store/datamodel/artifacts/.

[JosePizarro3]

I've merged the export-to-excel implementation as well

[coveralls]

Pull Request Test Coverage Report for Build 12391007429

Details

• 34 of 171 (19.88%) changed or added relevant lines in 8 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage decreased (-34.3%) to 47.419%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
bam_data_store/datamodel/property_types.py	0	2	0.0%
bam_data_store/metadata/entities.py	5	7	71.43%
bam_data_store/metadata/definitions.py	6	10	60.0%
bam_data_store/datamodel/collection_types.py	0	7	0.0%
bam_data_store/utils/utils.py	23	34	67.65%
bam_data_store/cli/entities_to_json.py	0	35	0.0%
bam_data_store/cli/cli.py	0	36	0.0%
bam_data_store/cli/entities_to_excel.py	0	40	0.0%

Totals
Change from base Build 12390657740:	-34.3%
Covered Lines:	147
Relevant Lines:	310

---

💛 - Coveralls

[coveralls]

Pull Request Test Coverage Report for Build 12709560814

Details

• 152 of 207 (73.43%) changed or added relevant lines in 9 files are covered.
• 1 unchanged line in 1 file lost coverage.
• Overall coverage increased (+96.6%) to 97.29%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
bam_masterdata/openbis/get_entities.py	2	3	66.67%
bam_masterdata/metadata/entities.py	13	15	86.67%
bam_masterdata/cli/entities_to_excel.py	51	54	94.44%
bam_masterdata/cli/entities_to_json.py	31	36	86.11%
bam_masterdata/utils/utils.py	27	33	81.82%
bam_masterdata/cli/fill_masterdata.py	2	9	22.22%
bam_masterdata/cli/cli.py	14	45	31.11%

Files with Coverage Reduction	New Missed Lines	%
bam_masterdata/openbis/get_entities.py	1	19.23%

Totals
Change from base Build 12691091810:	96.6%
Covered Lines:	16368
Relevant Lines:	16824

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💛 - Coveralls

[JosePizarro3]

@carlosmada22 these are my changes to generate JSONs and the excel in the typical format of openBIS from our classes in the datamodel/. This is a good opportunity for you to see a better CLI than argparse (using click); check the cli/ folder please.

Could you try checking out in this branch and doing:

bam_masterdata export_to_json

or:

bam_masterdata export_to_excel

And see whether it makes sense what is being printed out.

With this changes, we can start thinking about connecting excel with Python/JSON, and allow people to have a full environment for developing data models. There is left a TODO, which is in #35 (i.e., exporting/importing from WebProtege), but this we can do later.

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And btw, I had to fix a minor thing from the fill_masterdata.py: apparently, the data type has changed from SAMPLE to OBJECT at some point. See #42, I decided to separate those changes from this branch.