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Add the CURIE ID support to the mygene configuration
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Johnathan Schaff committed Jan 31, 2024
1 parent 3cd3521 commit 77b6f97
Showing 1 changed file with 82 additions and 54 deletions.
136 changes: 82 additions & 54 deletions src/config_web.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,14 +11,15 @@
# *****************************************************************************
# Elasticsearch Settings
# *****************************************************************************
ES_HOST = 'localhost:9200'
ES_INDEX = 'mygene_current'
ES_DOC_TYPE = 'gene'
# ES_HOST = 'localhost:9200'
ES_HOST = "es8.biothings.io:9200"
ES_INDEX = "mygene_current"
ES_DOC_TYPE = "gene"

# *****************************************************************************
# Web Application
# *****************************************************************************
API_VERSION = 'v3'
API_VERSION = "v3"
TAX_REDIRECT = "http://t.biothings.io/v1/taxon/{0}?include_children=1"
APP_LIST += [
(r"/{ver}/species/(\d+)/?", "tornado.web.RedirectHandler", {"url": TAX_REDIRECT}),
Expand All @@ -40,7 +41,7 @@
# *****************************************************************************
# User Input Control
# *****************************************************************************
DEFAULT_FIELDS = ['name', 'symbol', 'taxid', 'entrezgene']
DEFAULT_FIELDS = ["name", "symbol", "taxid", "entrezgene"]

TAXONOMY = {
"human": {"tax_id": "9606", "assembly": "hg38"},
Expand All @@ -51,7 +52,7 @@
"zebrafish": {"tax_id": "7955", "assembly": "danRer11"},
"thale-cress": {"tax_id": "3702", "assembly": "araTha1"},
"frog": {"tax_id": "8364", "assembly": "xenTro9"},
"pig": {"tax_id": "9823", "assembly": "susScr11"}
"pig": {"tax_id": "9823", "assembly": "susScr11"},
}

DATASOURCE_TRANSLATIONS = {
Expand All @@ -72,7 +73,6 @@
"ensemblgene:": "ensembl.gene:",
"ensembltranscript:": "ensembl.transcript:",
"ensemblprotein:": "ensembl.protein:",

# some specific datasources needs to be case-insentive
"hgnc:": r"HGNC:",
"hprd:": r"HPRD:",
Expand All @@ -90,84 +90,112 @@
}

SPECIES_TYPEDEF = {
'species': {
'type': list,
'default': ['all'],
'strict': False,
'max': 1000,
'translations': [
(re.compile(pattern, re.I), translation['tax_id'])
"species": {
"type": list,
"default": ["all"],
"strict": False,
"max": 1000,
"translations": [
(re.compile(pattern, re.I), translation["tax_id"])
for (pattern, translation) in TAXONOMY.items()
],
},
"species_facet_filter": {
"type": list,
"default": None,
"strict": False,
"max": 1000,
"translations": [
(re.compile(pattern, re.I), translation["tax_id"])
for (pattern, translation) in TAXONOMY.items()
]
],
},
'species_facet_filter': {
'type': list,
'default': None,
'strict': False,
'max': 1000,
'translations': [
(re.compile(pattern, re.I), translation['tax_id']) for
(pattern, translation) in TAXONOMY.items()
]
}
}
FIELD_FILTERS = {
'entrezonly': {'type': bool, 'default': False},
'ensemblonly': {'type': bool, 'default': False},
'exists': {'type': list, 'default': None, 'max': 1000, 'strict': False},
'missing': {'type': list, 'default': None, 'max': 1000, 'strict': False},
"entrezonly": {"type": bool, "default": False},
"ensemblonly": {"type": bool, "default": False},
"exists": {"type": list, "default": None, "max": 1000, "strict": False},
"missing": {"type": list, "default": None, "max": 1000, "strict": False},
}

DATASOURCE_TRANSLATION_TYPEDEF = [
(re.compile(pattern, re.I), translation) for
(pattern, translation) in DATASOURCE_TRANSLATIONS.items()
(re.compile(pattern, re.I), translation)
for (pattern, translation) in DATASOURCE_TRANSLATIONS.items()
]
TRIMMED_DATASOURCE_TRANSLATION_TYPEDEF = [
(re.compile(re.sub(r':.*', '', pattern).replace('\\', '') + '(?!\\.)', re.I),
re.sub(r':.*', '', translation).replace('\\', ''))
for(pattern, translation) in DATASOURCE_TRANSLATIONS.items()
(
re.compile(re.sub(r":.*", "", pattern).replace("\\", "") + "(?!\\.)", re.I),
re.sub(r":.*", "", translation).replace("\\", ""),
)
for (pattern, translation) in DATASOURCE_TRANSLATIONS.items()
]
ANNOTATION_KWARGS = copy.deepcopy(ANNOTATION_KWARGS)
ANNOTATION_KWARGS['*'].update(SPECIES_TYPEDEF)
ANNOTATION_KWARGS['*']['_source']['strict'] = False
ANNOTATION_KWARGS["*"].update(SPECIES_TYPEDEF)
ANNOTATION_KWARGS["*"]["_source"]["strict"] = False

QUERY_KWARGS = copy.deepcopy(QUERY_KWARGS)
QUERY_KWARGS['*'].update(SPECIES_TYPEDEF)
QUERY_KWARGS['*'].update(FIELD_FILTERS)
QUERY_KWARGS['*']['_source']['default'] = DEFAULT_FIELDS
QUERY_KWARGS['*']['_source']['strict'] = False
QUERY_KWARGS['GET']['q']['translations'] = DATASOURCE_TRANSLATION_TYPEDEF
QUERY_KWARGS['POST']['scopes']['translations'] = TRIMMED_DATASOURCE_TRANSLATION_TYPEDEF
QUERY_KWARGS['GET']['include_tax_tree'] = {'type': bool, 'default': False}
QUERY_KWARGS['POST']['scopes']['default'] = ["_id", "entrezgene", "ensembl.gene", "retired"]
QUERY_KWARGS['POST']['q']['jsoninput'] = True
QUERY_KWARGS["*"].update(SPECIES_TYPEDEF)
QUERY_KWARGS["*"].update(FIELD_FILTERS)
QUERY_KWARGS["*"]["_source"]["default"] = DEFAULT_FIELDS
QUERY_KWARGS["*"]["_source"]["strict"] = False
QUERY_KWARGS["GET"]["q"]["translations"] = DATASOURCE_TRANSLATION_TYPEDEF
QUERY_KWARGS["POST"]["scopes"]["translations"] = TRIMMED_DATASOURCE_TRANSLATION_TYPEDEF
QUERY_KWARGS["GET"]["include_tax_tree"] = {"type": bool, "default": False}
QUERY_KWARGS["POST"]["scopes"]["default"] = [
"_id",
"entrezgene",
"ensembl.gene",
"retired",
]
QUERY_KWARGS["POST"]["q"]["jsoninput"] = True


# *****************************************************************************
# Elasticsearch Query Pipeline
# *****************************************************************************
ES_QUERY_BUILDER = "web.pipeline.MygeneQueryBuilder"
AVAILABLE_FIELDS_EXCLUDED = ['all', 'accession_agg', 'refseq_agg']
AVAILABLE_FIELDS_EXCLUDED = ["all", "accession_agg", "refseq_agg"]

# *****************************************************************************
# Endpoints Specifics & Others
# *****************************************************************************

# kwargs for status check
STATUS_CHECK = {
'id': '1017',
'index': 'mygene_current'
}
STATUS_CHECK = {"id": "1017", "index": "mygene_current"}

# This essentially bypasses the es.get fallback as in myvariant...
# This essentially bypasses the es.get fallback as in myvariant ...
# The first regex matched integers, in which case the query becomes against
# entrezgeneall annotation queries are now multimatch against the following fields
ANNOTATION_ID_REGEX_LIST = [(re.compile(r'^\d+$'), ['entrezgene', 'retired'])]
base_regex_pattern = re.compile(r"^\d+$")
base_field_scope = ["entrezgene", "retired"]

# CURIE ID support
BIOLINK_MODEL_PREFIX_BIOTHINGS_GENE_MAPPING = {
"NCBIGene": {"type": "gene", "field": "entrezgene"},
"ENSEMBL": {"type": "gene", "field": "ensembl.gene"},
"UniProtKB": {"type": "gene", "field": "uniprot.Swiss-Prot"},
}
gene_pattern_field_mapping = []
for (
biolink_model,
biothings_parameters,
) in BIOLINK_MODEL_PREFIX_BIOTHINGS_GENE_MAPPING.items():
expression = re.compile(rf"({biolink_model}):(?P<term>[^:]+)", re.I)
field_match = biothings_parameters["field"]
pattern = (expression, field_match)
gene_pattern_field_mapping.append(pattern)

ANNOTATION_ID_REGEX_LIST = [
*gene_pattern_field_mapping,
(base_regex_pattern, base_field_scope),
]

# ANNOTATION_ID_REGEX_LIST = [] # [(re.compile(r'rs[0-9]+', re.I), 'dbsnp.rsid')]
ANNOTATION_DEFAULT_SCOPES = ["_id", "entrezgene", "ensembl.gene", "retired"]

# for docs
INCLUDE_DOCS = False
DOCS_STATIC_PATH = 'docs/_build/html'
DOCS_STATIC_PATH = "docs/_build/html"

# url template to redirect for 'include_tax_tree' parameter
INCLUDE_TAX_TREE_REDIRECT_ENDPOINT = 'http://t.biothings.io/v1/taxon'
INCLUDE_TAX_TREE_REDIRECT_ENDPOINT = "http://t.biothings.io/v1/taxon"

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