Merge up-to-date with main

smaht-dac · Feb 27, 2025 · 407d4df · 407d4df
2 parents 29547a5 + ec57b99
commit 407d4df
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,7 +7,7 @@ smaht-portal
 Change Log
 ----------
 
-0.139.0
+0.140.0
 =======
 `PR 354: SN Release Tracker title <https://github.com/smaht-dac/smaht-portal/pull/354>`_
 * 2025-02-21 / dmichaels
@@ -18,6 +18,13 @@ Change Log
     old way of doing it can be accessed using the legacy=true URL query argument.
 * Add calcprop to File, `release_tracker_title`, which displays in order of priority `override_release_tracker_title`, `CellCultureMixture.code`, `CellLine.code`, or `Tissue.display_title` for use as a header in the Release Tracker on the home page
 
+0.139.0
+=======
+`PR 360: fix: add resources to hard-coded disabled breadcrumbs <https://github.com/smaht-dac/smaht-portal/pull/360>`_
+
+* Disable breadcrumbs for resources pages
+
+
 0.138.0
 =======
 `PR 351: FileSearchView for type=File search <https://github.com/smaht-dac/smaht-portal/pull/351>`

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "encoded"
-version = "0.139.0"
+version = "0.140.0"
 description = "SMaHT Data Analysis Portal"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"

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/static/components/PageTitleSection.js b/src/encoded/static/components/PageTitleSection.js
@@ -413,7 +413,7 @@ export class StaticPageBreadcrumbs extends React.Component {
         var inner;
 
         // Hard-coded link groups to disable
-        const breadcrumbsToDisable = ['docs', 'data', 'about'];
+        const breadcrumbsToDisable = ['docs', 'data', 'about', 'resources'];
         const shouldDisable = ancestor.identifier
             .split('/')
             .some((ancestor) => breadcrumbsToDisable.includes(ancestor));
@@ -423,7 +423,11 @@ export class StaticPageBreadcrumbs extends React.Component {
         } else if (shouldDisable) {
             inner = <span>{ancestor.display_title}</span>;
         } else {
-            inner = <a href={ancestor['@id']} className="link-underline-hover">{ancestor.display_title}</a>;
+            inner = (
+                <a href={ancestor['@id']} className="link-underline-hover">
+                    {ancestor.display_title}
+                </a>
+            );
         }
         return (
             <div

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"
             ),
         ),