Refactor and improve kb_tests.py

[hkir-dev]

Related with issue #267

• Logging improved. Json formatted test results are written to a report file and simplified test results are printed to the console
• A new cli interface that enable users to define datasets added:

python -m uk.ac.ebi.vfb.neo4j.neo2neo.kb_tests_runner -k http://kb.virtualflybrain.org -u neo4j -p vfb -d Yu2013 -d Cachero2010

[hkir-dev]

Example report output is as follows:

Test Progress: 100%|████████████████████| 110/110

Failed Tests:          6/515    (1%)
Failed Datasets:       3/110    (2%)
Empty Datasets:        7/110    (6%)
Successful Datasets:   100/110          (90%)

=== Failed Datasets:

Dataset: Cachero2010

        Testing assertion: All anatomical individuals in dataset are typed.
        1 of total 119 individuals failed. First 5 failing individuals are: ['VFB_00017893']
        MATCH (ds:DataSet)<-[:has_source]-(i:Individual)-[:INSTANCEOF]->(c:Class) WHERE ds.short_form = 'Cachero2010' RETURN COUNT (DISTINCT i) as ind_count, COLLECT(i.short_form) as ind_list

Dataset: CostaJefferis_v2

        Testing assertion: All anatomical individuals in dataset have matching channel individuals.
        604 of total 604 individuals failed. First 5 failing individuals are: ['VFB_00016303', 'VFB_00016495', 'VFB_00016293', 'VFB_00016428', 'VFB_00016572']
        MATCH (ds:DataSet)<-[:has_source]-(i:Individual)<-[:depicts]-(j:Individual) WHERE ds.short_form = 'CostaJefferis_v2' RETURN COUNT (DISTINCT i) as ind_count, COLLECT(i.short_form) as ind_list

        Testing assertion: All anatomical individuals in dataset have matching registered channel individuals.
        604 of total 604 individuals failed. First 5 failing individuals are: ['VFB_00016303', 'VFB_00016495', 'VFB_00016293', 'VFB_00016428', 'VFB_00016572']
        MATCH (ds:DataSet)<-[:has_source]-(i:Individual)<-[:depicts]-(j:Individual)-[in_register_with]->(k:Individual) WHERE ds.short_form = 'CostaJefferis_v2' RETURN COUNT (DISTINCT i) as ind_count, COLLECT(i.short_form) as ind_list

        Testing assertion: All anatomical individuals in dataset have matching channel individuals with imaging method.
        604 of total 604 individuals failed. First 5 failing individuals are: ['VFB_00016303', 'VFB_00016495', 'VFB_00016293', 'VFB_00016428', 'VFB_00016572']
        MATCH (ds:DataSet)<-[:has_source]-(i:Individual)<-[:depicts]-(j:Individual)-[:is_specified_output_of]->(:Class) WHERE ds.short_form = 'CostaJefferis_v2' RETURN COUNT (DISTINCT i) as ind_count, COLLECT(i.short_form) as ind_list

        Testing assertion: All anatomical individuals in dataset have matching channel, typed individuals
        604 of total 604 individuals failed. First 5 failing individuals are: ['VFB_00016303', 'VFB_00016495', 'VFB_00016293', 'VFB_00016428', 'VFB_00016572']
        MATCH (ds:DataSet)<-[:has_source]-(i:Individual)<-[:depicts]-(j:Individual)-[:INSTANCEOF]->(c:Class { label: 'channel'}) WHERE ds.short_form = 'CostaJefferis_v2' RETURN COUNT (DISTINCT i) as ind_count, COLLECT(i.short_form) as ind_list

Dataset: Dickson2017

        Testing assertion: All anatomical individuals in dataset are typed.
        1 of total 5387 individuals failed. First 5 failing individuals are: ['VFB_00068747']
        MATCH (ds:DataSet)<-[:has_source]-(i:Individual)-[:INSTANCEOF]->(c:Class) WHERE ds.short_form = 'Dickson2017' RETURN COUNT (DISTINCT i) as ind_count, COLLECT(i.short_form) as ind_list

=== Empty Datasets:

  - Tsubouchi2017
  - LateralHorn2019
  - SplitDavis2017
  - Valdes-Aleman2021
  - SplitTurner_Evans2017
  - HeadMusclesMcKellar2020
  - McKellar2019