update IrodsDataRequest path display (#1749)

bihealth · Sep 1, 2023 · 16eb806 · 16eb806
1 parent 311a526
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -74,6 +74,8 @@ Changed
     - Hide internal fields from ISA-Tab templates (#1698, #1733)
     - Refactor ``IrodsDataRequest`` model and tests (#1706)
     - Update ``get_sheets_url()`` helper to only handle ``Project`` objects (#1771)
+    - Display full path under assay for iRODS data requests in UI (#1749)
+    - Return full path under assay from ``IrodsDataRequest.get_short_path()`` (#1749)
 - **Taskflowbackend**
     - Move iRODS object helpers from ``LandingZoneTaskflowMixin`` (#1699)
     - Move iRODS test cleanup to ``TaskflowTestMixin.clear_irods_test_data()`` (#1722)

diff --git a/samplesheets/models.py b/samplesheets/models.py
@@ -1421,14 +1421,19 @@ def is_collection(self):
             return irods.collections.exists(self.path)
 
     def get_short_path(self):
-        """Return shortened layout-friendly path"""
-        return '/'.join(self.path.split('/')[-2:])
+        """
+        Return shortened layout-friendly path, omitting the full path to the
+        assay root.
+        """
+        irods_backend = get_backend_api('omics_irods')
+        pp_len = len(irods_backend.get_projects_path().split('/'))
+        # NOTE: This only works for assays, needs to be changed if studies are
+        #       supported
+        return '/'.join(self.path.split('/')[pp_len + 5 :])
 
     def get_assay(self):
         """Return Assay object for request path or None if not found"""
         irods_backend = get_backend_api('omics_irods')
-        if not irods_backend:
-            return None
         a_uuid = irods_backend.get_uuid_from_path(self.path, 'assay')
         return Assay.objects.filter(sodar_uuid=a_uuid).first()
 

diff --git a/samplesheets/templates/samplesheets/irods_requests.html b/samplesheets/templates/samplesheets/irods_requests.html
@@ -18,38 +18,33 @@
     table#sodar-ss-request-table tbody tr td:nth-child(4) {
       white-space: nowrap;
     }
-
     table#sodar-ss-request-table thead tr th:nth-child(3),
     table#sodar-ss-request-table tbody tr td:nth-child(3) {
       width: 150px;
     }
-
     table#sodar-ss-request-table thead tr th:nth-child(4),
     table#sodar-ss-request-table tbody tr td:nth-child(4) {
       width: 120px;
     }
 
     table#sodar-ss-request-table thead tr th:nth-child(5),
     table#sodar-ss-request-table tbody tr td:nth-child(5) {
-  width: 75px;
+      width: 75px;
     }
-
     /* Date column */
     @media screen and (max-width: 900px) {
       table#sodar-ss-request-table thead tr th:nth-child(3),
       table#sodar-ss-request-table tbody tr td:nth-child(3) {
         display: none;
       }
     }
-
     /* User column */
     @media screen and (max-width: 700px) {
       table#sodar-ss-request-table thead tr th:nth-child(2),
       table#sodar-ss-request-table tbody tr td:nth-child(2) {
         display: none;
       }
     }
-
     /* Status column */
     @media screen and (max-width: 550px) {
       table#sodar-ss-request-table thead tr th:nth-child(4),
@@ -127,9 +122,13 @@ <h3>iRODS Delete Requests</h3>
           {% for irods_request in object_list %}
             <tr class="sodar-ss-request-item">
               <td>
-                <span class="sodar-ss-request-item-path"
-                      title="Assay: {{ irods_request.get_assay.get_display_name }}"
-                      data-toggle="tooltip">
+                <a href="{{ irods_request.get_assay.get_url }}"
+                   title="{{ irods_request.get_assay.get_display_name }}"
+                   class="sodar-ss-request-item-assay-link"
+                   data-tooltip="tooltip" data-placement="top">
+                  <i class="iconify text-danger" data-icon="mdi:table-large"></i>
+                </a>
+                <span class="sodar-ss-request-item-path">
                   {{ irods_request.get_short_path }}
                 </span>
                 {% if irods_request.description %}
@@ -232,7 +231,6 @@ <h3>iRODS Delete Requests</h3>
   {# Tour content #}
   <script type="text/javascript">
     tourEnabled = true;
-
     tour.addStep('irods_req_info', {
         title: 'iRODS Delete Requests',
         text: 'In this view you can manage requests for deleting specific ' +
@@ -241,7 +239,6 @@ <h3>iRODS Delete Requests</h3>
         advanceOn: '.docs-link click',
         showCancelLink: true
     });
-
     tour.addStep('irods_req_contributor', {
         title: 'As Project Contributor',
         text: 'As a project contributor, you can see your own requests along ' +
@@ -252,7 +249,6 @@ <h3>iRODS Delete Requests</h3>
         advanceOn: '.docs-link click',
         showCancelLink: true
     });
-
     tour.addStep('irods_req_owner', {
         title: 'As Project Owner or Delegate',
         text: 'As a project owner or delegate, you see a list of all active ' +
@@ -264,8 +260,15 @@ <h3>iRODS Delete Requests</h3>
         advanceOn: '.docs-link click',
         showCancelLink: true
     });
-
     if ($('.sodar-ss-request-item').length) {
+        tour.addStep('irods_req_assay', {
+            title: 'Request assay',
+            text: 'This icon displays the assay for the request and links to ' +
+                  'it in the main sample sheets view.',
+            attachTo: '.sodar-ss-request-item-assay-link right',
+            advanceOn: '.docs-link click',
+            showCancelLink: true
+        });
         tour.addStep('irods_req_path', {
             title: 'Request Path',
             text: 'The partial path of the request is displayed here, ' +
@@ -277,7 +280,6 @@ <h3>iRODS Delete Requests</h3>
             advanceOn: '.docs-link click',
             showCancelLink: true
         });
-
         if ($('.sodar-ss-request-item-description').length) {
             tour.addStep('irods_req_desc', {
                 title: 'Request Description',
@@ -289,15 +291,13 @@ <h3>iRODS Delete Requests</h3>
                 showCancelLink: true
              });
          }
-
         tour.addStep('irods_req_status', {
             title: 'Request Status',
             text: 'The current status of the request is displayed here.',
             attachTo: '.sodar-ss-request-item-status left',
             advanceOn: '.docs-link click',
             showCancelLink: true
         });
-
         tour.addStep('irods_req_dropdown', {
             title: 'Request Dropdown',
             text: 'This dropdown contains links to actions the user is ' +
@@ -306,7 +306,6 @@ <h3>iRODS Delete Requests</h3>
             advanceOn: '.docs-link click',
             showCancelLink: true
         });
-
         if ($('.sodar-ss-request-item-check').length) {
             tour.addStep('irods_req_check', {
                 title: 'Batch Accepting or Rejecting Requests',
@@ -323,7 +322,6 @@ <h3>iRODS Delete Requests</h3>
              });
          }
     }
-
     tour.addStep('irods_req_ops_dropdown', {
         title: 'Request Operations Dropdown',
         text: 'This dropdown lists operations you can perform on requests. ' +
@@ -334,7 +332,6 @@ <h3>iRODS Delete Requests</h3>
         advanceOn: '.docs-link click',
         showCancelLink: true
     });
-
     tour.addStep('sheets_btn_back', {
         title: 'Back to Project Sample Sheets',
         text: 'Click on this button to return to the project sample sheets.',
@@ -343,5 +340,4 @@ <h3>iRODS Delete Requests</h3>
         showCancelLink: true
     });
   </script>
-
 {% endblock javascript %}