Merge pull request #281 from BioAnalyticResource/dev

Updates

Author: asherpasha

api/models/interactions_vincent_v2.py

@@ -36,18 +36,34 @@ class TagLookupTable(db.Model):
     __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)
+    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)
+    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)
@@ -59,12 +75,8 @@ class SourceTagJoinTable(db.Model):
     __tablename__ = "source_tag_join_table"
 
     source_id: db.Mapped[int] = db.mapped_column(
-        db.Integer(),
-        db.ForeignKey("external_source.source_id"),
-        primary_key=True
+        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
+        db.String(20), db.ForeignKey("tag_lookup_table.tag_name"), primary_key=True
     )

api/resources/efp_image.py

@@ -153,7 +153,7 @@ def get(self, species=""):
 
         # This will only work on the BAR
         if os.environ.get("BAR"):
-            if species in ["arabidopsis", "arachis", "cannabis", "maize", "rice", "sorghum", "soybean"]:
+            if species in ["arabidopsis", "arachis", "cannabis", "grape", "maize", "rice", "sorghum", "soybean"]:
                 efp_base_path = "/var/www/html/efp_" + species + "/data"
             else:
                 return BARUtils.error_exit("Invalid species.")

api/resources/interactions.py

@@ -314,13 +314,12 @@ def get(self, paper_id=""):
         try:
             interactions_database = PostInteractions
             itnsjoin_database = PostInteractionsSourceMiJoin
-            query = db.select(
-                interactions_database,
-                itnsjoin_database
-                ).select_from(interactions_database).join(
-                        itnsjoin_database,
-                        interactions_database.interaction_id == itnsjoin_database.interaction_id
-                    ).where(itnsjoin_database.source_id == paper_id)
+            query = (
+                db.select(interactions_database, itnsjoin_database)
+                .select_from(interactions_database)
+                .join(itnsjoin_database, interactions_database.interaction_id == itnsjoin_database.interaction_id)
+                .where(itnsjoin_database.source_id == paper_id)
+            )
             rows = db.session.execute(query).all()
             for i, m in rows:
                 result.append(
@@ -382,9 +381,7 @@ def get(self, tag=""):
             # Step 1: Get source_ids that contain the searched tag
 
             matching_source_ids = []
-            query_source = db.select(src_tag_join_database.source_id).where(
-                src_tag_join_database.tag_name == tag
-            )
+            query_source = db.select(src_tag_join_database.source_id).where(src_tag_join_database.tag_name == tag)
             rows_source = db.session.execute(query_source).all()
             matching_source_ids = [row[0] for row in rows_source]
 
@@ -393,11 +390,7 @@ def get(self, tag=""):
 
             # Step 2: Get all tags for those sources
             query = (
-                db.select(
-                    ext_src_database,
-                    src_tag_join_database.tag_name,
-                    tag_lkup_database.tag_group
-                )
+                db.select(ext_src_database, src_tag_join_database.tag_name, tag_lkup_database.tag_group)
                 .join(src_tag_join_database, ext_src_database.source_id == src_tag_join_database.source_id)
                 .join(tag_lkup_database, src_tag_join_database.tag_name == tag_lkup_database.tag_name)
                 .where(ext_src_database.source_id.in_(matching_source_ids))  # Keep all tags for matched sources
@@ -425,7 +418,7 @@ def get(self, tag=""):
                         "image_url": ex.image_url,
                         "grn_title": ex.grn_title,
                         "cyjs_layout": ex.cyjs_layout,
-                        "tag": "|".join(src_tag_match[ex.source_id])
+                        "tag": "|".join(src_tag_match[ex.source_id]),
                     }
                     result.append(one_source[source_id])
 
@@ -494,7 +487,7 @@ def get(self, number=""):
                         "url": row.url,
                         "image_url": row.image_url,
                         "grn_title": row.grn_title,
-                        "cyjs_layout": row.cyjs_layout
+                        "cyjs_layout": row.cyjs_layout,
                     }
                 )
 
@@ -530,7 +523,7 @@ def get(self, stringAGI=""):
                     es.comments,
                     es.cyjs_layout,
                     stjt.tag_name,
-                    tlt.tag_group
+                    tlt.tag_group,
                 )
                 .join(i_s_mi_join_table, i_s_mi_join_table.source_id == es.source_id)
                 .join(i, i.interaction_id == i_s_mi_join_table.interaction_id)
@@ -557,20 +550,14 @@ def get(self, stringAGI=""):
                         "source_name": row.source_name,
                         "comments": row.comments,
                         "cyjs_layout": row.cyjs_layout,
-                        "tags": []
+                        "tags": [],
                     }
 
                 tag_entry = f"{row.tag_name}:{row.tag_group}"
                 if tag_entry not in result_dict[source_id]["tags"]:  # DISTINCT
                     result_dict[source_id]["tags"].append(tag_entry)
 
-            result = [
-                {
-                    **data,
-                    "tags": "|".join(data["tags"])  # overwrites tags
-                }
-                for data in result_dict.values()
-            ]
+            result = [{**data, "tags": "|".join(data["tags"])} for data in result_dict.values()]  # overwrites tags
 
             if len(result) == 0:
                 return BARUtils.error_exit("Invalid AGI"), 400
@@ -603,7 +590,7 @@ def get(self, AGI_1="", AGI_2=""):
                     es.comments,
                     es.cyjs_layout,
                     stjt.tag_name,
-                    tlt.tag_group
+                    tlt.tag_group,
                 )
                 .join(i_s_mi_join_table, i_s_mi_join_table.source_id == es.source_id)
                 .join(i, i.interaction_id == i_s_mi_join_table.interaction_id)
@@ -630,18 +617,14 @@ def get(self, AGI_1="", AGI_2=""):
                         "source_name": row.source_name,
                         "comments": row.comments,
                         "cyjs_layout": row.cyjs_layout,
-                        "tags": set()
+                        "tags": set(),
                     }
 
-                result_dict[source_id]["tags"].add(f"{row.tag_name}:{row.tag_group}")  # ensures uniqueness automatically with `set`
+                result_dict[source_id]["tags"].add(
+                    f"{row.tag_name}:{row.tag_group}"
+                )  # ensures uniqueness automatically with `set`
 
-            result = [
-                {
-                    **data,
-                    "tags": "|".join(sorted(data["tags"]))
-                }
-                for data in result_dict.values()
-            ]
+            result = [{**data, "tags": "|".join(sorted(data["tags"]))} for data in result_dict.values()]
 
             if len(result) == 0:
                 return BARUtils.error_exit("Both AGI invalid"), 400
@@ -664,11 +647,7 @@ def get(self):
             stjt = SourceTagJoinTable
             tlt = TagLookupTable
             query = (
-                db.select(
-                    es,
-                    stjt.tag_name,
-                    tlt.tag_group
-                )
+                db.select(es, stjt.tag_name, tlt.tag_group)
                 .join(stjt, es.source_id == stjt.source_id)
                 .join(tlt, stjt.tag_name == tlt.tag_name)
             )
@@ -695,7 +674,7 @@ def get(self):
                         "image_url": ex.image_url,
                         "grn_title": ex.grn_title,
                         "cyjs_layout": ex.cyjs_layout,
-                        "tag": "|".join(src_tag_match[ex.source_id])
+                        "tag": "|".join(src_tag_match[ex.source_id]),
                     }
                     result.append(one_source[source_id])
 

api/utils/mfinder_utils.py

@@ -150,7 +150,9 @@ def get_gene_id_hash_map(input):
             if item[1] not in hash_of_ids.values():
                 hash_of_ids[iter] = item[1]
                 iter += 1
-            return_str += f"{MfinderUtils.find_key(hash_of_ids, item[0])} {MfinderUtils.find_key(hash_of_ids, item[1])} 1\n"
+            return_str += (
+                f"{MfinderUtils.find_key(hash_of_ids, item[0])} {MfinderUtils.find_key(hash_of_ids, item[1])} 1\n"
+            )
 
         return hash_of_ids, return_str
 

requirements.txt

@@ -27,7 +27,7 @@ jsonschema==4.25.1
 jsonschema-specifications==2025.9.1
 limits==5.5.0
 markdown-it-py==4.0.0
-MarkupSafe==3.0.2
+MarkupSafe==3.0.3
 marshmallow==4.0.1
 mccabe==0.7.0
 mdurl==0.1.2

tests/resources/test_interactions.py

@@ -210,26 +210,20 @@ def test_single_itrn(self):
                     "pearson_correlation_coeff": None,
                     "entity_1": "AT4G25470",
                     "entity_2": "AT5G50720",
-                    "interaction_type_id": 1
+                    "interaction_type_id": 1,
                 }
-            ]
+            ],
         }
         self.assertEqual(response.json, expected)
 
         # Input not a number
         response = self.app_client.get("/interactions/single_interaction/g")
-        expected = {
-            "wasSuccessful": False,
-            "error": "ID given was not a number!"
-        }
+        expected = {"wasSuccessful": False, "error": "ID given was not a number!"}
         self.assertEqual(response.json, expected)
 
         # Not a valid interaction ID
         response = self.app_client.get("/interactions/single_interaction/3")
-        expected = {
-            "wasSuccessful": False,
-            "error": "Invalid interaction ID"
-        }
+        expected = {"wasSuccessful": False, "error": "Invalid interaction ID"}
         self.assertEqual(response.json, expected)
 
     def test_itrn_by_ref(self):
@@ -245,18 +239,12 @@ def test_itrn_by_ref(self):
 
         # Input not a number
         response = self.app_client.get("/interactions/interactions_by_ref/k")
-        expected = {
-            "wasSuccessful": False,
-            "error": "ID given was not a number!"
-        }
+        expected = {"wasSuccessful": False, "error": "ID given was not a number!"}
         self.assertEqual(response.json, expected)
 
         # Not a valid paper ID
         response = self.app_client.get("/interactions/interactions_by_ref/1")
-        expected = {
-            "wasSuccessful": False,
-            "error": "Invalid paper ID"
-        }
+        expected = {"wasSuccessful": False, "error": "Invalid paper ID"}
         self.assertEqual(response.json, expected)
 
     def test_all_tags(self):
@@ -283,10 +271,7 @@ def test_search_by_tag(self):
 
         # Invalid tag name
         response = self.app_client.get("/interactions/search_by_tag/p")
-        expected = {
-            "wasSuccessful": False,
-            "error": "Invalid tag name"
-        }
+        expected = {"wasSuccessful": False, "error": "Invalid tag name"}
         self.assertEqual(response.json, expected)
 
     def test_get_all_papers(self):
@@ -318,34 +303,25 @@ def test_get_paper(self):
                     "url": "www.ncbi.nlm.nih.gov/pubmed/25736223",
                     "image_url": "https://bar.utoronto.ca/GRN_Images/25736223%232.jpg",
                     "grn_title": "Park et al.(The Plant Journal, 2015) CBF Regulon Low Temperature Network",
-                    "cyjs_layout": "{\"name\": \"breadthfirst\", \"animate\" : \"true\"}"
+                    "cyjs_layout": '{"name": "breadthfirst", "animate" : "true"}',
                 }
-            ]
+            ],
         }
         self.assertEqual(response.json, expected)
 
         # Input not an integer, a string
         response = self.app_client.get("/interactions/get_paper/p")
-        expected = {
-            "wasSuccessful": False,
-            "error": "Input number is not an integer!"
-        }
+        expected = {"wasSuccessful": False, "error": "Input number is not an integer!"}
         self.assertEqual(response.json, expected)
 
         # Input not an integer, a float
         response = self.app_client.get("/interactions/get_paper/2.2")
-        expected = {
-            "wasSuccessful": False,
-            "error": "Input number is not an integer!"
-        }
+        expected = {"wasSuccessful": False, "error": "Input number is not an integer!"}
         self.assertEqual(response.json, expected)
 
         # Invalid source ID
         response = self.app_client.get("/interactions/get_paper/3")
-        expected = {
-            "wasSuccessful": False,
-            "error": "Invalid source ID"
-        }
+        expected = {"wasSuccessful": False, "error": "Invalid source ID"}
         self.assertEqual(response.json, expected)
 
     def test_get_paper_by_agi(self):
@@ -361,10 +337,7 @@ def test_get_paper_by_agi(self):
 
         # Invalid AGI
         response = self.app_client.get("/interactions/get_paper_by_agi/AT1G00000")
-        expected = {
-            "wasSuccessful": False,
-            "error": "Invalid AGI"
-        }
+        expected = {"wasSuccessful": False, "error": "Invalid AGI"}
         self.assertEqual(response.json, expected)
 
     def test_get_paper_by_agi_pair(self):
@@ -380,10 +353,7 @@ def test_get_paper_by_agi_pair(self):
 
         # Both AGI invalid
         response = self.app_client.get("/interactions/get_paper_by_agi_pair/AT1G00000/AT2G00000")
-        expected = {
-            "wasSuccessful": False,
-            "error": "Both AGI invalid"
-        }
+        expected = {"wasSuccessful": False, "error": "Both AGI invalid"}
         self.assertEqual(response.json, expected)
 
     def test_get_all_grns(self):