remove SPECIAL_FILE_LINK_HEADERS hack, refactor (#817, #1641)

bihealth · Apr 21, 2023 · d1afebf · d1afebf
1 parent 49b0a38
commit d1afebf
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Showing 3 changed files with 26 additions and 11 deletions.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -8,7 +8,26 @@ Changelog for the SODAR project. Loosely follows the
 Unreleased
 ==========
 
-TODO
+Added
+-----
+
+- **Samplesheets**
+    - ``ProjectIrodsFileListAPIView`` in REST API (#1619)
+    - ``SIMPLE_LINK_TEMPLATE`` helper for simple link creation
+
+Changed
+-------
+
+- **General**
+    - Update URL patterns to use path (#1631)
+- **Samplesheets**
+    - Refactor ``meta_ms`` to remove ``SPECIAL_FILE_LINK_HEADERS`` use (#1641)
+
+Removed
+-------
+
+- **Samplesheets**
+    - ``SPECIAL_FILE_LINK_HEADERS`` hack (#817, #1641)
 
 
 v0.13.2 (2023-04-18)

diff --git a/samplesheets/assayapps/meta_ms/plugins.py b/samplesheets/assayapps/meta_ms/plugins.py
@@ -4,6 +4,7 @@
 
 # from samplesheets.models import GenericMaterial, Process
 from samplesheets.plugins import SampleSheetAssayPluginPoint
+from samplesheets.rendering import SIMPLE_LINK_TEMPLATE
 from samplesheets.utils import get_top_header
 from samplesheets.views import MISC_FILES_COLL, RESULTS_COLL
 
@@ -87,7 +88,6 @@ def update_row(self, row, table, assay):
             if not top_header or i >= th_colspan:
                 top_header = get_top_header(table, i)
                 th_colspan += top_header['colspan']
-
             # Data files
             if (
                 header['obj_cls'] == 'GenericMaterial'
@@ -103,16 +103,15 @@ def update_row(self, row, table, assay):
                 row[i]['link'] = (
                     base_url + '/' + coll_name + '/' + row[i]['value']
                 )
-
             # Report file links within processes
             elif (
                 header['obj_cls'] == 'Process'
                 and header['value'].lower() == 'report file'
             ):
-                row[i]['link'] = (
-                    base_url + '/' + RESULTS_COLL + '/' + row[i]['value']
+                row[i]['value'] = SIMPLE_LINK_TEMPLATE.format(
+                    label=row[i]['value'],
+                    url=base_url + '/' + RESULTS_COLL + '/' + row[i]['value'],
                 )
-
         return row
 
     def get_shortcuts(self, assay):

diff --git a/samplesheets/rendering.py b/samplesheets/rendering.py
@@ -80,9 +80,8 @@
     'factor_values',
     'parameter_values',
 ]
-# HACK: Special cases for inline file linking (see issue #817)
-SPECIAL_FILE_LINK_HEADERS = ['report file']
 STUDY_TABLE_CACHE_ITEM = 'sheet/tables/study/{study}'
+SIMPLE_LINK_TEMPLATE = '{label} <{url}>'
 
 
 # Table building ---------------------------------------------------------------
@@ -222,9 +221,7 @@ def _add_header(self, name, header_type=None, obj=None):
             header['col_type'] = 'DATE'
         elif name.lower() == 'external links':
             header['col_type'] = 'EXTERNAL_LINKS'
-        elif (
-            name.lower() == 'name' and header['item_type'] == 'DATA'
-        ) or name.lower() in SPECIAL_FILE_LINK_HEADERS:  # HACK for issue #817
+        elif name.lower() == 'name' and header['item_type'] == 'DATA':
             header['col_type'] = 'LINK_FILE'
         # Recognize ONTOLOGY by headers
         elif obj.is_ontology_field(name, header_type):