update isa template dependency (#1667)

bihealth · May 11, 2023 · 82f2748 · 82f2748
1 parent 78997eb
commit 82f2748
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -8,11 +8,17 @@ Changelog for the SODAR project. Loosely follows the
 Unreleased
 ==========
 
+Changed
+-------
+
+- **Samplesheets**
+    - Update ISA-Tab template dependency to ``cubi-isa-templates`` (#1667)
+
 Fixed
 -----
 
 - **General**
-    - Docker build crash from ``django-autocomplete-light==3.9.5`` and ``whitenoise`` (#1666)
+    - ``django-autocomplete-light`` Docker build crash with ``whitenoise`` (#1666)
 
 
 v0.13.3 (2023-05-10)

diff --git a/requirements/base.txt b/requirements/base.txt
@@ -106,8 +106,9 @@ django-webpack-loader==1.6.0
 fastobo==0.12.2
 pronto==2.5.0  # For OWL conversion
 
-# CUBI-TK for sheet templates
--e git+https://github.com/bihealth/cubi-tk.git@0c0250cdfd546eaac1e0364df62213ad3c97ef7c#egg=cubi-tk
+# CUBI ISA-Tab templates
+cookiecutter==2.1.1
+-e git+https://github.com/bihealth/cubi-isa-templates.git@f71cde73648d37734414b971db13821e4d6969ff#egg=cubi-isa-templates
 
 # Taskflow requirements
 tooz==3.0.0

diff --git a/samplesheets/constants.py b/samplesheets/constants.py
@@ -10,6 +10,7 @@
 
 # Hide template fields listed here from the template UI (see issue #1443)
 HIDDEN_SHEET_TEMPLATE_FIELDS = [
+    '__output_dir',
     'a_measurement_types',
     'a_technology_types',
     'assay_technology_types',

diff --git a/samplesheets/forms.py b/samplesheets/forms.py
@@ -213,13 +213,13 @@ def clean(self):
 
     def save(self):
         extra_context = {
-            k: v for k, v in self.cleaned_data.items() if k != 'i_dir_name'
+            k: v for k, v in self.cleaned_data.items() if k != '__output_dir'
         }
         for k in self.json_fields:
             if not isinstance(extra_context[k], dict):
                 extra_context[k] = json.loads(extra_context[k])
         tpl_dir_name = self.cleaned_data['i_dir_name']
-        extra_context['i_dir_name'] = tpl_dir_name
+        extra_context['__output_dir'] = tpl_dir_name
         if 'is_triplet' in self.sheet_tpl.configuration:
             extra_context['is_triplet'] = self.sheet_tpl.configuration[
                 'is_triplet'

diff --git a/samplesheets/tests/test_ui.py b/samplesheets/tests/test_ui.py
@@ -2,7 +2,7 @@
 
 import json
 
-from cubi_tk.isa_tpl import _TEMPLATES as TK_TEMPLATES
+from cubi_isa_templates import _TEMPLATES as ISA_TEMPLATES
 
 from django.urls import reverse
 from django.utils.http import urlencode
@@ -264,7 +264,7 @@ class TestSheetTemplateCreateFormView(TestProjectSheetsVueAppBase):
 
     def test_render_hidden_fields(self):
         """Test rendering hidden fields in the sheet template form"""
-        for t in TK_TEMPLATES:
+        for t in ISA_TEMPLATES:
             url = (
                 reverse(
                     'samplesheets:template_create',

diff --git a/samplesheets/tests/test_views.py b/samplesheets/tests/test_views.py
@@ -3,7 +3,7 @@
 import json
 import os
 
-from cubi_tk.isa_tpl import _TEMPLATES as TK_TEMPLATES
+from cubi_isa_templates import _TEMPLATES as ISA_TEMPLATES
 from urllib.parse import urlencode
 from zipfile import ZipFile
 
@@ -753,7 +753,7 @@ def test_post_batch(self):
         """Test POST request with supported templates and default values"""
         templates = {
             t.name: t
-            for t in TK_TEMPLATES
+            for t in ISA_TEMPLATES
             if t.name in settings.SHEETS_ENABLED_TEMPLATES
         }
 

diff --git a/samplesheets/views.py b/samplesheets/views.py
@@ -9,7 +9,7 @@
 import requests
 import zipfile
 
-from cubi_tk.isa_tpl import _TEMPLATES as TK_TEMPLATES
+from cubi_isa_templates import _TEMPLATES as ISA_TEMPLATES
 from irods.exception import CollectionDoesNotExist
 from packaging import version
 
@@ -1155,7 +1155,7 @@ def get_context_data(self, **kwargs):
         # HACK: Skip non-working templates in cubi-tk
         for t in [
             t
-            for t in TK_TEMPLATES
+            for t in ISA_TEMPLATES
             if t.name in settings.SHEETS_ENABLED_TEMPLATES
         ]:
             templates.append(
@@ -1204,7 +1204,7 @@ class SheetTemplateCreateView(
 
     def _get_sheet_template(self):
         t_name = self.request.GET.get('sheet_tpl')
-        return {t.name: t for t in TK_TEMPLATES}[t_name]
+        return {t.name: t for t in ISA_TEMPLATES}[t_name]
 
     def get_context_data(self, *args, **kwargs):
         context = super().get_context_data(*args, **kwargs)