added psivec route

app/controllers/alternativeSplicing.py

@@ -1,6 +1,7 @@
 from flask import abort
 import app.models as models
 from flask import Response
+from app.config import db
 
 def get_transcript_events(enst_number):
     """
@@ -91,3 +92,50 @@ def get_exons_for_position(start_pos: int, end_pos: int):
     else:
         abort(404, "No data found that satisfies the given filters")
 
+
+def get_psi_values(transcript_ID: str = None, enst_number: str =None, psivec_ID: int = None, alternative_splicing_event_transcripts_ID: str = None, sample_ID: str = None, limit=100):
+    """
+    This function response for the request: /alternativeSplicing/getPsiValue/
+    with the possibility to filter by psivec_ID, alternative
+    splicing event transcripts ID and sample ID
+    :param psivec_ID: ID of the psivec
+    :param alternative_splicing_event_transcripts_ID: ID of the alternative splicing event transcripts
+    :param sample_ID: ID of the sample
+    :return: psi value for the given parameters, ordered by psi value
+    """
+    # Build the transcript query
+    transcript_query = db.select(models.Transcript.transcript_ID)
+    if transcript_ID:
+        transcript_query = transcript_query.where(models.Transcript.transcript_ID == transcript_ID)
+    if enst_number:
+        transcript_query = transcript_query.where(models.Transcript.enst_number == enst_number)
+
+    # Build the alternative splicing events query
+    as_query = db.select(models.AlternativeSplicingEventTranscripts.alternative_splicing_event_transcripts_ID).where(
+        models.AlternativeSplicingEventTranscripts.transcript_ID.in_(transcript_query)
+    )
+    if alternative_splicing_event_transcripts_ID:
+        as_query = as_query.where(
+            models.AlternativeSplicingEventTranscripts.alternative_splicing_event_transcripts_ID == alternative_splicing_event_transcripts_ID
+        )
+
+    # Build the psi values query
+    psi_query = db.select(models.PsiVec).where(
+        models.PsiVec.alternative_splicing_event_transcripts_ID.in_(as_query)
+    )
+    if psivec_ID:
+        psi_query = psi_query.where(models.PsiVec.psivec_ID == psivec_ID)
+    if sample_ID:
+        psi_query = psi_query.where(models.PsiVec.sample_ID == sample_ID)
+
+    # Apply limit and sort results
+    psi_query = psi_query.order_by(models.PsiVec.psi_value.desc()).limit(limit)
+
+    psi_values = db.session.execute(psi_query).scalars().all()
+
+    if psi_values:
+        schema = models.PsiVecSchema(many=True)
+        return schema.dump(psi_values)
+    else:
+        abort(404, "No data found that satisfies the given filters")
+

app/models.py

@@ -607,6 +607,22 @@ class GseaRankingGenes(db.Model):
     gene_ID = db.Column(db.Integer, db.ForeignKey('gene.gene_ID'))
     gene_symbol = relationship("Gene", foreign_keys=[gene_ID])
 
+class PsiVec(db.Model):
+    __tablename__ = 'psivec'
+    psivec_ID = db.Column(db.Integer, primary_key=True)
+
+    alternative_splicing_event_transcripts_ID = db.Column(db.Integer, db.ForeignKey('alternative_splicing_event_transcripts.alternative_splicing_event_transcripts_ID'), nullable=False)
+    alternative_splicing_event_transcripts = relationship("AlternativeSplicingEventTranscripts", foreign_keys=[alternative_splicing_event_transcripts_ID])
+
+    sample_ID = db.Column(db.String(32))
+    psi_value = db.Column(db.Float)
+
+
+
+####################################
+############# SCHEMAS ##############
+####################################
+
 class DatasetSchema(ma.SQLAlchemyAutoSchema):
     class Meta:
         model = Dataset
@@ -1158,3 +1174,11 @@ class Meta:
 
     dataset_1 = ma.Nested(DatasetSchema)
     dataset_2 = ma.Nested(DatasetSchema)
+
+class PsiVecSchema(ma.SQLAlchemyAutoSchema):
+    class Meta:
+        model = PsiVec
+        sqla_session = db.session
+
+    alternative_splicing_event_transcripts = ma.Nested(AlternativeSplicingEventsTranscriptsSchema)
+

swagger.yml

@@ -74,50 +74,6 @@ paths:
                   sponge_db_version:
                     type: integer
                     description: SPONGEdb version used
-  # /dataset:
-  #   get:
-  #     operationId: dataset.read
-  #     tags:
-  #     - Dataset
-  #     summary: Get information about all cancer types/datasets or specific one.
-  #     description: Get information about all available datasets to start browsing or search for a specific cancer type/dataset.
-  #     parameters:
-  #     - $ref: '#/components/parameters/VersionParam'
-  #     - name: disease_name
-  #       in: query
-  #       description: Name of the specific cancer type/dataset. Fuzzy search is available (e.g. "kidney clear cell carcinoma" or just "kidney").
-  #       required: false
-  #       schema:
-  #         type: string
-  #     responses:
-  #       "200":
-  #         description: Successfully read information about all cancer types/datasets or specific one from database.
-  #         content:
-  #           application/json:
-  #             schema:
-  #               type: object
-  #               properties:
-  #                 dataset_ID:
-  #                   type: integer
-  #                   description: Internal database ID of the cancer type/dataset.
-  #                 disease_name:
-  #                   type: string
-  #                   description: Name of the cancer type/dataset.
-  #                 data_origin:
-  #                   type: string
-  #                   description: Cancer type/dataset origin (database name, etc.).
-  #                 disease_type:
-  #                   type: string
-  #                   description: Type of the disease (e.g. cancer).
-  #                 download_url:
-  #                   type: string
-  #                   description: URL to cancer type/dataset annotation.
-  #                 disease_subtype:
-  #                   type: string
-  #                   description: Subtype of specific cancer type (NA if no relevant subtype is present)
-  #                 sponge_db_version:
-  #                   type: integer
-  #                   description: SPONGEdb version used
   /dataset/spongeRunInformation:
     get:
       operationId: dataset.read_spongeRunInformation
@@ -3481,6 +3437,71 @@ paths:
                     ense_number:
                       type: string
                       description: Ense number of the exon.
+  /alternativeSplicing/getPsiValues:
+    get:
+      operationId: alternativeSplicing.get_psi_values
+      tags:
+      - AlternativeSplicing
+      summary: Retrieve all psi values for a specific event type of a transcript of interest.
+      description: Retrieve all psi values for a specific event type of a transcript of interest.
+      parameters:
+      - name: transcript_ID
+        in: query
+        description: Internal database ID of the transcript of interest.
+        required: false
+        schema:
+          type: integer
+      - name: enst_number
+        in: query
+        description: A enst number of a transcript of interest (e.g. ENST00000387314)
+        required: false
+        schema:
+          type: string
+      - name: psivec_ID
+        in: query
+        description: Internal database ID of the psi values of the transcript of interest.
+        required: false
+        schema:
+          type: integer
+      - name: alternative_splicing_event_transcripts_ID
+        in: query
+        description: Internal database ID of the alternative splicing event transcripts of the transcript of interest.
+        required: false
+        schema:
+          type: integer
+      - name: sample_ID
+        in: query
+        description: A sample ID to filter for
+        schema:
+          type: string
+        required: false
+      - name: limit
+        in: query
+        description: Limit the number of results. Defaults to 100.
+        schema:
+          type: integer
+        required: false
+      responses:
+        "200":
+          description: Retrieve all psi values for a specific event type of a transcript of interest.
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  properties:
+                    psivec_ID:
+                      type: integer
+                      description: Internal database ID of the psi values of the transcript of interest.
+                    alternative_splicing_event_transcripts_ID:
+                      type: integer
+                      description: Internal database ID of the alternative splicing event transcripts of the transcript of interest.
+                    sample_ID:
+                      type: string
+                      description: ID of the specific sample.
+                    psi_value:
+                      type: number
+                      description: Psi value of the specific event type.
   /spongEffects/getSpongEffectsRuns:
     get:
       operationId: spongEffects.get_spongeffects_runs