Generate per-file reports for compendia files

[gaurav]

This PR adds per-file reports for compendia files that are written into the reports/content/ directory. We also generate an overall content report for compendia files. Since these are JSON files, I've added jq to the Babel image for use in debugging.

This is what the overall content report looks like right now:

{
  "biolink_types": {
    "biolink:Activity": 41367,
    "biolink:Agent": 4222,
    "biolink:AnatomicalEntity": 144778,
    "biolink:Behavior": 4156,
    "biolink:BiologicalEntity": 108,
    "biolink:BiologicalProcess": 26865,
    "biolink:Cell": 8804,
    "biolink:CellularComponent": 12132,
    "biolink:ChemicalEntity": 7406121,
    "biolink:ChemicalMixture": 499,
    "biolink:ClinicalAttribute": 107356,
    "biolink:Cohort": 7353,
    "biolink:ComplexMolecularMixture": 177,
    "biolink:Device": 77193,
    "biolink:Disease": 340566,
    "biolink:DiseaseOrPhenotypicFeature": 29,
    "biolink:Drug": 173458,
    "biolink:Event": 235,
    "biolink:Food": 8468,
    "biolink:Gene": 52825216,
    "biolink:GeneFamily": 27917,
    "biolink:GenomicEntity": 39793,
    "biolink:GeographicLocation": 4667,
    "biolink:GrossAnatomicalStructure": 10321,
    "biolink:Human": 39,
    "biolink:InformationContentEntity": 53702,
    "biolink:MacromolecularComplex": 626,
    "biolink:MolecularActivity": 195552,
    "biolink:MolecularEntity": 14,
    "biolink:MolecularMixture": 10174352,
    "biolink:NamedThing": 31,
    "biolink:NucleicAcidEntity": 449,
    "biolink:OrganismAttribute": 983,
    "biolink:OrganismTaxon": 3205738,
    "biolink:Pathway": 52880,
    "biolink:Phenomenon": 4666,
    "biolink:PhenotypicFeature": 357159,
    "biolink:PhysicalEntity": 6328,
    "biolink:PhysiologicalProcess": 31047,
    "biolink:Polypeptide": 832,
    "biolink:PopulationOfIndividualOrganisms": 4074,
    "biolink:Procedure": 426906,
    "biolink:Protein": 253569392,
    "biolink:Publication": 48564,
    "biolink:SmallMolecule": 106140712
  },
  "count_lines": 435545847,
  "counters": {
    "clique_count": 435545847,
    "cliques_by_description_count": {
      "0": 435144564,
      "1": 389676,
      "19": 1,
      "2": 9652,
      "3": 1720,
      "4": 196,
      "5": 27,
      "6": 7,
      "7": 3,
      "8": 1
    },
    "cliques_by_id_count": {
      "1": 305289449,
      "10": 4454,
      "100": 1,
      "101": 4,
      "103": 3,
      "107": 1,
      "109": 2,
      "11": 11362,
      "111": 1,
      "113": 1,
      "115": 1,
      "117": 2,
      "1181": 1,
      "12": 2077,
      "121": 1,
      "123": 1,
      "125": 2,
      "129": 1,
      "13": 7280,
      "131": 1,
      "133": 1,
      "137": 2,
      "14": 1244,
      "141": 1,
      "145": 1,
      "149": 1,
      "15": 5140,
      "155": 1,
      "156": 1,
      "16": 396,
      "17": 4185,
      "177": 1,
      "179": 1,
      "18": 208,
      "19": 4106,
      "2": 116298876,
      "20": 104,
      "201": 1,
      "21": 4415,
      "217": 1,
      "22": 88,
      "23": 3188,
      "24": 38,
      "25": 524,
      "26": 36,
      "261": 1,
      "27": 241,
      "28": 29,
      "29": 136,
      "291": 1,
      "3": 13186810,
      "30": 14,
      "303": 1,
      "31": 104,
      "32": 15,
      "33": 92,
      "34": 7,
      "35": 60,
      "36": 10,
      "37": 42,
      "38": 10,
      "39": 41,
      "4": 325258,
      "40": 5,
      "41": 33,
      "42": 3,
      "43": 49,
      "44": 2,
      "45": 32,
      "46": 2,
      "47": 20,
      "48": 3,
      "49": 17,
      "5": 274011,
      "50": 4,
      "51": 19,
      "52": 1,
      "53": 13,
      "54": 1,
      "545": 1,
      "55": 6,
      "57": 11,
      "59": 4,
      "6": 34922,
      "60": 1,
      "61": 3,
      "62": 3,
      "63": 6,
      "64": 1,
      "65": 11,
      "66": 2,
      "67": 11,
      "69": 4,
      "7": 56675,
      "71": 2,
      "72": 1,
      "73": 8,
      "74": 1,
      "75": 2,
      "77": 3,
      "79": 2,
      "8": 9716,
      "81": 6,
      "83": 7,
      "84": 1,
      "85": 2,
      "86": 1,
      "87": 6,
      "89": 5,
      "9": 20114,
      "91": 5,
      "93": 5,
      "95": 4,
      "99": 3
    },
    "cliques_by_label_count": {
      "0": 11903945,
      "1": 420628921,
      "10": 262,
      "11": 105,
      "12": 36,
      "13": 27,
      "14": 15,
      "15": 8,
      "16": 8,
      "17": 3,
      "18": 6,
      "19": 3,
      "2": 2716465,
      "22": 3,
      "23": 2,
      "24": 1,
      "26": 1,
      "27": 1,
      "29": 1,
      "3": 231320,
      "4": 32580,
      "42": 1,
      "5": 14426,
      "6": 8130,
      "7": 5551,
      "8": 2482,
      "9": 1544
    },
    "cliques_by_unique_description_count": {
      "0": 435144564,
      "1": 392272,
      "18": 1,
      "2": 7825,
      "3": 1046,
      "4": 116,
      "5": 15,
      "6": 5,
      "7": 3
    },
    "cliques_by_unique_label_count": {
      "0": 11903945,
      "1": 421075499,
      "10": 26,
      "11": 11,
      "12": 6,
      "13": 7,
      "14": 4,
      "15": 4,
      "16": 2,
      "17": 3,
      "18": 1,
      "19": 2,
      "2": 2476928,
      "20": 1,
      "22": 2,
      "23": 1,
      "24": 1,
      "26": 1,
      "28": 1,
      "3": 67163,
      "34": 1,
      "4": 15830,
      "5": 4640,
      "6": 1251,
      "7": 344,
      "8": 130,
      "9": 43
    }
  },
  "prefixes": {
    "CAS": 3546369,
    "CHEBI": 165470,
    "CHEMBL.COMPOUND": 2399641,
    "CL": 2726,
    "ComplexPortal": 1252,
    "DOID": 11443,
    "DRUGBANK": 14955,
    "DrugCentral": 4995,
    "EC": 8633,
    "EFO": 12093,
    "EMAPA": 945,
    "ENSEMBL": 33346859,
    "FB": 30285,
    "FBbt": 114,
    "GO": 42837,
    "GTOPDB": 12347,
    "HGNC": 43861,
    "HGNC.FAMILY": 1779,
    "HMDB": 217920,
    "HP": 17498,
    "ICD10": 2431,
    "ICD9": 2219,
    "INCHIKEY": 110336171,
    "KEGG.COMPOUND": 15802,
    "KEGG.DISEASE": 40,
    "KEGG.REACTION": 5,
    "MEDDRA": 68217,
    "MESH": 343115,
    "MGI": 80206,
    "MONDO": 23620,
    "MP": 10,
    "NCBIGene": 49400812,
    "NCBITaxon": 2525280,
    "NCIT": 56325,
    "OMIM": 27515,
    "OMIM.PS": 546,
    "PANTHER.FAMILY": 26138,
    "PANTHER.PATHWAY": 175,
    "PR": 226207,
    "PUBCHEM.COMPOUND": 122954081,
    "REACT": 107383,
    "RGD": 57172,
    "RHEA": 64447,
    "RXCUI": 122610,
    "SGD": 7161,
    "SMPDB": 30248,
    "SNOMEDCT": 142613,
    "TCDB": 23,
    "UBERON": 14393,
    "UMLS": 3237718,
    "UNII": 121952,
    "UniProtKB": 251772975,
    "WBbt": 18,
    "WormBase": 48781,
    "ZFA": 609,
    "ZFIN": 38078,
    "dictyBase": 13892,
    "orphanet": 10783
  },
  "report_path": "babel_outputs/reports/content/compendia_report.json"
}

Should be merged after PR #201

[cbizon]

One idea - rather than
"count_cliques_with_65_ids": 11,
What about something like:

"count_cliques_with_n_ids": [
{ "n": 65,
 "num_cliques": 11},
...
]

[gaurav]

One idea - rather than "count_cliques_with_65_ids": 11, What about something like:

"count_cliques_with_n_ids": [
{ "n": 65,
 "num_cliques": 11},
...
]

How about:

    "cliques_by_unique_description_count": {
      "0": 435144564,
      "1": 392272,
      "18": 1,
      "2": 7825,
      "3": 1046,
      "4": 116,
      "5": 15,
      "6": 5,
      "7": 3
    },

That's what I've currently implemented and this is definitely the easier format to work with on the intermediate files, but I can convert the final report into the "count": [{ "n": 5, "num_cliques": 10 }] format if that would be easier to work with.