Adding bioentity endpoints

src/indra_cogex/apps/bioentity/api.py

@@ -0,0 +1,313 @@
+"""
+This module provides Flask-RESTful APIs for querying bioentity information.
+
+Namespaces:
+-----------
+bioentity_ns : flask_restx.Namespace
+    Namespace for BioEntity related queries.
+
+Models:
+----------
+uniprot_mnemonic_ids_model : flask_restx.Model
+    Model for a list of UniProt mnemonic IDs.
+uniprot_ids_model : flask_restx.Model
+    Model for a list of UniProt IDs.
+hgnc_ids_model : flask_restx.Model
+    Model for a list of HGNC IDs.
+kinase_genes_model : flask_restx.Model
+    Model for a list of kinase gene names.
+phosphatase_genes_model : flask_restx.Model
+    Model for a list of phosphatase gene names.
+transcription_factor_genes_model : flask_restx.Model
+    Model for a list of transcription factor gene names.
+
+Resources:
+----------
+UniprotIdsFromUniprotMnemonicIds : flask_restx.Resource
+    Resource for converting UniProt mnemonic IDs to UniProt IDs.
+HgncIdsFromUniprotIds : flask_restx.Resource
+    Resource for mapping UniProt IDs to HGNC IDs.
+HgncNamesFromHgncIds : flask_restx.Resource
+    Resource for retrieving HGNC names from HGNC IDs.
+CheckIfKinase : flask_restx.Resource
+    Resource for checking if given genes are kinases.
+CheckIfPhosphatase : flask_restx.Resource
+    Resource for checking if given genes are phosphatases.
+CheckIfTranscriptionFactor : flask_restx.Resource
+    Resource for checking if given genes are transcription factors.
+"""
+
+from flask import request
+from flask_restx import Namespace, Resource, fields
+
+from indra.databases import hgnc_client, uniprot_client
+
+bioentity_ns = Namespace("BioEntity", description="Queries for BioEntity", path="/api")
+
+uniprot_mnemonic_ids_model = bioentity_ns.model(
+    'get_uniprot_ids_from_uniprot_mnemonic_ids_model',
+    {
+        'uniprot_mnemonic_ids': fields.List(
+            fields.String,
+            required=True,
+            description='List of UniProt mnemonic IDs', example=['CLH1_HUMAN']
+        )
+    }
+)
+uniprot_ids_model = bioentity_ns.model(
+    'get_hgnc_ids_from_uniprot_ids_model',
+    {
+        'uniprot_ids': fields.List(
+            fields.String,
+            required=True,
+            description='List of UniProt IDs',
+            example=['Q00610']
+        )
+    }
+)
+hgnc_ids_model = bioentity_ns.model(
+    'get_hgnc_names_from_hgnc_ids_model',
+    {
+        'hgnc_ids': fields.List(
+            fields.String,
+            required=True,
+            description='List of HGNC IDs',
+            example=['2092']
+        )
+    }
+)
+kinase_genes_model = bioentity_ns.model(
+    'get_is_kinase_model',
+    {
+        'genes': fields.List(
+            fields.String,
+            required=True,
+            description='List of gene names',
+            example=['CHEK1']
+        )
+    }
+)
+phosphatase_genes_model = bioentity_ns.model(
+    'get_is_phosphatase_model',
+    {
+        'genes': fields.List(
+            fields.String,
+            required=True,
+            description='List of gene names',
+            example=['MTM1']
+        )
+    }
+)
+transcription_factor_genes_model = bioentity_ns.model(
+    'get_is_transcription_factor_model',
+    {
+        'genes': fields.List(
+            fields.String,
+            required=True,
+            description='List of gene names',
+            example=['STAT1']
+        )
+    }
+)
+
+
+@bioentity_ns.expect(uniprot_mnemonic_ids_model)
+@bioentity_ns.route("/get_uniprot_ids_from_uniprot_mnemonic_ids")
+class UniprotIdsFromUniprotMnemonicIds(Resource):
+    """A Flask-RESTful resource for converting UniProt mnemonic IDs to UniProt IDs.
+
+    Methods
+    -------
+    post()
+        Receives a JSON payload with a list of UniProt mnemonic IDs and returns a
+        mapping of these IDs to their corresponding UniProt IDs.
+    """
+
+    def post(self):
+        """Maps UniProt mnemonic IDs to UniProt IDs.
+
+        This method expects a JSON payload with a key "uniprot_mnemonic_ids"
+        containing a list of UniProt mnemonic IDs. It uses the UniProt client to
+        convert each mnemonic ID to a UniProt ID. Then, it adds the mapping from the
+        mnemonic ID to the UniProt ID to the result.
+
+        Returns
+        -------
+        :
+            A dictionary mapping UniProt mnemonic IDs to UniProt IDs.
+        """
+        uniprot_mnemonic_ids = request.json["uniprot_mnemonic_ids"]
+        mapping = dict()
+        for uniprot_mnemonic_id in uniprot_mnemonic_ids:
+            uniprot_id = uniprot_client.get_id_from_mnemonic(uniprot_mnemonic_id)
+            if uniprot_id:
+                mapping[uniprot_mnemonic_id] = uniprot_id
+        return mapping
+
+
+@bioentity_ns.expect(uniprot_ids_model)
+@bioentity_ns.route("/get_hgnc_ids_from_uniprot_ids")
+class HgncIdsFromUniprotIds(Resource):
+    """A Flask-RESTful resource to map UniProt IDs to HGNC IDs.
+
+    Methods
+    -------
+    post()
+        Receives a JSON payload containing a list of UniProt IDs and returns a mapping
+        of UniProt IDs to HGNC IDs.
+    """
+
+    def post(self):
+        """Maps UniProt IDs to HGNC IDs.
+
+        This method expects a JSON payload with a list of UniProt IDs under the key
+        "uniprot_ids". It returns a dictionary mapping each UniProt ID to its
+        corresponding HGNC ID, if available.
+
+        Returns
+        -------
+        :
+            A dictionary where keys are UniProt IDs and values are HGNC IDs.
+        """
+        uniprot_ids = request.json["uniprot_ids"]
+        mapping = dict()
+        for uniprot_id in uniprot_ids:
+            hgnc_id = uniprot_client.get_hgnc_id(uniprot_id)
+            if hgnc_id:
+                mapping[uniprot_id] = hgnc_id
+        return mapping
+
+
+@bioentity_ns.expect(hgnc_ids_model)
+@bioentity_ns.route("/get_hgnc_names_from_hgnc_ids")
+class HgncNamesFromHgncIds(Resource):
+    """A Flask-RESTful resource for retrieving HGNC names from HGNC IDs.
+
+    Methods
+    -------
+    post()
+        Receives a JSON payload containing a list of HGNC IDs and returns a
+        dictionary mapping each HGNC ID to its corresponding HGNC name.
+    """
+
+    def post(self):
+        """Maps HGNC IDs to their corresponding names.
+
+        This method expects a JSON payload with a list of HGNC IDs under the key
+        "hgnc_ids". It retrieves the corresponding HGNC names using the `hgnc_client`
+        and returns a dictionary mapping each HGNC ID to its name.
+
+        Returns
+        -------
+        :
+            A dictionary where keys are HGNC IDs and values are HGNC names.
+        """
+        hgnc_ids = request.json["hgnc_ids"]
+        mapping = dict()
+        for hgnc_id in hgnc_ids:
+            hgnc_name = hgnc_client.get_hgnc_name(hgnc_id)
+            if hgnc_name:
+                mapping[hgnc_id] = hgnc_name
+        return mapping
+
+
+@bioentity_ns.expect(kinase_genes_model)
+@bioentity_ns.route("/is_kinase")
+class CheckIfKinase(Resource):
+    """A Flask-RESTful resource that checks if given genes are kinases.
+
+    Methods
+    -------
+    post()
+        Receives a JSON payload with a list of genes and returns a mapping of each
+        gene to a boolean indicating if it is a kinase.
+    """
+
+    def post(self):
+        """Determines if the given genes are kinases.
+
+        This method expects a JSON payload with a list of genes under the key "genes".
+        It checks each gene to determine if it is a kinase using the
+        `hgnc_client.is_kinase` method and returns a mapping of each gene to a boolean
+        indicating whether it is a kinase.
+
+        Returns
+        -------
+        :
+            A dictionary where the keys are gene names and the values are booleans
+            indicating whether each gene is a kinase.
+        """
+        genes = request.json["genes"]
+        mapping = dict()
+        for gene in genes:
+            gene_is_kinase = hgnc_client.is_kinase(gene)
+            mapping[gene] = gene_is_kinase
+        return mapping
+
+
+@bioentity_ns.expect(phosphatase_genes_model)
+@bioentity_ns.route("/is_phosphatase")
+class CheckIfPhosphatase(Resource):
+    """A Flask-RESTful resource for checking if a list of genes are phosphatases.
+
+    Methods
+    -------
+    post()
+        Receives a JSON payload with a list of genes and returns a mapping of each
+        gene to a boolean indicating if it is a phosphatase.
+    """
+
+    def post(self):
+        """Determines if the given genes are phosphatases.
+
+        This method expects a JSON payload with a list of gene identifiers under the
+        key "genes". It checks each gene to determine if it is a phosphatase using the
+        `hgnc_client.is_phosphatase` method. The result is a dictionary mapping each
+        gene to a boolean indicating whether it is a phosphatase.
+
+        Returns
+        -------
+        :
+            A dictionary where keys are gene identifiers and values are booleans
+            indicating if the gene is a phosphatase.
+        """
+        genes = request.json["genes"]
+        mapping = dict()
+        for gene in genes:
+            gene_is_phosphate = hgnc_client.is_phosphatase(gene)
+            mapping[gene] = gene_is_phosphate
+        return mapping
+
+
+@bioentity_ns.expect(transcription_factor_genes_model)
+@bioentity_ns.route("/is_transcription_factor")
+class CheckIfTranscriptionFactor(Resource):
+    """A Flask-RESTful resource that checks if given genes are transcription factors.
+
+    Methods
+    -------
+    post()
+        Receives a JSON payload with a list of genes and returns a mapping of each
+        gene to a boolean indicating whether it is a transcription factor.
+    """
+
+    def post(self):
+        """Determines if the given genes are transcription factors.
+
+        This method expects a JSON payload with a list of genes under the key "genes".
+        It checks each gene to determine if it is a transcription factor using the
+        `hgnc_client.is_transcription_factor` method and returns a mapping of genes
+        to their transcription factor status.
+
+        Returns
+        -------
+        :
+            A dictionary where keys are gene names and values are booleans indicating
+            whether the gene is a transcription factor.
+        """
+        genes = request.json["genes"]
+        mapping = dict()
+        for gene in genes:
+            gene_is_transcription_factor = hgnc_client.is_transcription_factor(gene)
+            mapping[gene] = gene_is_transcription_factor
+        return mapping

src/indra_cogex/apps/queries_web/__init__.py

@@ -14,7 +14,7 @@
 from inspect import isfunction, signature
 
 from flask import jsonify, request
-from flask_restx import Api, Resource, abort, fields
+from flask_restx import Resource, abort, fields, Namespace, Model
 
 from indra_cogex.apps.proxies import client
 from indra_cogex.client import queries, subnetwork
@@ -26,12 +26,12 @@
 from .helpers import ParseError, get_docstring, parse_json, process_result
 
 __all__ = [
-    "api",
     "query_ns",
 ]
 
 logger = logging.getLogger(__name__)
 
+query_ns = Namespace("CoGEx Queries", "Queries for INDRA CoGEx", path="/api/")
 
 def get_example_data():
     """Get example data for gene continuous analysis."""
@@ -42,15 +42,6 @@ def get_example_data():
 
 continuous_analysis_example_names, continuous_analysis_example_data = get_example_data()
 
-
-api = Api(
-    title="INDRA CoGEx Query API",
-    description="REST API for INDRA CoGEx queries",
-    doc="/apidocs",
-)
-
-query_ns = api.namespace("CoGEx Queries", "Queries for INDRA CoGEx", path="/api/")
-
 examples_dict = {
     "tissue": fields.List(fields.String, example=["UBERON", "UBERON:0001162"]),
     "gene": fields.List(fields.String, example=["HGNC", "9896"]),
@@ -171,7 +162,7 @@ def get_example_data():
             )
 
     # Get the parameters name for the other parameter that is not 'client'
-    query_model = api.model(
+    query_model = query_ns.model(
         model_name,
         {
             param_name: examples_dict[param_name]

src/indra_cogex/apps/rest_api.py

@@ -0,0 +1,17 @@
+from flask_restx import Api
+
+from .bioentity.api import bioentity_ns
+from .queries_web import query_ns
+
+__all__ = [
+    "api",
+]
+
+api = Api(
+    title="INDRA CoGEx Query API",
+    description="REST API for INDRA CoGEx queries",
+    doc="/apidocs",
+)
+
+api.add_namespace(query_ns)
+api.add_namespace(bioentity_ns)

src/indra_cogex/apps/wsgi.py

@@ -22,7 +22,7 @@
 from indra_cogex.apps.gla.gene_blueprint import gene_blueprint
 from indra_cogex.apps.gla.metabolite_blueprint import metabolite_blueprint
 from indra_cogex.apps.home import home_blueprint
-from indra_cogex.apps.queries_web import api
+from indra_cogex.apps.rest_api import api
 from indra_cogex.client.neo4j_client import Neo4jClient
 from indra_cogex.client.enrichment.utils import build_caches