merge v0.15.1 release

CHANGELOG.rst

@@ -5,6 +5,25 @@ Changelog for the SODAR project. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+v0.15.1 (2024-09-12)
+====================
+
+Changed
+-------
+
+- **Samplesheets**
+    - Upgrade Vue app dependencies (#1986)
+
+Fixed
+-----
+
+- **Landingzones**
+    - Invalid CSS classes set by zone status update (#1995)
+- **Samplesheets**
+    - ``generic`` assay plugin inline links pointing to ``ResultsReports`` (#1982)
+    - ``generic`` assay plugin cache update crash with row path built from ontology column (#1984)
+
+
 v0.15.0 (2024-08-08)
 ====================
 

config/settings/base.py

@@ -611,7 +611,7 @@ def set_logging(level=None):
 
 
 # General API settings
-SODAR_API_DEFAULT_VERSION = '0.15.0'
+SODAR_API_DEFAULT_VERSION = '0.15.1'
 SODAR_API_ALLOWED_VERSIONS = [
     '0.7.0',
     '0.7.1',
@@ -634,6 +634,7 @@ def set_logging(level=None):
     '0.14.1',
     '0.14.2',
     '0.15.0',
+    '0.15.1',
 ]
 SODAR_API_MEDIA_TYPE = 'application/vnd.bihealth.sodar+json'
 SODAR_API_DEFAULT_HOST = env.url(

docs_manual/source/api_documentation.rst

@@ -45,7 +45,7 @@ expected version.
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.15.0
+    Accept: application/vnd.bihealth.sodar+json; version=0.15.1
 
 Specific sections of the SODAR API may require their own accept header. See the
 exact header requirement in the respective documentation on each section of the

docs_manual/source/api_examples.rst

@@ -43,7 +43,7 @@ the SODAR API:
     # Use core_headers for project management API endpoints
     core_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar-core+json; version=0.13.4'}
     # Use sodar_headers for sample sheet and landing zone API endpoints
-    sodar_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar+json; version=0.15.0'}
+    sodar_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar+json; version=0.15.1'}
 
 .. note::
 

docs_manual/source/api_irodsinfo.rst

@@ -22,4 +22,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.15.0
+    Accept: application/vnd.bihealth.sodar+json; version=0.15.1

docs_manual/source/api_landingzones.rst

@@ -32,4 +32,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.15.0
+    Accept: application/vnd.bihealth.sodar+json; version=0.15.1

docs_manual/source/api_samplesheets.rst

@@ -68,4 +68,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.15.0
+    Accept: application/vnd.bihealth.sodar+json; version=0.15.1

docs_manual/source/conf.py

@@ -26,7 +26,7 @@
 author = 'BIH Core Unit Bioinformatics'
 
 # The full version, including alpha/beta/rc tags
-release = '0.15.0'
+release = '0.15.1'
 
 
 # -- General configuration ---------------------------------------------------

docs_manual/source/metadata_advanced.rst

@@ -179,7 +179,7 @@ investigation file.
 - Inline links
     * Comments define semicolon-separated lists of columns to be linked to
       collections.
-    * *SODAR Assay Link Results* |rarr| ``ResultsReports``
+    * *SODAR Assay Link ResultsReports* |rarr| ``ResultsReports``
     * *SODAR Assay Link MiscFiles* |rarr| ``MiscFiles``
     * *SODAR Assay Link Row* |rarr| ``RowPath``
     * For example:

docs_manual/source/sodar_release_notes.rst

@@ -8,6 +8,16 @@ list of changes in current and previous releases, see the
 :ref:`full changelog<sodar_changelog>`.
 
 
+v0.15.1 (2024-09-12)
+====================
+
+Release for minor updates, maintenance and bug fixes.
+
+- Fix generic assay plugin issues
+- Upgrade critical dependencies
+- Minor updates and bug fixes
+
+
 v0.15.0 (2024-08-08)
 ====================
 

landingzones/static/landingzones/js/landingzones.js

@@ -51,7 +51,8 @@ var updateZoneStatus = function() {
                     ) {
                         statusTd.text(zoneStatus);
                         statusTd.removeClass();
-                        statusTd.addClass(statusStyles[zoneStatus] + ' text-white');
+                        statusTd.addClass(
+                            'sodar-lz-zone-status ' + statusStyles[zoneStatus] + ' text-white');
                         statusInfoSpan.text(zoneStatusInfo);
                         if (['PREPARING', 'VALIDATING', 'MOVING', 'DELETING'].includes(zoneStatus)) {
                             statusTd.append(

samplesheets/assayapps/generic/plugins.py

@@ -12,7 +12,7 @@
 
 # Local constants
 APP_NAME = 'samplesheets.assayapps.generic'
-RESULTS_COMMENT = 'SODAR Assay Link Results'
+RESULTS_COMMENT = 'SODAR Assay Link ResultsReports'
 MISC_FILES_COMMENT = 'SODAR Assay Link MiscFiles'
 DATA_COMMENT_PREFIX = 'SODAR Assay Row Path'
 DATA_LINK_COMMENT = 'SODAR Assay Link Row'
@@ -65,9 +65,13 @@ def _link_from_comment(cell, header, top_header, target_cols, url):
             return True
         # Special case for Material Names
         if (
-            top_header['value']
-            in th.DATA_FILE_HEADERS + th.MATERIAL_NAME_HEADERS
-        ) and (header['value'] == 'Name'):
+            (
+                top_header['value']
+                in th.DATA_FILE_HEADERS + th.MATERIAL_NAME_HEADERS
+            )
+            and top_header['value'].lower() in target_cols
+            and (header['value'] == 'Name')
+        ):
             cell['link'] = f"{url}/{cell['value']}"
             return True
         # Handle everything else
@@ -83,11 +87,11 @@ def _get_col_value(cls, target_col, row, table):
         """
         Return value of last matched column.
 
-        :param target_col: Column name to look for
+        :param target_col: Column name string to look for.
         :param row: List of dicts (a row returned by SampleSheetTableBuilder)
         :param table: Full table with headers (dict returned by
                       SampleSheetTableBuilder)
-        :return: String with cell value of last matched column
+        :return: String with cell value of last matched column.
         """
         # Returns last match of row
         value = None
@@ -96,7 +100,12 @@ def _get_col_value(cls, target_col, row, table):
                 header = table['field_header'][i]
                 if header['value'].lower() == target_col.lower():
                     value = row[i]['value']
-        return value
+
+        if isinstance(value, str):
+            return value
+        elif isinstance(value, list) and len(value) == 1:  # OntologyTermRefs
+            return value[0]['name']
+        return None
 
     def get_row_path(self, row, table, assay, assay_path):
         """

samplesheets/vueapp/package.json

@@ -1,6 +1,6 @@
 {
   "name": "samplesheets",
-  "version": "0.15.0",
+  "version": "0.15.1",
   "private": true,
   "scripts": {
     "serve": "vue-cli-service serve",