test node endpoints, including tags, grns, papers, by agi and by ref. Committing files include interactions database, interactions, model, output json files, cfg, init.sh and test file

Author: TeresasaZ

api/models/interactions_vincent_v2.py

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+from api import db
+from sqlalchemy import Enum
+from sqlalchemy.orm import relationship
+from sqlalchemy.dialects.mysql import TEXT
+from sqlalchemy import ForeignKey
+from typing import List
+from datetime import datetime
+
+
+class Interactions(db.Model):
+    __bind_key__ = "interactions_vincent_v2"
+    __tablename__ = "interactions"
+
+    interaction_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True)
+    pearson_correlation_coeff: db.Mapped[float] = db.mapped_column(db.Float, nullable=True, primary_key=False)
+    entity_1: db.Mapped[str] = db.mapped_column(db.String(50), nullable=False, primary_key=False)
+    entity_2: db.Mapped[str] = db.mapped_column(db.String(50), nullable=False, primary_key=False)
+    interaction_type_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=False)
+    children: db.Mapped[List["InteractionsSourceMiJoin"]] = relationship()
+
+
+class InteractionsSourceMiJoin(db.Model):
+    __bind_key__ = "interactions_vincent_v2"
+    __tablename__ = "interactions_source_mi_join_table"
+
+    interaction_id: db.Mapped[int] = db.mapped_column(ForeignKey("interactions.interaction_id"), primary_key=True)
+    source_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=False)
+    external_db_id: db.Mapped[str] = db.mapped_column(db.String(30), nullable=False, primary_key=False)
+    mode_of_action: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=False)
+    mi_detection_method: db.Mapped[str] = db.mapped_column(db.String(10), nullable=False, primary_key=False)
+    mi_detection_type: db.Mapped[str] = db.mapped_column(db.String(10), nullable=False, primary_key=False)
+
+
+class TagLookupTable(db.Model):
+    __bind_key__ = "interactions_vincent_v2"
+    __tablename__ = "tag_lookup_table"
+
+    tag_name: db.Mapped[str] = db.mapped_column(db.String(20), nullable=False, primary_key=True)
+    tag_group: db.Mapped[str] = db.mapped_column(Enum("Gene", "Experiment", "Condition", "Misc"), nullable=False, primary_key=False)
+
+
+class ExternalSource(db.Model):
+    __bind_key__ = "interactions_vincent_v2"
+    __tablename__ = "external_source"
+
+    source_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, comment="surrogate key", primary_key=True)
+    source_name: db.Mapped[str] = db.mapped_column(db.String(500), nullable=False, comment="name of the source, can be a pubmed identifier like “PMIDXXXXXXX” or “Asher’s sql dump”", primary_key=False)
+    comments: db.Mapped[str] = db.mapped_column(TEXT(), nullable=False, comment="Comments regarding the source", primary_key=False)
+    date_uploaded: db.Mapped[datetime] = db.mapped_column(db.Date(), nullable=False, comment="When it was uploaded to database", primary_key=False)
+    url: db.Mapped[str] = db.mapped_column(db.String(350), nullable=True, comment="URL if available to paper/source (does not have to be a DOI, can be a link to a databases’ source)", primary_key=False)
+    image_url: db.Mapped[str] = db.mapped_column(db.String(300), nullable=True, primary_key=False)
+    grn_title: db.Mapped[str] = db.mapped_column(db.String(200), nullable=True, primary_key=False)
+    cyjs_layout: db.Mapped[str] = db.mapped_column(db.String(1000), nullable=True, primary_key=False)
+    children: db.Mapped[List["SourceTagJoinTable"]] = relationship()
+
+
+class SourceTagJoinTable(db.Model):
+    __bind_key__ = "interactions_vincent_v2"
+    __tablename__ = "source_tag_join_table"
+
+    source_id: db.Mapped[int] = db.mapped_column(
+        db.Integer(),
+        db.ForeignKey("external_source.source_id"),
+        primary_key=True
+    )
+    tag_name: db.Mapped[str] = db.mapped_column(
+        db.String(20),
+        db.ForeignKey("tag_lookup_table.tag_name"),
+        primary_key=True
+    )