Merge pull request #1084 from ScilifelabDataCentre/develop

Remove xmas message and adapt to repo rename
ScilifelabDataCentre · Jan 15, 2024 · 1c6804d · 1c6804d
2 parents 09676db + 42207ca
commit 1c6804d
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Showing 41 changed files with 124 additions and 124 deletions.
diff --git a/.github/workflows/dockerhub.yml b/.github/workflows/dockerhub.yml
@@ -20,7 +20,7 @@ jobs:
   push_to_registry:
     # only generate images when in the named repo
     # (to avoid running the action in forks)
-    if: github.repository == 'ScilifelabDataCentre/covid-portal'
+    if: github.repository == 'ScilifelabDataCentre/pathogens-portal'
     name: Publish Docker Image
     runs-on: ubuntu-latest
     # Cancel earlier job if there is a new one for the same branch/release
@@ -32,7 +32,7 @@ jobs:
       matrix:
         include:
           - dockerfile: Dockerfiles/Dockerfile
-            images: ghcr.io/scilifelabdatacentre/covid-portal
+            images: ghcr.io/scilifelabdatacentre/pathogens-portal
     permissions:
       contents: read
       packages: write

diff --git a/.github/workflows/trivy-scheduled.yaml b/.github/workflows/trivy-scheduled.yaml
@@ -32,7 +32,7 @@ jobs:
       - name: Run Trivy vulnerability scanner
         uses: aquasecurity/[email protected]
         with:
-          image-ref: 'ghcr.io/${{ env.REPOSITORY_OWNER }}/covid-portal:develop'
+          image-ref: 'ghcr.io/${{ env.REPOSITORY_OWNER }}/pathogens-portal:develop'
           format: 'sarif'
           output: 'trivy-results.sarif'
           severity: 'CRITICAL,HIGH'

diff --git a/CONTRIBUTING/adding_editing_information.md b/CONTRIBUTING/adding_editing_information.md
@@ -16,15 +16,15 @@ __Table of contents:__
 
 ## How to propose changes or additions
 
-All information displayed on the Portal is contained within [this GitHub repository](https://github.com/ScilifelabDataCentre/covid-portal). Some of the sections use information that is stored in the `data` folder in .JSON format while other sections use information that is stored in the `content` folder in Markdown format.
+All information displayed on the Portal is contained within [this GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal). Some of the sections use information that is stored in the `data` folder in .JSON format while other sections use information that is stored in the `content` folder in Markdown format.
 
 ### Using the web interface
 
 - Navigate to the folder and file that is indicated below in the corresponding section.
 - Click on the top right corner of the document ("Edit this file"). This should create a fork of the original repository in your own GitHub account. You should see a page where you can directly edit the content.
 - Make changes as described below; do not forget to change the last update date on top of the document if needed.
 - Scroll to the bottom of the page. Describe what you have changed and press 'Propose changes'
-- You should now find yourself on a page where you can create a pull request. Check that the pull request will be sent to the base repository `SciLifeLabDataCentre/covid-portal` and base `develop`. You can also review the changes you made. Click on "Create pull request" if everything looks good.
+- You should now find yourself on a page where you can create a pull request. Check that the pull request will be sent to the base repository `SciLifeLabDataCentre/pathogens-portal` and base `develop`. You can also review the changes you made. Click on "Create pull request" if everything looks good.
 - Once created, a member of the Portal team will review your changes.
 Once approved, they will be merged and published.
 
@@ -33,14 +33,14 @@ Once approved, they will be merged and published.
 If you prefer, you can edit the website files on your computer in your favourite text editor. Fork this repository to your account. Then, clone the forked repository to your machine:
 
 ```bash
-git clone [email protected]:[YOUR-USERNAME]/covid-portal.git
-cd covid-portal
+git clone [email protected]:[YOUR-USERNAME]/pathogens-portal.git
+cd pathogens-portal
 ```
 
 To make it easier to pull in changes made by others, you can add the main repository as a remote:
 
 ```bash
-git remote add upstream https://github.com/ScilifelabDataCentre/covid-portal.git
+git remote add upstream https://github.com/ScilifelabDataCentre/pathogens-portal.git
 ```
 
 Then you can fetch changes at any time from this remote:
@@ -59,7 +59,7 @@ git push
 
 Once you're finished with your edits and they are committed and pushed to your forked repository, it's time to open a pull request. In short:
 
-- Visit the main repository: [https://github.com/ScilifelabDataCentre/covid-portal](https://github.com/ScilifelabDataCentre/covid-portal)
+- Visit the main repository: [https://github.com/ScilifelabDataCentre/pathogens-portal](https://github.com/ScilifelabDataCentre/pathogens-portal)
 - Click the button that reads _"New Pull Request"_
 - Click the text link near the top that says _"compare across forks"_
 - In the right-hand _"head repository"_ drop down, select your username / fork.
@@ -70,7 +70,7 @@ Once approved, they will be merged and published.
 
 #### Testing with a local copy of the Portal
 
-Because the Portal is built on Hugo, it is quite easy to run a full version of the Portal on your computer and see how your changes look while doing that. See [this page for information on how to do that](https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md).
+Because the Portal is built on Hugo, it is quite easy to run a full version of the Portal on your computer and see how your changes look while doing that. See [this page for information on how to do that](https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md).
 
 ## Available datasets
 

diff --git a/CONTRIBUTING/running_a_local_copy.md b/CONTRIBUTING/running_a_local_copy.md
@@ -29,8 +29,8 @@ $ hugo serve
   Cleaned          |  0 |  0
 
 Built in 123 ms
-Watching for changes in /Users/philewels/GitHub/covid-portal/{archetypes,content,layouts,static}
-Watching for config changes in /Users/philewels/GitHub/covid-portal/config.yaml
+Watching for changes in /Users/philewels/GitHub/pathogens-portal/{archetypes,content,layouts,static}
+Watching for config changes in /Users/philewels/GitHub/pathogens-portal/config.yaml
 Environment: "development"
 Serving pages from memory
 Running in Fast Render Mode. For full rebuilds on change: hugo server --disableFastRender

diff --git a/README.md b/README.md
@@ -26,23 +26,23 @@ It uses the [Bootstrap](https://getbootstrap.com/) framework. In addition, it us
 
 ### Adding and editing information in different sections
 
-We prepared detailed instructions on how to add or edit information in each specific section of the portal, see [the page on adding and editing information in the CONTRIBUTING folder](https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/adding_editing_information.md).
+We prepared detailed instructions on how to add or edit information in each specific section of the portal, see [the page on adding and editing information in the CONTRIBUTING folder](https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/adding_editing_information.md).
 
 ### Testing changes with a local copy of the portal
 
-Users who are technically more advanced are welcome to make contributions by running a local copy of the portal on their own computers, we prepared [instructions on how to do that here](https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md).
+Users who are technically more advanced are welcome to make contributions by running a local copy of the portal on their own computers, we prepared [instructions on how to do that here](https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md).
 
 ### Using ImJoy Plugins
 
-This website supports [ImJoy](https://imjoy.io) plugins which can be used to visualize, annotate, run analysis directly from the website. See [an example here](https://covid19dataportal.se/highlights/immunofluorescence/). Please see the file [CONTRIBUTING/ImJoy.md](https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/ImJoy.md) for examples of usage.
+This website supports [ImJoy](https://imjoy.io) plugins which can be used to visualize, annotate, run analysis directly from the website. See [an example here](https://covid19dataportal.se/highlights/immunofluorescence/). Please see the file [CONTRIBUTING/ImJoy.md](https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/ImJoy.md) for examples of usage.
 
 ### The Swedish COVID-19 Sample Collection Database
 
 The portal team works closely with [Biobank Sverige](https://biobanksverige.se) to develop and maintain the [The Swedish COVID-19 Sample Collection Database](https://biobanks.covid19dataportal.se). The database contains biobanks collections from multiple biobanks across Sweden. Research staff can use the database to search for and request access to samples that could be beneficial for their work. New collections are submitted to the portal team by Biobank Sverige as they become available. The code behind The Swedish COVID-19 Sample Collection Database is maintained by the portal team and is available on [GitHub](https://github.com/ScilifelabDataCentre/covid-sample-collection-database).
 
 ### Data visualisations
 
-Unless otherwise specified, the data visualisations on the portal have been developed in-house by the portal team. A link to the code underlying each visualisation is provided on the portal page on which it is displayed. All visualisations on the portal can be found on our dedicated [GitHub repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations).
+Unless otherwise specified, the data visualisations on the portal have been developed in-house by the portal team. A link to the code underlying each visualisation is provided on the portal page on which it is displayed. All visualisations on the portal can be found on our dedicated [GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations).
 
 ## How to get help
 

diff --git a/content/english/about/_index.md b/content/english/about/_index.md
@@ -20,19 +20,19 @@ The _Swedish Pathogens Portal_ provides information about available datasets, re
 
 The Portal is operated by the [SciLifeLab Data Centre](https://scilifelab.se/data/) and [partners](partner_organisations). We welcome community contributions to the Portal and provide information on the different ways that the community can contribute, for more details see [contribute](/contribute/) page. In addition to running the Portal, the team can also either provide support on data-related questions surrounding pandemic preparedness research or help find suitable support services. For more general data support, please see our related research data management service([RDM Guidelines](https://data-guidelines.scilifelab.se/)).
 
-This website is built using [Hugo](https://gohugo.io/) in combination with [Bootstrap](https://getbootstrap.com/) for styling, [DataTables](https://datatables.net/) for tables, and [Vega/Vega-Lite](https://vega.github.io/vega-lite/) and [Plotly](https://plotly.com/) for interactive graphics. All code used for the Portal is open source (held under an [MIT licence](https://choosealicense.com/licenses/mit/)) and [is available on GitHub](https://github.com/ScilifelabDataCentre/covid-portal). We encourage the reuse of our code, either for generating another national portal, or recreating certain features.
+This website is built using [Hugo](https://gohugo.io/) in combination with [Bootstrap](https://getbootstrap.com/) for styling, [DataTables](https://datatables.net/) for tables, and [Vega/Vega-Lite](https://vega.github.io/vega-lite/) and [Plotly](https://plotly.com/) for interactive graphics. All code used for the Portal is open source (held under an [MIT licence](https://choosealicense.com/licenses/mit/)) and [is available on GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal). We encourage the reuse of our code, either for generating another national portal, or recreating certain features.
 
 #### History of the Portal
 
 The Swedish Pathogens Portal was originally launched as the 'Swedish COVID-19 Data Portal' in June 2020 on assignment and with funding from the Swedish Research Council a.k.a. Vetenskapsrådet (more details [here](https://www.vr.se/english/just-now/news/news-archive/2020-06-03-new-national-portal-makes-research-data-on-covid-19-accessible.html)). The Portal was actually the first national node of the [European COVID-19 Data Platform](https://covid19dataportal.eu/), which was initiated and funded by the European Commission (more details [here](https://www.embl.org/news/science/embl-ebi-launches-covid-19-data-portal/)) and you can find an overview of other national nodes [here](/partners/). The Portal focused on SARS-CoV-2 and COVID-19 research data exclusively until the end of 2021. We released a [news item](/updates/first_year/) summarising our activities in 2021.
 
 From 2022, the Portal expanded to cover other research relevant to pandemic preparedness and became a part of the [SciLifeLab Pandemic Laboratory Preparedness programme](https://www.scilifelab.se/pandemic-response/pandemic-laboratory-preparedness/). The SciLifeLab Pandemic Laboratory Preparedness Programme is funded by the earmarked governmental funding to SciLifeLab ([Research proposition Prop. 202/21:60](https://www.regeringen.se/rattsliga-dokument/proposition/2020/12/forskning-frihet-framtid--kunskap-och-innovation-for-sverige/)).
 
-From the start, the Portal has been operated by the SciLifeLab Data Centre and partners. However, it has received considerable input from the community. Indeed, many people contributed to building the initial site, and to content throughout. An overview of some of the contributors that have been instrumental to establishing and advancing the Portal can be found on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal/graphs/contributors).
+From the start, the Portal has been operated by the SciLifeLab Data Centre and partners. However, it has received considerable input from the community. Indeed, many people contributed to building the initial site, and to content throughout. An overview of some of the contributors that have been instrumental to establishing and advancing the Portal can be found on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal/graphs/contributors).
 
 #### Portal team
 
-Many people from SciLifeLab, NBIS, other organisations, and the community have been involved in the Portal since its conception in early 2020. A complete list of contributors can be found on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal/graphs/contributors). Below, we show the current team of people actively working on the Portal.
+Many people from SciLifeLab, NBIS, other organisations, and the community have been involved in the Portal since its conception in early 2020. A complete list of contributors can be found on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal/graphs/contributors). Below, we show the current team of people actively working on the Portal.
 
 The team are happy to help with using the Portal, to take suggestions regarding new and existing sections, and to answer any questions that you may have. Please just get in touch using for [contact](/contact/) form.
 

diff --git a/content/english/contribute.md b/content/english/contribute.md
@@ -22,9 +22,9 @@ There are multiple ways to add/edit information on the Portal. Choose any method
     </div>
     <div class="col-md-6">
       <h3><i class="bi bi-github"></i> Send a GitHub pull request</h3>
-      <p>All information which is displayed on the Portal is <a href="https://github.com/ScilifelabDataCentre/covid-portal/tree/develop">stored on GitHub</a>. The information is stored as .JSON files or as Markdown files, making it human-readable and easy to edit. If you know your way around the web interface of GitHub or GitHub CLI, you can easily edit or add information yourself and send us a pull request.</p>
-      <p>The information for each section of the Portal is stored in a particular folder and needs to be formatted in a certain way. To make it easier for you to contribute, <a href="https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/adding_editing_information.md">we have written detailed instructions</a> for each of the sections. Moreover, you can even easily <a href="https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md">run a local copy of the Portal on your computer</a> and see all changes live before sending them to us. If you run into an issue, send us an email so that we can help you.</p>
-      <p><b><a href="https://github.com/ScilifelabDataCentre/covid-portal/blob/develop/CONTRIBUTING/adding_editing_information.md">Contribute through GitHub <i class="bi bi-arrow-right-circle-fill"></i></a></b></p>
+      <p>All information which is displayed on the Portal is <a href="https://github.com/ScilifelabDataCentre/pathogens-portal/tree/develop">stored on GitHub</a>. The information is stored as .JSON files or as Markdown files, making it human-readable and easy to edit. If you know your way around the web interface of GitHub or GitHub CLI, you can easily edit or add information yourself and send us a pull request.</p>
+      <p>The information for each section of the Portal is stored in a particular folder and needs to be formatted in a certain way. To make it easier for you to contribute, <a href="https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/adding_editing_information.md">we have written detailed instructions</a> for each of the sections. Moreover, you can even easily <a href="https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/running_a_local_copy.md">run a local copy of the Portal on your computer</a> and see all changes live before sending them to us. If you run into an issue, send us an email so that we can help you.</p>
+      <p><b><a href="https://github.com/ScilifelabDataCentre/pathogens-portal/blob/develop/CONTRIBUTING/adding_editing_information.md">Contribute through GitHub <i class="bi bi-arrow-right-circle-fill"></i></a></b></p>
     </div>
   </div>
 </div>