SN Submission updates (#357)

* Update samplesource columns and submission search * samplesource facets * fix test * add tissue facet * add submitted_id to columns * Update category enums * reset poetry.lock * reset poetry.lock * Update cell sample pattern
smaht-dac · Feb 27, 2025 · 4426fbe · 4426fbe
1 parent e428d18
commit 4426fbe
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Showing 8 changed files with 38 additions and 5 deletions.
diff --git a/poetry.lock b/poetry.lock
diff --git a/src/encoded/commands/write_submission_spreadsheets.py b/src/encoded/commands/write_submission_spreadsheets.py
@@ -1371,10 +1371,11 @@ def get_comment_search(property_: Property, indent: str) -> List[str]:
     
     If property is file_format, include query for specific File type
     """
+    search_text = "Use URL to search for the submitted_id or identifer of relevant items"
     if property_.search:
         if property_.name == "file_format":
-            return [f"Search:{indent}{property_.search}&valid_item_types={property_.item}"]
-        return [f"Search:{indent}{property_.search}"]
+            return [f"{search_text}:{indent}{property_.search}&valid_item_types={property_.item}"]
+        return [f"{search_text}:{indent}{property_.search}"]
     return []
 
 

diff --git a/src/encoded/schemas/assay.json b/src/encoded/schemas/assay.json
@@ -102,7 +102,9 @@
                 "Hi-C",
                 "Dip-C",
                 "Repeat Element Targeted Sequencing",
-                "ATAC-seq"
+                "ATAC-seq",
+                "NT-seq",
+                "Strand-seq"
             ]
         },
         "cell_isolation_method": {

diff --git a/src/encoded/schemas/cell_culture.json b/src/encoded/schemas/cell_culture.json
@@ -152,6 +152,9 @@
         }
     },
     "columns": {
+        "submitted_id": {
+            "title": "Submitted ID"
+        },
         "submission_centers.display_title": {
             "title": "Submitted By"
         },

diff --git a/src/encoded/schemas/cell_culture_mixture.json b/src/encoded/schemas/cell_culture_mixture.json
@@ -103,5 +103,13 @@
         "submitted_id": {
             "pattern": "^[A-Z0-9]{3,}_CELL-CULTURE-MIXTURE_[A-Z0-9-_.]{4,}$"
         }
+    },
+    "columns": {
+        "submitted_id": {
+            "title": "Submitted ID"
+        },
+        "submission_centers.display_title": {
+            "title": "Submitted By"
+        }
     }
 }
diff --git a/src/encoded/schemas/sample_source.json b/src/encoded/schemas/sample_source.json
@@ -61,5 +61,18 @@
             "type": "integer",
             "minimum": 1
         }
+    },
+    "facets": {
+        "submission_centers.display_title": {
+            "title": "Submitted By"
+        }
+    },
+    "columns": {
+        "submitted_id": {
+            "title": "Submitted ID"
+        },
+        "submission_centers.display_title": {
+            "title": "Submitted By"
+        }
     }
 }
diff --git a/src/encoded/schemas/tissue.json b/src/encoded/schemas/tissue.json
@@ -163,6 +163,12 @@
     "facets": {
         "submission_centers.display_title": {
             "title": "Submitted By"
+        },
+        "donor.display_title": {
+            "title": "Donor"
+        },
+        "status": {
+            "title": "Status"
         }
     },
     "columns": {

diff --git a/src/encoded/tests/test_write_submission_spreadsheets.py b/src/encoded/tests/test_write_submission_spreadsheets.py
@@ -601,7 +601,7 @@ def test_get_ordered_properties(
                 "Type:  string\n"
                 "Link:  Yes\n"
                 "Required:  No\n"
-                "Search:  test.url.com\n"
+                "Use URL to search for the submitted_id or identifer of relevant items:  test.url.com\n"
                 "Nested:  Yes"
             ),
         ),