Merge pull request #18 from ScilifelabDataCentre/develop

New collection added

.github/workflows/dockerhub.yml

@@ -0,0 +1,75 @@
+---
+# Build and publish docker image(s)
+# Publishing to Dockerhub requires a username and token
+# as the secrets DOCKERHUB_USERNAME and DOCKERHUB_TOKEN
+# remember to change repo-name and set dockerfile(s)/image name(s) in the matrix
+
+name: Publish Docker image
+on:
+  # generate image whenever there is a push to the listed branches
+  push:
+    branches:
+      - main
+      - develop
+  # generate images for releases, using the tag name
+  # the newest one will be latest as well
+  release:
+    types: [published]
+jobs:
+  push_to_registry:
+    # only generate images when in the named repo
+    # (to avoid running the action in forks)
+    if: github.repository == 'ScilifelabDataCentre/covid-sample-collection-database'
+    name: Publish Docker Image
+    runs-on: ubuntu-latest
+    # Cancel earlier job if there is a new one for the same branch/release
+    concurrency:
+      group: ${{ github.ref }}-docker-build
+      cancel-in-progress: true
+    # Define the images/tags to build; will run in parallell
+    strategy:
+      matrix:
+        include:
+          - dockerfile: Dockerfiles/Dockerfile
+            images: |
+              docker.io/scilifelabdatacentre/covid-sample-collection-database
+              ghcr.io/scilifelabdatacentre/covid-sample-collection-database
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+      # only needed when publishing to Dockerhub
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          # available in scilifelabdatacentre, ask admin for help
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      # only needed when publishing to Github (ghcr.io)
+      - name: Log in to Github Container Repository
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          # will run as the user who triggered the action, using its token
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Docker Meta
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ matrix.images }}
+          tags: |
+            type=ref,event=branch
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+      - name: Build and Publish
+        uses: docker/build-push-action@v3
+        with:
+          file: ${{ matrix.dockerfile }}
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfiles/Dockerfile

@@ -1,5 +1,6 @@
-FROM klakegg/hugo:0.83.1-onbuild AS build
+FROM klakegg/hugo:0.104.3-ubuntu-onbuild AS build
 
-FROM nginx:1.21-alpine
-COPY Dockerfiles/default.conf /etc/nginx/conf.d/default.conf
+FROM nginxinc/nginx-unprivileged:alpine
 COPY --from=build /target /usr/share/nginx/html
+
+EXPOSE 8080

config.yaml

@@ -3,7 +3,7 @@ languageCode: "en-us"
 title: "The Swedish COVID-19 Sample Collection Database"
 params:
   title: "The Swedish COVID-19 Sample Collection Database"
-  description: "The Swedish COVID-19 Sample Collection Database, part of the COVID-19 Data Portal Sweden"
+  description: "The Swedish COVID-19 Sample Collection Database, part of the Swedish COVID-19 and Pandemic Preparedness Portal"
 markup:
   goldmark:
     renderer:

content/collections/NAT/1.md

@@ -0,0 +1,38 @@
+---
+id: c19dp:collection:SE_NAT_1
+biobank: c19dp:biobank:SE_NAT
+name: National sample collection stored at National Pandemic Center (NPC)
+acronym:
+parent_collection:
+local_id: N/A
+bbmri_id:
+country: SE
+description: Personnel within Sweden's regions have worked intensively with both sample collection and handling of COVID-19-related samples. A large amount of samples are thereafter sequenced at the National Pandemic Center (NPC), Karolinska Institutet (KI; Stockholm), which also results in an extensive sample collection stored at the NPC. The regions are legally responsible for "their" subset of the sample collection. In theory, the sample collection at NPC is an enormous resource for research.
+website_url:
+bioresource_reference:
+ethics_id: N/A
+sampling_startdate: 2020-03-01T11:00:00+0000
+sampling_enddate:
+storage_duration:
+collection_type: [Hospital, Disease specific, Sample]
+collection_category: "National sample collection"
+data_categories: [Biological samples, Medical records]
+order_of_magnitude: 6
+timestamp: 2022-11-02T11:00:00+0000
+biobank_label:
+sub_collections:
+diagnosis_available: []
+order_of_magnitude_donors:
+autopsy:
+minors:
+inclusion_criteria:
+exclusion_criteria:
+materials: [Nasal swab,Throat swab]
+head_firstname:
+head_lastname:
+head_role:
+display_collection_contact: FALSE
+contact: c19dp:biobank:SE_NAT
+publications_list:
+contact_priority: 1
+---

content/collections/NAT/_index.md

@@ -0,0 +1,17 @@
+---
+id: c19dp:biobank:SE_NAT
+name: National sample collections
+acronym: National sample collections
+juridical_person: NA
+country: SE
+biobank_sverige: TRUE
+ivo_regnum:
+bbmri_id:
+website_url: https://biobanksverige.se/kontakta-oss/biobankssamordnare-och-nej-talonger/
+description:
+address:
+contact: c19dp:contact:SE_NAT
+contact_priority: 1
+collections:
+email: [email protected]
+---

layouts/collections/single.html

@@ -110,19 +110,21 @@ <h4>General information</h4>
             <div class="col-auto pl-0 font-weight-bold">Ethical approval number:</div>
             <div class="col pl-0">{{ .Params.ethics_id }}</div>
           </div>
+          {{ if eq .Params.name "National sample collection stored at National Pandemic Center (NPC)" }}
+          {{ else }}
           <div class="row ml-0 mt-3">
             <h4>Donor information</h4>
-          </div>
+          </div> {{ end }}
           {{ if .Params.diagnosis_available }}<div class="row ml-0">
             <div class="col-auto pl-0 font-weight-bold">Diagnoses:</div>
             <div class="col pl-0">
               {{ range .Params.diagnosis_available}}
-                {{ if eq . "urn:miriam:icd:U07.1" }}
-                <span class="m-1 badge badge-primary">Laboratory-confirmed COVID-19 diagnosis; U07.1</span>
-                {{ end }}
-                {{ if eq . "urn:miriam:icd:U07.2" }}
-                <span class="m-1 badge badge-primary">Suspect or probable COVID-19 diagnosis; U07.2</span>
-                {{ end }}
+              {{ if eq . "urn:miriam:icd:U07.1" }}
+              <span class="m-1 badge badge-primary">Laboratory-confirmed COVID-19 diagnosis; U07.1</span>
+              {{ end }}
+              {{ if eq . "urn:miriam:icd:U07.2" }}
+              <span class="m-1 badge badge-primary">Suspect or probable COVID-19 diagnosis; U07.2</span>
+              {{ end }}
               {{ end }}
             </div>
           </div>{{ end }}
@@ -154,31 +156,33 @@ <h4>Donor information</h4>
           {{ $info_about_autopsy := string .Params.autopsy }}
           {{ if $info_about_autopsy }}<div class="row ml-0">
             <div class="col-auto pl-0 font-weight-bold">Samples from deceased (autopsy):</div>
-            <div class="col pl-0">{{ if eq $info_about_autopsy "true" }}yes{{ else if eq $info_about_autopsy "false" }}no{{ end }}</div>
+            <div class="col pl-0">
+              {{ if eq $info_about_autopsy "true" }}yes{{ else if eq $info_about_autopsy "false" }}no{{ end }}</div>
           </div> {{ end }}
           {{ $info_about_minors := string .Params.minors }}
           {{ if $info_about_minors }}<div class="row ml-0">
             <div class="col-auto pl-0 font-weight-bold">Samples from minors (&lt;18 years old):</div>
-            <div class="col pl-0">{{ if eq $info_about_minors "true" }}yes{{ else if eq $info_about_minors "false" }}no{{ end }}</div>
+            <div class="col pl-0">
+              {{ if eq $info_about_minors "true" }}yes{{ else if eq $info_about_minors "false" }}no{{ end }}</div>
           </div> {{ end }}
           {{ if .Params.inclusion_criteria }}<div class="row ml-0">
             <div class="mb-3">
               <b>Inclusion criteria:</b> {{ .Params.inclusion_criteria }}
             </div>
-            </div>{{ end }}
+          </div>{{ end }}
           {{ if .Params.exclusion_criteria }}<div class="row ml-0">
             <div class="mb-3">
               <b>Exclusion criteria:</b> {{ .Params.exclusion_criteria }}
             </div>
-            </div>{{ end }}
+          </div>{{ end }}
           <div class="row ml-0 mt-3">
             <h4>Sample information</h4>
           </div>
           <div class="row ml-0">
             <div class="col-auto pl-0 font-weight-bold">Materials:</div>
             <div class="col pl-0">{{ range (.GetTerms "materials") }}
               <span class="m-1 badge badge-danger taxonomy-term"><a href="{{ .Permalink }}">{{ .LinkTitle }}</a></span>
-            {{ end }}
+              {{ end }}
             </div>
           </div>
         </div>
@@ -188,17 +192,40 @@ <h4>Sample information</h4>
               <div class="card-text">
                 {{ if .Params.display_collection_contact }}
                 <h5>Collection contact information</h5>
-                {{ if .Params.head_firstname }}<div class="row"><div class="col">Collection head: {{ .Params.head_firstname }} {{ .Params.head_lastname }} {{ if .Params.head_role }}({{ .Params.head_role }}){{ end }}</div></div>{{ end }}
-                <div class="row"><div class="col">Contact person: {{ .Params.collection_contact.first_name }} {{ .Params.collection_contact.last_name }}</div></div>
-                <div class="row"><div class="col"><i class="bi bi-envelope-fill mr-2"></i><span>{{ .Params.collection_contact.email }} </span></div></div>
-                {{ if .Params.website_url }}<div class="row"><div class="col"><i class="bi bi-globe mr-2"></i><a href="{{ .Params.website_url }}" target="_blank"><span>Collection homepage</span></a></div></div>{{ end }}
+                {{ if .Params.head_firstname }}<div class="row">
+                  <div class="col">Collection head: {{ .Params.head_firstname }} {{ .Params.head_lastname }}
+                    {{ if .Params.head_role }}({{ .Params.head_role }}){{ end }}</div>
+                </div>{{ end }}
+                <div class="row">
+                  <div class="col">Contact person: {{ .Params.collection_contact.first_name }}
+                    {{ .Params.collection_contact.last_name }}</div>
+                </div>
+                <div class="row">
+                  <div class="col"><i class="bi bi-envelope-fill mr-2"></i><span>{{ .Params.collection_contact.email }}
+                    </span></div>
+                </div>
+                {{ if .Params.website_url }}<div class="row">
+                  <div class="col"><i class="bi bi-globe mr-2"></i><a href="{{ .Params.website_url }}"
+                      target="_blank"><span>Collection homepage</span></a></div>
+                </div>{{ end }}
                 {{ end }}
                 <h5>Biobank contact information</h5>
-                <div class="row"><div class="col">{{ .Parent.Params.name }}</div></div>
-                {{ if .Parent.Params.ivo_regnum }}<div class="row"><div class="col">Registration number at IVO: {{ .Parent.Params.ivo_regnum }}</div></div>{{ end }}
-                {{ if .Parent.Params.email }}<div class="row"><div class="col"><i class="bi bi-envelope-fill mr-2"></i>{{ .Parent.Params.email }}</div></div>{{ end }}
-                {{ if .Parent.Params.website_url }}<div class="row"><div class="col"><i class="bi bi-globe mr-2"></i><a href="{{ .Parent.Params.website_url }}" target="_blank"><span>Biobank homepage</span></a></div></div>{{ end }}
-                <div class="row mt-2"><div class="col"><a href="{{ .Parent.RelPermalink }}" class=""><span>All collections of {{ .Parent.Params.name }}</span> <i class="bi bi-arrow-right-circle-fill"></i></a></div></div>
+                <div class="row">
+                  <div class="col">{{ .Parent.Params.name }}</div>
+                </div>
+                {{ if .Parent.Params.ivo_regnum }}<div class="row">
+                  <div class="col">Registration number at IVO: {{ .Parent.Params.ivo_regnum }}</div>
+                </div>{{ end }}
+                {{ if .Parent.Params.email }}<div class="row">
+                  <div class="col"><i class="bi bi-envelope-fill mr-2"></i>{{ .Parent.Params.email }}</div>
+                </div>{{ end }}
+                {{ if .Parent.Params.website_url }}<div class="row">
+                  <div class="col"><i class="bi bi-globe mr-2"></i><a href="{{ .Parent.Params.website_url }}"
+                      target="_blank"><span>Biobank homepage</span></a></div>
+                </div>{{ end }}
+                <div class="row mt-2">
+                  <div class="col"><a href="{{ .Parent.RelPermalink }}" class=""><span>All collections of
+                        {{ .Parent.Params.name }}</span> <i class="bi bi-arrow-right-circle-fill"></i></a></div>
                 </div>
               </div>
             </div>
@@ -207,5 +234,6 @@ <h5>Biobank contact information</h5>
       </div>
     </div>
   </div>
+</div>
 
-{{ end }}
+{{ end }}

layouts/index.html

@@ -61,6 +61,7 @@
           <div id="collapseCollectionTypes" class="collapse" aria-labelledby="headingCollectionTypes">
           <div class="card-body">
               <div class="custom-control"><input type="checkbox" name="collectiontypes" class="form-check-input" value="Healthcare sample collection">Healthcare sample collection</div>
+              <div class="custom-control"><input type="checkbox" name="collectiontypes" class="form-check-input" value="National sample collection">National sample collection</div>
               <div class="custom-control"><input type="checkbox" name="collectiontypes" class="form-check-input" value="Research sample collection">Research sample collection</div>
           </div>
         </div>