jsstevenson

{
    "pre_mapped": {
        "id": "ga4gh:VA.FLe4-pSUs7vjdVtVD4TmUNL4JhrBbqTd",
        "type": "Allele",
        "extensions": [
            {
                "name": "vrs_ref_allele_seq",
                "value": "Y"
            }
        ],

jsstevenson

{
    "schemaVersion": 1,
    "label": "QC",
    "message": "N/A",
    "color": "white",
    "logoSvg": "<svg id=\"Layer_1\" data-name=\"Layer 1\" xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 135.54 133.3\"><defs><style>.cls-1{fill:#fff;}.cls-2{fill:#231f20;}</style></defs><path class=\"cls-1\" d=\"M85.31,20.58l-4-16.64s0,0,0,0c-1.11-.14-2.21-.26-3.33-.35s-2.24-.15-3.36-.18-2.26,0-3.4,0c-.82,0-1.66.06-2.49.11L63.21,19.66c-.22,0-.43.11-.65.15l0,.11c-1.58.3-3.13.68-4.65,1.12s-3,1-4.45,1.53L40.52,11.64c-.58.32-1.17.63-1.74,1-1,.56-1.91,1.14-2.83,1.74s-1.84,1.23-2.73,1.88-1.77,1.31-2.63,2l-.73.6L34.72,35c-.15.16-.28.33-.42.48v0c-1.12,1.18-2.17,2.42-3.17,3.7s-1.95,2.59-2.84,4h-.06v0l-16.83-1c-.31.62-.62,1.23-.91,1.85-.46,1-.88,2-1.29,3.07-.28.69-.53,1.39-.79,2.09-.12.35-.26.7-.38,1.05-.36,1-.69,2.1-1,3.17-.1.33-.17.68-.26,1l13.4,10.13a54.29,54.29,0,0,0-.56,10.73L5.25,84.54c.09.52.16,1,.26,1.55.21,1.08.44,2.16.7,3.23s.54,2.14.85,3.2.65,2.12,1,3.16c.14.42.31.82.46,1.24h0L25.22,97l0,0h.13a51.6,51.6,0,0,0,5.88,9

jsstevenson

{
  "oboscore": {
    "dashboard_score_max_impact": {
      "dashboard": 1,
      "impact": 1,
      "impact_external": 3,
      "no_base": 5,
      "overall_error": 20,
      "overall_info": 5,
      "overall_warning": 10,

jsstevenson

notes

Each kind of response is slightly different, but this tries to make them more consistent in a few ways:

• No more gene vs normalized gene object. Everything is a GA4GH core Gene. This means no more associated_with vs xref, so one less kind of MatchType.
• The outermost level includes the query, additional parameters passed to the API endpoint (I think (...?) this is good practice to include) and service information
• The outermost level also includes a match key that points to what the individual Python QueryHandler methods would return. IMO it makes more sense to move this stuff into the REST API response because these are things that you don't otherwise typically include in Python-to-Python methods (e.g. another class doesn't need to know what version of Gene Normalizer is running, it's literally sharing the environment).
• match objects include source metadata and warnings. In some of the responses, we have previously included source metadata closer to the actual source matches, b

jsstevenson

dgidb-example

2023-12-15

Querying DGIdb GraphQL API

Load packages:

library("ghql")

jsstevenson

[ issue-132-tests ⚙ venv] ~/code/fusor % ipython
Python 3.11.0 (main, Sep  6 2023, 12:48:52) [Clang 14.0.3 (clang-1403.0.22.14.1)]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.16.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from gene.database import create_db

In [2]: db = create_db()

In [3]: db.get_source_metadata("NCBI")

jsstevenson

normalized_id	normalized_xrefs	normalized_strand	normalized_hgnc_types	normalized_ensembl_types	normalized_ncbi_types	normalized_hgnc_locations	normalized_ensembl_locations	normalized_ncbi_locations	incoming_concept_id	incoming_strand	incoming_locations	incoming_gene_type
hgnc:30046	['ensembl:ENSG00000254093', 'ensembl:ENSG00000258724', 'ncbigene:54984']	-	['gene with protein product']	['protein_coding']		[{'type': 'ChromosomeLocation', 'species_id': 'taxonomy:9606', 'chr': '8', 'start': 'p23.1', 'end': 'p23.1'}]	[{'type': 'SequenceLocation', 'start': 10725398, 'end': 10839847, 'sequence_id': 'ga4gh:SQ.209Z7zJ-mFypBEWLk4rNC6S_OxY5p7bs'}]		ncbigene:54984	+	"[{""type"": ""ChromosomeLocation"", ""species_id"": ""taxonomy:9606"", ""chr"": ""8"", ""start"": ""p23.1"", ""end"": ""p23.1""}, {""type"": ""SequenceLocation"", ""start"": 10764960, ""end"": 10839875, ""sequence_id"": ""ga4gh:SQ.209Z7zJ-mFypBEWLk4rNC6S_OxY5p7bs""}, {""type"": ""SequenceLocation"", ""start"": 2507387, ""end"": 2582240, ""sequence_id"": ""g

jsstevenson

('ncbigene:100131223', {'src_name': 'NCBI', 'concept_id': 'ncbigene:100131223', 'symbol': 'LOC100131223', 'strand': '-', 'locations': [{'type': <VRSTypes.SEQUENCE_LOCATION: 'SequenceLocation'>, 'start': 28120833, 'end': 28121467, 'sequence_id': 'ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO'}], 'label_and_type': 'ncbigene:100131223##identity', 'item_type': 'identity'})
('ncbigene:440585', {'src_name': 'NCBI', 'xrefs': ['hgnc:34347'], 'concept_id': 'ncbigene:440585', 'symbol': 'FAM183A', 'strand': '+', 'locations': [{'type': <VRSTypes.SEQUENCE_LOCATION: 'SequenceLocation'>, 'start': 43142961, 'end': 43156396, 'sequence_id': 'ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO'}], 'label_and_type': 'ncbigene:440585##identity', 'item_type': 'identity'})
('ncbigene:51668', {'src_name': 'NCBI', 'xrefs': ['hgnc:25019'], 'concept_id': 'ncbigene:51668', 'symbol': 'HSPB11', 'strand': '-', 'locations': [{'type': <VRSTypes.SEQUENCE_LOCATION: 'SequenceLocation'>, 'start': 53911575, 'end': 53946305, 'sequence_id': 'ga4gh:SQ.Ya6Rs7DHhDe

jsstevenson

(gene-normalization) ~/code/gene-normalization (issue-112) % ipython
Python 3.9.12 (main, Mar 26 2022, 15:51:15)
Type 'copyright', 'credits' or 'license' for more information
IPython 8.2.0 -- An enhanced Interactive Python. Type '?' for help.

In [2]: import boto3

In [3]: g = boto3.resource("dynamodb").Table("gene_concepts")

In [4]: from boto3.dynamodb.conditions import Key

jsstevenson

//
// top level qs:
// * any Array-style components require members?
// * any scalar-style components require values? (ie can be Optional?)
const example = {
    // ** reading frame preserved
    // mandatory?
    // how to (if needed?) represent 'unknown'?
    // not required to be included -- fusor // null
    // curation tool -- should be yes or no