merge v0.13.4 release

CHANGELOG.rst

@@ -5,6 +5,27 @@ Changelog for the SODAR project. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+v0.13.4 (2023-05-15)
+====================
+
+Changed
+-------
+
+- **Samplesheets**
+    - Update ISA-Tab template dependency to ``cubi-isa-templates`` (#1667)
+    - Allow assay tables with no materials after sample (#1676)
+
+Fixed
+-----
+
+- **General**
+    - ``django-autocomplete-light`` Docker build crash with ``whitenoise`` (#1666)
+    - Chrome install script issues (#1677)
+- **Samplesheets**
+    - Multi-file upload not working (#1670)
+    - Template create form allowing multiple ISA-Tabs per project (#1672)
+
+
 v0.13.3 (2023-05-10)
 ====================
 

config/settings/base.py

@@ -586,7 +586,7 @@ def set_logging(level=None):
 
 
 # General API settings
-SODAR_API_DEFAULT_VERSION = '0.13.3'
+SODAR_API_DEFAULT_VERSION = '0.13.4'
 SODAR_API_ALLOWED_VERSIONS = [
     '0.7.0',
     '0.7.1',
@@ -604,6 +604,7 @@ def set_logging(level=None):
     '0.13.1',
     '0.13.2',
     '0.13.3',
+    '0.13.4',
 ]
 SODAR_API_MEDIA_TYPE = 'application/vnd.bihealth.sodar+json'
 SODAR_API_DEFAULT_HOST = env.url(

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=0.12.0'}
     # Use sodar_headers for sample sheet and landing zone API endpoints
-    sodar_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar+json; version=0.13.2'}
+    sodar_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar+json; version=0.13.4'}
 
 .. note::
 

docs_manual/source/api_landingzones.rst

@@ -30,4 +30,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.13.3
+    Accept: application/vnd.bihealth.sodar+json; version=0.13.4

docs_manual/source/api_samplesheets.rst

@@ -32,4 +32,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.13.3
+    Accept: application/vnd.bihealth.sodar+json; version=0.13.4

docs_manual/source/app_samplesheets_create.rst

@@ -47,6 +47,11 @@ In case of a successful import, you will be redirected to the main sample sheets
 view, where you should see the study and assay tables for your imported sample
 sheets.
 
+.. note::
+
+    Importing ISA-Tab files with empty study or assay tables is not allowed.
+    Study tables must also contain source and sample materials.
+
 Parser Warnings
 ---------------
 

docs_manual/source/app_samplesheets_edit.rst

@@ -222,7 +222,7 @@ Names of all nodes must be filled out before the row can be saved into the
 database. Exceptions for this include unnamed processes, which will be
 autofilled, as well as *File* type materials which can remain unnamed.
 Characteristics, factor values and other metadata fields can be filled or left
-empty at tihs point. Their values can be edited freely just like any other cell
+empty at this point. Their values can be edited freely just like any other cell
 after saving the row.
 
 .. hint::

docs_manual/source/conf.py

@@ -26,7 +26,7 @@
 author = 'BIH Core Unit Bioinformatics'
 
 # The full version, including alpha/beta/rc tags
-release = '0.13.3'
+release = '0.13.4'
 
 
 # -- General configuration ---------------------------------------------------

docs_manual/source/sodar_release_notes.rst

@@ -8,6 +8,17 @@ list of changes in current and previous releases, see the
 :ref:`full changelog<sodar_changelog>`.
 
 
+v0.13.4 (2023-05-15)
+====================
+
+Release for minor sample sheet updates, maintenance and bug fixes.
+
+- Update ISA-Tab template dependency to ``cubi-isa-templates``
+- Allow assay tables with no materials after sample
+- Fix sample sheet creation form resubmit handling
+- Fix django-autocomplete-light Docker build crash
+
+
 v0.13.3 (2023-05-10)
 ====================
 

requirements/base.txt

@@ -71,6 +71,10 @@ mistune==2.0.4
 # Django-plugins (with Django v3.0+ support)
 -e git+https://github.com/mikkonie/django-plugins.git@42e86e7904e5c09f1da32173862b26843eda5dd8#egg=django-plugins
 
+# Pin to avoid issue with v3.9.5
+# See issue #166 and bihealth/sodar-core#1225
+django-autocomplete-light==3.9.4
+
 # SODAR Core
 django-sodar-core==0.12.0
 # -e git+https://github.com/bihealth/sodar-core.git@55d46268e5da4ef8a26913ce3b2c584d794d275c#egg=django-sodar-core
@@ -102,8 +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@13ec5a83c9f7871d64064bbae658a0009d4bf113#egg=cubi-isa-templates
 
 # Taskflow requirements
 tooz==3.0.0

samplesheets/forms.py

@@ -32,6 +32,25 @@
 # Local constants
 ERROR_MSG_INVALID_PATH = 'Not a valid iRODS path for this project'
 ERROR_MSG_EXISTING = 'An active request already exists for this path'
+TPL_DIR_FIELD = '__output_dir'
+
+
+class MultipleFileInput(forms.ClearableFileInput):
+    allow_multiple_selected = True
+
+
+class MultipleFileField(forms.FileField):
+    def __init__(self, *args, **kwargs):
+        kwargs.setdefault('widget', MultipleFileInput())
+        super().__init__(*args, **kwargs)
+
+    def clean(self, data, initial=None):
+        single_file_clean = super().clean
+        if isinstance(data, (list, tuple)):
+            result = [single_file_clean(d, initial) for d in data]
+        else:
+            result = single_file_clean(data, initial)
+        return result
 
 
 class SheetImportForm(forms.Form):
@@ -40,12 +59,9 @@ class SheetImportForm(forms.Form):
     directory.
     """
 
-    file_upload = forms.FileField(
+    file_upload = MultipleFileField(
         allow_empty_file=False,
         help_text='Zip archive or ISA-Tab files for a single investigation',
-        widget=forms.ClearableFileInput(
-            attrs={'allow_multiple_selected': True}
-        ),
     )
 
     class Meta:
@@ -68,21 +84,18 @@ def __init__(
 
     def clean(self):
         files = self.files.getlist('file_upload')
-
         # Zip archive upload
         if len(files) == 1:
-            file = self.cleaned_data.get('file_upload')
+            file = self.cleaned_data.get('file_upload')[0]
             try:
                 self.isa_zip = self.sheet_io.get_zip_file(file)
             except OSError as ex:
                 self.add_error('file_upload', str(ex))
                 return self.cleaned_data
-
         # Multi-file checkup
         else:
             inv_found = False
             study_found = False
-
             for file in files:
                 if file.content_type in ARCHIVE_TYPES:
                     self.add_error(
@@ -100,14 +113,12 @@ def clean(self):
                     inv_found = True
                 elif file.name.startswith('s_'):
                     study_found = True
-
             if not inv_found:
                 self.add_error(
                     'file_upload',
                     'Investigation file not found among uploaded files',
                 )
                 return self.cleaned_data
-
             if not study_found:
                 self.add_error(
                     'file_upload', 'Study file not found among uploaded files'
@@ -145,6 +156,14 @@ def save(self, *args, **kwargs):
 class SheetTemplateCreateForm(forms.Form):
     """Form for creating sample sheets from an ISA-Tab template."""
 
+    @classmethod
+    def _get_tsv_data(cls, path, file_names):
+        ret = {}
+        for n in file_names:
+            with open(os.path.join(path, n)) as f:
+                ret[n] = {'path': n, 'tsv': f.read()}
+        return ret
+
     def __init__(
         self, project=None, sheet_tpl=None, current_user=None, *args, **kwargs
     ):
@@ -157,18 +176,21 @@ def __init__(
         self.current_user = current_user
         self.sheet_tpl = sheet_tpl
         self.json_fields = []
-        self.fields['i_dir_name'] = forms.CharField(
-            label='Directory Name',
-            help_text='Investigation directory name and assay prefix',
-        )
-        self.initial['i_dir_name'] = clean_sheet_dir_name(project.title)
 
         for k, v in sheet_tpl.configuration.items():
             # Skip fields generated by cookiecutter
             if isinstance(v, str) and ('{{' in v or '{%' in v):
                 continue
-            field_kwargs = {'label': k}
-            if isinstance(v, str):
+            field_kwargs = {
+                'label': k if k != TPL_DIR_FIELD else 'Output Directory'
+            }
+            if k == TPL_DIR_FIELD:
+                field_kwargs[
+                    'help_text'
+                ] = 'Investigation directory and assay prefix'
+                self.fields[k] = forms.CharField(**field_kwargs)
+                self.initial[k] = clean_sheet_dir_name(project.title)
+            elif isinstance(v, str):
                 if not v:  # Allow empty value if default is not set
                     field_kwargs = {'required': False}
                 self.fields[k] = forms.CharField(**field_kwargs)
@@ -189,18 +211,15 @@ def __init__(
             if k in HIDDEN_SHEET_TEMPLATE_FIELDS:
                 self.fields[k].widget = forms.widgets.HiddenInput()
 
-    @classmethod
-    def _get_tsv_data(cls, path, file_names):
-        ret = {}
-        for n in file_names:
-            with open(os.path.join(path, n)) as f:
-                ret[n] = {'path': n, 'tsv': f.read()}
-        return ret
-
     def clean(self):
+        # Do not allow creating multiple investigations
+        inv = Investigation.objects.filter(project=self.project).first()
+        if inv:
+            self.add_error(None, 'Sample sheets already exist in project')
+            return self.cleaned_data
         # Force regex for dir name
-        self.cleaned_data['i_dir_name'] = clean_sheet_dir_name(
-            self.cleaned_data['i_dir_name']
+        self.cleaned_data[TPL_DIR_FIELD] = clean_sheet_dir_name(
+            self.cleaned_data[TPL_DIR_FIELD]
         )
         # Validate JSON
         for k in self.json_fields:
@@ -212,14 +231,10 @@ def clean(self):
         return self.cleaned_data
 
     def save(self):
-        extra_context = {
-            k: v for k, v in self.cleaned_data.items() if k != 'i_dir_name'
-        }
+        extra_context = {k: v for k, v in self.cleaned_data.items()}
         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
         if 'is_triplet' in self.sheet_tpl.configuration:
             extra_context['is_triplet'] = self.sheet_tpl.configuration[
                 'is_triplet'
@@ -232,12 +247,12 @@ def save(self):
                 output_dir=td,
                 no_input=True,
             )
-
             isa_data = {
                 'investigation': {},
                 'studies': {},
                 'assays': {},
             }
+            tpl_dir_name = self.cleaned_data[TPL_DIR_FIELD]
             path = os.path.join(td, tpl_dir_name)
             i_name = [n for n in os.listdir(path) if n.startswith('i_')][0]
             i_path = os.path.join(path, i_name)