[GLT-4053] added user guide for completing case sign-offs (#186)

.mkdocs.yml

@@ -5,35 +5,30 @@ site_author: Genome Sequence Informatics, Ontario Institute for Cancer Research
 site_favicon: images/favicon.ico
 repo_url: https://github.com/oicr-gsi/dimsum
 
-theme: 
+theme:
   name: readthedocs
   highlightjs: true
   h1js_languages:
     - yaml
     - bash
   logo: images/dimsum_logo.svg
-
 
 nav:
   - User Manual:
-    - Overview: index.md
-    - Cases: user_manual/cases.md
-    - Common Features: user_manual/features.md
-    - QC Dashboard: user_manual/qc_dashboard.md
-    - Detail Pages: user_manual/details.md 
-    - Notifications: user_manual/notifications.md
-    - Runs Page: user_manual/runs.md
-    - Omissions Page: user_manual/omissions.md
-    - Projects Page: user_manual/projects.md
+      - Overview: index.md
+      - Cases: user_manual/cases.md
+      - Common Features: user_manual/features.md
+      - QC Dashboard: user_manual/qc_dashboard.md
+      - Detail Pages: user_manual/details.md
+      - Notifications: user_manual/notifications.md
+      - Runs Page: user_manual/runs.md
+      - Omissions Page: user_manual/omissions.md
+      - Projects Page: user_manual/projects.md
   - Guides:
-    - Complete Run Sign-Offs: user_manual/guides/sign_off_run.md
-    - Review Data Entry: user_manual/guides/review_data_entry.md
-    - Review Case Sign-Offs: user_manual/guides/review_sign_offs.md
-
-
+      - Complete Run Sign-Offs: user_manual/guides/sign_off_run.md
+      - Complete Case Sign-Offs: user_manual/guides/sign_off_case.md
+      - Review Data Entry: user_manual/guides/review_data_entry.md
+      - Review Case Sign-Offs: user_manual/guides/review_sign_offs.md
 
 extra_css:
   - css/extra.css
-
-
-

.vscode/settings.json

@@ -21,7 +21,10 @@
         "editor.formatOnSaveMode": "file",
         "editor.defaultFormatter": "esbenp.prettier-vscode"
     },
-    "editor.tabSize": 2
+    "[markdown]": {
+        "editor.formatOnSave": false // Formatting breaks multi-level lists and doesn't respect config
+    },
+    "editor.tabSize": 2,
     "java.saveActions.organizeImports": true,
     "java.sources.organizeImports.staticStarThreshold": 2
 }

docs/user_manual/guides/sign_off_case.md

@@ -0,0 +1,38 @@
+# Complete Case Sign-Offs
+
+The final three QC steps are completed at the case level. These sign-offs are recorded in another
+system (Nabu), but can be completed from Dimsum.
+
+| QC Step | Description | Requirements |
+| ------- | ----------- | ------------ |
+| Analysis Review | Confirmation that the analysis data is good | Approval for each deliverable type - clinical report and/or data release |
+| Release Approval | Approval to release deliverables to the collaborator | Approval for each deliverable type - clinical report and/or data release |
+| Release | Confirmation that a specific deliverable was delivered | Approval for each specific deliverable |
+
+When a case is stopped, release approval and release QC steps are still required in order to
+indicate that any partial results or failed deliverable have been delivered as required.
+
+1. Find and select the cases you wish to sign off.
+    1. Cases can be found on the main QC Dashboard, or on the Cases table on the Project, Donor,
+       Case, or Requisition Details pages.
+    2. Use the sorting and filter functions if necessary to help find the cases.
+    3. Select the cases using the checkboxes at the left side of the table.
+    4. You can use the checkbox in the header to select all cases currently shown in the table. If
+       there are multiple pages of cases in the table, this only selects the current page.
+    5. Note that all the options you choose will apply to every case that you select. If you wish to
+       set a different status or note for some cases, you will need to select and sign them off them
+       separately.
+2. Click the <img src="../../../images/signoff_button.png" alt="Sign Off button" width="64"> button at the top or bottom of the table
+3. In the dialog that appears, choose the QC step and deliverable type you wish to sign off and
+   click "Submit."
+
+   <img src="../../../images/case_qc_dialog_1.png" alt="Case QC Dialog" width="400">
+
+4. In the next dialog, choose the QC status and enter a note if desired. If signing off the Release
+   QC step, you will also need to specify which deliverable you wish to sign off. Click "Submit"
+   when you are done.
+
+   <img src="../../../images/case_qc_dialog_2.png" alt="Release QC Dialog" width="400">
+
+5. Another dialog should confirm that your sign-offs were saved successfully. Once you close the
+   dialog, the page will refresh to show the updated cases.