Merge branch 'dev' into landingzone

CHANGELOG.rst

@@ -8,19 +8,36 @@ Changelog for the SODAR project. Loosely follows the
 Unreleased
 ==========
 
+Added
+-----
+
+- **Samplesheets**
+    User setting for study and assay table height (#1283)
+
 Changed
 -------
 
 - **General**
     - Upgrade to django-sodar-core v0.13.0 (#1617)
     - Upgrade to python-irodsclient v1.1.8 (#1538)
+- **Samplesheets**
+    - Sample sheet table viewport background color (#1692)
+    - Contract sheet table height to fit content (#1693)
 
 Fixed
 -----
 
+- **Ontologyaccess**
+    - Batch import tests failing from forbidden obolibrary access (#1694)
 - **Samplesheets**
     - ``perform_project_sync()`` crash with no iRODS collections created (#1687)
 
+Removed
+-------
+
+- **Samplesheets**
+    - ``SHEETS_TABLE_HEIGHT`` Django setting (#1283)
+
 
 v0.13.4 (2023-05-15)
 ====================

config/settings/base.py

@@ -748,8 +748,6 @@ def set_logging(level=None):
 SHEETS_ENABLE_CACHE = True
 # iRODS file query limit
 SHEETS_IRODS_LIMIT = env.int('SHEETS_IRODS_LIMIT', 50)
-# Study/assay table height
-SHEETS_TABLE_HEIGHT = env.int('SHEETS_TABLE_HEIGHT', 400)
 # Minimum edit config version
 SHEETS_CONFIG_VERSION = '0.8.0'
 # Min default column width

docs_manual/source/admin_settings.rst

@@ -154,8 +154,6 @@ Sample Sheets Settings
     Allow critical altamISA warnings on import (boolean).
 ``SHEETS_IRODS_LIMIT``
     iRODS file query limit (integer).
-``SHEETS_TABLE_HEIGHT``
-    Default study/assay table height.
 ``SHEETS_MIN_COLUMN_WIDTH``
     Minimum default column width in study/assay tables (integer).
 ``SHEETS_MAX_COLUMN_WIDTH``

docs_manual/source/sodar_release_notes.rst

@@ -13,6 +13,8 @@ v0.14.0 (WIP)
 
 Major feature update.
 
+- Add user setting for maximum sample sheet table height
+- Contract sample sheet table height to fit content in browsing mode
 - Upgrade to SODAR Core v0.13.0
 
 

ontologyaccess/tests/test_io.py

@@ -3,8 +3,6 @@
 import fastobo
 import os
 
-from urllib.request import urlopen
-
 from test_plus.test import TestCase
 
 from ontologyaccess.io import OBOFormatOntologyIO
@@ -23,25 +21,14 @@
     'is_obsolete': 'EX:0000006',
     'no_def': 'EX:0000007',
 }
-OBO_BATCH_URLS = [
-    'http://purl.obolibrary.org/obo/hp.obo',
-    'http://purl.obolibrary.org/obo/ms.obo',
-    'http://purl.obolibrary.org/obo/pato.obo',
-    # 'http://purl.obolibrary.org/obo/cl.obo',  # TODO: Fix (see #1064)
-    # TODO: Also see issue #944
-]
-OWL_BATCH_URLS = [
-    'http://purl.obolibrary.org/obo/duo.owl',
-    'http://data.bioontology.org/ontologies/ROLEO/submissions/3/download?'
-    'apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb',
-]
 
 
 class TestOBOFormatOntologyIO(TestCase):
     """Tests for the OBOFormatOntologyIO class"""
 
     def setUp(self):
         self.obo_io = OBOFormatOntologyIO()
+        self.req_headers = {'User-Agent': 'Mozilla'}
 
     def test_import(self):
         """Test importing an example ontology"""
@@ -74,27 +61,7 @@ def test_import(self):
         term = ontology.get_term_by_id(EX_OBO_TERM_IDS['no_def'])
         self.assertIsNone(term.definition)
 
-    def test_import_batch(self):
-        """Test importing ontologies in a batch (this may take a while)"""
-        for url in OBO_BATCH_URLS:
-            self.assertEqual(OBOFormatOntology.objects.count(), 0)
-            self.assertEqual(OBOFormatOntologyTerm.objects.count(), 0)
-
-            file_name = url.split('/')[-1]
-            obo_doc = fastobo.load(urlopen(url))
-            ontology = self.obo_io.import_obo(
-                obo_doc=obo_doc, name=file_name.split('.')[0].upper(), file=url
-            )
-
-            self.assertIsNotNone(ontology, msg=file_name)
-            self.assertEqual(
-                OBOFormatOntology.objects.count(), 1, msg=file_name
-            )
-            self.assertNotEqual(
-                OBOFormatOntologyTerm.objects.count(), 0, msg=file_name
-            )
-            ontology.delete()
-
+    '''
     def test_import_batch_owl(self):
         """Test importing OWL ontologies in batch (this may take a while)"""
         for url in OWL_BATCH_URLS:
@@ -116,5 +83,7 @@ def test_import_batch_owl(self):
                 OBOFormatOntologyTerm.objects.count(), 0, msg=file_name
             )
             ontology.delete()
+    '''
 
-    # TODO: Test import_omim()
+    # TODO: Test importing OWL with a local file
+    # TODO: Test import_omim() with a local file

samplesheets/plugins.py

@@ -71,7 +71,6 @@
     'SHEETS_MAX_COLUMN_WIDTH',
     'SHEETS_MIN_COLUMN_WIDTH',
     'SHEETS_SYNC_INTERVAL',
-    'SHEETS_TABLE_HEIGHT',
     'SHEETS_VERSION_PAGINATION',
     'SHEETS_IGV_OMIT_BAM',
     'SHEETS_IGV_OMIT_VCF',
@@ -173,6 +172,16 @@ class ProjectAppPlugin(
             'source project',
             'user_modifiable': True,
         },
+        'sheet_table_height': {
+            'scope': SODAR_CONSTANTS['APP_SETTING_SCOPE_USER'],
+            'type': 'INTEGER',
+            'label': 'Sample sheet table height',
+            'options': [250, 400, 600, 800],
+            'default': 400,
+            'description': 'Maximum display height for study and assay tables '
+            'in pixels',
+            'user_modifiable': True,
+        },
         'public_access_ticket': {
             'scope': SODAR_CONSTANTS['APP_SETTING_SCOPE_PROJECT'],
             'type': 'STRING',

samplesheets/tests/test_views_ajax.py

@@ -55,7 +55,12 @@
 )
 from samplesheets.utils import get_node_obj, get_ext_link_labels
 from samplesheets.views import SheetImportMixin
-from samplesheets.views_ajax import ALERT_ACTIVE_REQS
+from samplesheets.views_ajax import (
+    ALERT_ACTIVE_REQS,
+    RENDER_HEIGHT_HEADERS,
+    RENDER_HEIGHT_ROW,
+    RENDER_HEIGHT_SCROLLBAR,
+)
 
 
 conf_api = SheetConfigAPI()
@@ -225,7 +230,6 @@ def test_get(self):
             'external_link_labels': get_ext_link_labels(),
             'ontology_url_template': settings.SHEETS_ONTOLOGY_URL_TEMPLATE,
             'ontology_url_skip': settings.SHEETS_ONTOLOGY_URL_SKIP,
-            'table_height': settings.SHEETS_TABLE_HEIGHT,
             'min_col_width': settings.SHEETS_MIN_COLUMN_WIDTH,
             'max_col_width': settings.SHEETS_MAX_COLUMN_WIDTH,
             'allow_editing': app_settings.get_default(
@@ -329,7 +333,6 @@ def test_no_sheets(self):
             'irods_webdav_enabled': settings.IRODS_WEBDAV_ENABLED,
             'irods_webdav_url': settings.IRODS_WEBDAV_URL,
             'external_link_labels': None,
-            'table_height': settings.SHEETS_TABLE_HEIGHT,
             'min_col_width': settings.SHEETS_MIN_COLUMN_WIDTH,
             'max_col_width': settings.SHEETS_MAX_COLUMN_WIDTH,
             'allow_editing': app_settings.get_default(
@@ -507,6 +510,21 @@ def test_get(self):
         self.assertNotIn('shortcuts', ret_data['tables']['study'])
         self.assertEqual(len(ret_data['tables']['assays']), 1)
         self.assertIn('uuid', ret_data['tables']['study']['table_data'][0][0])
+        self.assertIn('table_heights', ret_data)
+        self.assertEqual(
+            ret_data['table_heights']['study'],
+            RENDER_HEIGHT_HEADERS
+            + len(ret_data['tables']['study']['table_data']) * RENDER_HEIGHT_ROW
+            + RENDER_HEIGHT_SCROLLBAR,
+        )
+        a_uuid = str(self.assay.sodar_uuid)
+        self.assertEqual(
+            ret_data['table_heights']['assays'][a_uuid],
+            RENDER_HEIGHT_HEADERS
+            + len(ret_data['tables']['assays'][a_uuid]['table_data'])
+            * RENDER_HEIGHT_ROW
+            + RENDER_HEIGHT_SCROLLBAR,
+        )
         self.assertIn('display_config', ret_data)
         self.assertNotIn('edit_context', ret_data)
 
@@ -530,6 +548,15 @@ def test_get_edit(self):
         self.assertNotIn('shortcuts', ret_data['tables']['study'])
         self.assertEqual(len(ret_data['tables']['assays']), 1)
         self.assertIn('uuid', ret_data['tables']['study']['table_data'][0][0])
+        self.assertIn('table_heights', ret_data)
+        default_height = app_settings.get(
+            APP_NAME, 'sheet_table_height', user=self.user
+        )
+        self.assertEqual(ret_data['table_heights']['study'], default_height)
+        a_uuid = str(self.assay.sodar_uuid)
+        self.assertEqual(
+            ret_data['table_heights']['assays'][a_uuid], default_height
+        )
         self.assertIn('display_config', ret_data)
         self.assertIn('study_config', ret_data)
         self.assertIn('edit_context', ret_data)
@@ -557,7 +584,7 @@ def test_get_track_hubs(self):
                 )
             )
         self.assertEqual(response.status_code, 200)
-        # TODO fill out ... assays are not yet tested, as well as shortcuts
+        # TODO: Assert track hub data
 
     def test_get_study_cache(self):
         """Test cached study table creation on retrieval"""

samplesheets/views_ajax.py

@@ -69,6 +69,10 @@
     'label': 'extract_label',
     'performer': 'performer',
 }
+# Approximate magic numbers for header/row height
+RENDER_HEIGHT_HEADERS = 79
+RENDER_HEIGHT_ROW = 39
+RENDER_HEIGHT_SCROLLBAR = 12
 
 ALERT_ACTIVE_REQS = (
     'Active iRODS delete requests in this project require your attention. '
@@ -315,7 +319,6 @@ def get(self, request, *args, **kwargs):
             'irods_webdav_enabled': settings.IRODS_WEBDAV_ENABLED,
             'irods_webdav_url': get_webdav_url(project, request.user),
             'external_link_labels': None,
-            'table_height': settings.SHEETS_TABLE_HEIGHT,
             'min_col_width': settings.SHEETS_MIN_COLUMN_WIDTH,
             'max_col_width': settings.SHEETS_MAX_COLUMN_WIDTH,
             'allow_editing': app_settings.get(
@@ -498,12 +501,27 @@ def get(self, request, *args, **kwargs):
 class StudyTablesAjaxView(SODARBaseProjectAjaxView):
     """View to retrieve study tables built from the sample sheet graph"""
 
-    def get_permission_required(self):
-        """Override get_permisson_required() to provide the approrpiate perm"""
-        if bool(self.request.GET.get('edit')):
-            return 'samplesheets.edit_sheet'
+    def _get_table_height(self, table, user, edit):
+        """
+        Return table height in pixels.
 
-        return 'samplesheets.view_sheet'
+        :param table: Study or assay render table
+        :param user: User object making the request
+        :param edit: Edit mode enabled (boolean)
+        :return: Integer
+        """
+        default_height = app_settings.get(
+            APP_NAME, 'sheet_table_height', user=user
+        )
+        if edit:  # When editing we always set tables to fixed user setting
+            return default_height
+        # Else limit return value to user setting
+        return min(
+            RENDER_HEIGHT_HEADERS
+            + RENDER_HEIGHT_SCROLLBAR
+            + len(table['table_data']) * RENDER_HEIGHT_ROW,
+            default_height,
+        )
 
     def _get_display_config(self, investigation, user, sheet_config=None):
         """Get or create display configuration for an investigation"""
@@ -567,6 +585,12 @@ def _get_display_config(self, investigation, user, sheet_config=None):
             )
         return display_config
 
+    def get_permission_required(self):
+        """Override get_permisson_required() to provide the approrpiate perm"""
+        if bool(self.request.GET.get('edit')):
+            return 'samplesheets.edit_sheet'
+        return 'samplesheets.view_sheet'
+
     def get(self, request, *args, **kwargs):
         from samplesheets.plugins import get_irods_content
 
@@ -608,6 +632,19 @@ def get(self, request, *args, **kwargs):
             ret_data['render_error'] = str(ex)
             return Response(ret_data, status=200)
 
+        # Add table heights
+        ret_data['table_heights'] = {
+            'study': self._get_table_height(
+                ret_data['tables']['study'], request.user, edit
+            ),
+            'assays': {},
+        }
+        for k, v in ret_data['tables']['assays'].items():
+            ret_data['table_heights']['assays'][k] = self._get_table_height(
+                v, request.user, edit
+            )
+        # logger.debug('Table heights = {}'.format(ret_data['table_heights']))
+
         # Get iRODS content if NOT editing and collections have been created
         if not edit:
             logger.debug('Retrieving iRODS content for study..')
@@ -639,7 +676,6 @@ def get(self, request, *args, **kwargs):
                 'samples': {},
                 'protocols': [],
             }
-
             # Add sample info
             s_assays = {}
             for assay in study.assays.all().order_by('pk'):
@@ -660,7 +696,6 @@ def get(self, request, *args, **kwargs):
                     if sample.unique_name in s_assays
                     else [],
                 }
-
             # Add Protocol info
             for protocol in Protocol.objects.filter(study=study).order_by(
                 'name'

samplesheets/vueapp/src/App.vue

@@ -50,6 +50,7 @@
             :grid-options="gridOptions.study"
             :grid-uuid="currentStudyUuid"
             :row-data="rowData.study"
+            :table-height="tableHeights.study"
             :initial-filter="initialFilter">
         </sheet-table>
 
@@ -80,6 +81,7 @@
               :grid-options="gridOptions.assays[assayUuid]"
               :grid-uuid="assayUuid"
               :row-data="rowData.assays[assayUuid]"
+              :table-height="tableHeights.assays[assayUuid]"
               :initial-filter="initialFilter">
           </sheet-table>
         </span>
@@ -271,6 +273,7 @@ export default {
       sampleColId: null,
       sampleIdx: null,
       sourceColSpan: null,
+      tableHeights: null,
       unsavedRow: null, // Info of currently unsaved row, or null if none
       updatingRow: false, // Row update in progress (bool)
       unsavedData: false, // Other updated data (bool)
@@ -415,15 +418,15 @@ export default {
         if (this.editMode && 'study_config' in data) {
           this.editStudyConfig = data.study_config
         }
-
         // Editing: Get edit context
         if (this.editMode && 'edit_context' in data) {
           this.editContext = data.edit_context
         }
 
+        // Get table heights
+        this.tableHeights = data.table_heights
         // Get display config
         this.studyDisplayConfig = data.display_config
-
         // Store colspan
         this.sourceColSpan = data.tables.study.top_header[0].colspan
 
@@ -1314,6 +1317,10 @@ export default {
   border: 0 !important;
 }
 
+.ag-body-viewport {
+  background-color: #eee;
+}
+
 .ag-header-group-cell {
   border-right: 1px solid #dfdfdf !important;
 }