Merge with upstream master

.github/workflows/check_pr_label.yml

@@ -0,0 +1,21 @@
+name: Check Label on PR
+on:
+  pull_request:
+    types: [opened, synchronize, labeled, unlabeled]
+
+jobs:
+  check-pr_label:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout PR
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags
+
+      - name: Check if the PR contains the label validation or no validation
+        id: prlabel_check
+        if: |
+          ! contains( github.event.pull_request.labels.*.name, 'validation') &&  ! contains( github.event.pull_request.labels.*.name, 'no validation')
+        run: |
+          echo "Neither 'validation' nor 'no validation' labels are present."
+          exit 1 # Exit with a failure

run_dir/design/deliveries.html

@@ -145,7 +145,13 @@ <h3>
                 <td class="bioinfo-status-expand"><a href="#bioinfo-fc-{{ project_id }}-{{ flowcell_id }}" class="bioinfo-expand">
                     <span class="fa fa-chevron-right"></span></a></td>
                 <td></td>
-                <td class="bioinfo-granularity"><samp><a class="text-decoration-none" href="/flowcells/{{ flowcell_id }}">{{ flowcell_id }}</a></samp></td>
+                {% set url_addition = "" %}
+                {% if flowcell.get("instrument_type") == "element"%}
+                  {% set url_addition = "_element" %}
+                {% elif flowcell.get("instrument_type") == "ont"%}
+                  {% set url_addition = "_ont" %}
+                {% end %}
+                <td class="bioinfo-granularity"><samp><a class="text-decoration-none" href="/flowcells{{url_addition}}/{{ flowcell_id }}">{{ flowcell_id }}</a></samp></td>
                 <td><span class="bioinfo-status badge {{ status_css.get(flowcell['flowcell_status'], 'bg-primary') }}">{{ flowcell['flowcell_status'] }}</span></td>
                   <td class="bi-run-pwf hide-incoming {% if flowcell['checklist']['total'] == flowcell['checklist']['completed'] %} table-success {% else %} table-warning {% end %}">
                     <div class="progress">

run_dir/design/project_samples_old.html

@@ -135,23 +135,34 @@ <h4>User project description
     <li class="nav-item"><a class="nav-link" href="#tab_running_notes_content" role="tab" data-toggle="tab">Running Notes</a></li>
     <li class="nav-item"><a class="nav-link" href="#tab_com_content" role="tab" data-toggle="tab" id="tab_communication">User communication</a></li>
     <li class="nav-item"><a class="nav-link" href="#tab_links_content" role="tab" data-toggle="tab">Links</a></li>
-    {% if not multiqc %}
-    <li class="nav-item" data-toggle="tooltip" data-html="true" data-placement="bottom" title="No MultiQC report available" ><a class="nav-link disabled">Open MultiQC reports</a></li>
-    {% else %}
-     <li class="nav-item dropdown">
-       <a class="nav-link dropdown-toggle" data-toggle="dropdown" href="#" role="button" aria-haspopup="true" aria-expanded="false">Open MultiQC reports</a>
-       <div class="dropdown-menu">
-         {% for key in multiqc %}
+    <li class="nav-item dropdown"><a class="nav-link dropdown-toggle" href="#" role="button" data-toggle="dropdown" id="reports_dropdown">Reports</a>
+      <div class="dropdown-menu" aria-labelledby="reports_dropdown">
+        {% if not reports%}
+          <a class="dropdown-item" href="#" disabled>No reports to show</a>
+        {% end %}
+        {% if 'multiqc' in reports%}
+        {% for key in reports['multiqc'] %}
           {% if 'qc' in key %}
             {% set rep_name = ' QC' %}
           {% else %}
             {% set rep_name = ' '+key.strip('_').capitalize() %}
           {% end %}
-         <a class="dropdown-item" href="/multiqc_report/{{ project }}?type={{ key }}" target="_blank">Open{{ rep_name }} MultiQC report</a>
+         <a class="dropdown-item" href="/multiqc_report/{{ project }}?type={{ key }}" target="_blank">MultiQC {{ rep_name }}</a>
          {% end %}
-       </div>
-     </li>
-    {% end %}
+        {% end %}
+        {% if 'project_summary' in reports %}
+          <a class="dropdown-item" href="/proj_summary_report/{{ project }}" target="_blank">Project Summary</a>
+        {% end %}
+        {% if 'sample_summary_reports' in reports %}
+        <h6 class="dropdown-header">Single Cell Sample Summary</h6>
+          {% for sample, values in reports['sample_summary_reports'].items() %}
+            {% for method, report in values.items() %}
+              <a class="dropdown-item" href="/singlecell_sample_summary_report/{{ project }}/{{ sample }}/{{ report }}" target="_blank"> {{ sample }} {{ method }} </a>
+            {% end %}
+          {% end %}
+        {% end %}
+      </div>
+    </li>
     <li class="nav-item"><a class="nav-link" href="/bioinfo/{{ project }}" target="_blank">Open bioinfo tab</a></li>
     <li class="nav-item"><a class="nav-link" href="#tab_agreements_content" role="tab" data-toggle="tab" id="tab_agreements">Agreements</a></li>
   </ul>

status/bioinfo_analysis.py

@@ -4,6 +4,7 @@
 
 import dateutil
 
+from status.reports import MultiQCReportHandler
 from status.util import SafeHandler
 
 
@@ -282,8 +283,8 @@ def get(self, project_id):
             if application in app_classes[key]:
                 application = key
                 break
-        # to check if multiqc report exists (get_multiqc() is defined in util.BaseHandler)
-        multiqc = self.get_multiqc(project_id) or ""
+
+        multiqc = MultiQCReportHandler.get_multiqc(self.application, project_id) or ""
         self.write(
             t.generate(
                 gs_globals=self.application.gs_globals,

status/clone_project.py

@@ -28,32 +28,21 @@ class LIMSProjectCloningHandler(SafeHandler):
     """
 
     def get(self, project_identifier):
-        # Check if the project_identifier matches a project id.
-        # If not, assuming it's a project name, try to get the project id from the project name,
-        # since the LIMS API only accepts project ids
-        if not re.match("^(P[0-9]{3,7})", project_identifier):
-            try:
-                projectid = (
-                    self.application.projects_db.view("projects/name_to_id")[
-                        project_identifier
-                    ]
-                    .rows[0]
-                    .value
-                )
-            except IndexError:
-                self.set_status(404)
-                return self.write({"error": "Project not found"})
-        else:
-            projectid = project_identifier
+        projectid = self.get_project_id(project_identifier)
+        if not projectid:
+            self.set_status(404)
+            return self.write({"error": "Project not found"})
+
         proj_values = self.get_project_data_from_lims(projectid, "get")
         if not proj_values:
             self.set_status(404)
             self.write({"error": "Project not found"})
             return
+
         self.set_header("Content-type", "application/json")
         self.write(proj_values)
 
-    def post(self, projectid):
+    def post(self, project_identifier):
         if not (
             self.get_current_user().is_proj_coord
             or self.get_current_user().is_any_admin
@@ -63,6 +52,11 @@ def post(self, projectid):
                 "Error: You do not have the permissions for this operation!"
             )
 
+        projectid = self.get_project_id(project_identifier)
+        if not projectid:
+            self.set_status(404)
+            return self.write({"error": "Project not found"})
+
         new_proj = self.get_project_data_from_lims(projectid, "post")
         if "error" in new_proj:
             self.set_status(400)
@@ -72,7 +66,7 @@ def post(self, projectid):
         self.set_status(201)
         self.write(new_proj)
 
-    def get_project_data_from_lims(self, projectid, type):
+    def get_project_data_from_lims(self, projectid, req_type):
         copy_udfs = {
             "Customer project reference",
             "Project Comment",
@@ -128,7 +122,7 @@ def get_project_data_from_lims(self, projectid, type):
                 udfs[udf] = existing_project.udf[udf]
         proj_values["udfs"] = udfs
 
-        if type == "get":
+        if req_type == "get":
             return proj_values
 
         else:
@@ -149,3 +143,24 @@ def get_project_data_from_lims(self, projectid, type):
                 return {"error": e.message}
 
             return {"project_id": new_project.id, "project_name": new_project.name}
+
+    def get_project_id(self, project_identifier):
+        """Return projectid for the provided identifier"""
+        # Check if the project_identifier matches a project id.
+        # If not, assuming it's a project name, try to get the project id from the project name,
+        # since the LIMS API only accepts project ids
+        projectid = None
+        if re.match("^(P[0-9]{3,7})", project_identifier):
+            projectid = project_identifier
+        else:
+            try:
+                projectid = (
+                    self.application.projects_db.view("projects/name_to_id")[
+                        project_identifier
+                    ]
+                    .rows[0]
+                    .value
+                )
+            except IndexError:
+                pass
+        return projectid

status/deliveries.py

@@ -159,6 +159,7 @@ def get(self):
 
                             # define bioinfo checklist
                             sample_data = flowcells[flowcell_id][lane_id][sample_id]
+                            instrument_type = sample_data.get("instrument_type")
                             checklist = self.__fill_checklist(sample_data)
                             if checklist["total"] and len(checklist["total"]) == len(
                                 checklist["passed"]
@@ -233,6 +234,7 @@ def get(self):
                     flowcell_status = self.__aggregate_status(flowcell_statuses)
                     runs_bioinfo[flowcell_id]["flowcell_status"] = flowcell_status
                     runs_bioinfo[flowcell_id]["checklist"] = flowcell_checklists
+                    runs_bioinfo[flowcell_id]["instrument_type"] = instrument_type
 
                     # add flowcell_status to the status_list (needed for filtering)
                     if flowcell_status not in status_list:

status/flowcell.py

@@ -470,8 +470,9 @@ def __init__(self, application, request, **kwargs):
         super(SafeHandler, self).__init__(application, request, **kwargs)
 
     def get(self, name):
-        reports_dir = self.application.minknow_reports_path
-        report_path = os.path.join(reports_dir, f"report_{name}.html")
+        report_path = os.path.join(
+            self.application.report_path["minknow"], f"report_{name}.html"
+        )
 
         self.write(open(report_path).read())
 
@@ -483,8 +484,9 @@ def __init__(self, application, request, **kwargs):
         super(SafeHandler, self).__init__(application, request, **kwargs)
 
     def get(self, name):
-        reports_dir = self.application.toulligqc_reports_path
-        report_path = os.path.join(reports_dir, f"report_{name}.html")
+        report_path = os.path.join(
+            self.application.report_path["toulligqc"], f"report_{name}.html"
+        )
 
         self.write(open(report_path).read())
 
@@ -758,10 +760,16 @@ def get(self, name):
                 barcodes=self.fetch_barcodes(name),
                 args=self.fetch_args(name),
                 has_minknow_report=os.path.exists(
-                    f"{self.application.minknow_reports_path}/report_{name}.html"
+                    os.path.join(
+                        self.application.report_path["minknow"],
+                        f"report_{name}.html",
+                    )
                 ),
                 has_toulligqc_report=os.path.exists(
-                    f"{self.application.toulligqc_reports_path}/report_{name}.html"
+                    os.path.join(
+                        self.application.report_path["tooulligqc"],
+                        f"report_{name}.html",
+                    )
                 ),
                 user=self.get_current_user(),
             )