Merge pull request #37 from abcd-j/upstream-changes

Bring in upstream changes

catalog/README.md

@@ -20,16 +20,16 @@ The `artwork` and `assets` directories contain images and web assets (such as Ja
 
 ## Serving the content
 
-Since this site is self-contained and static, no further build processes, server-side implementations, or access to content delivery networks (CDNs) are necessary in order to serve the content. All that is needed is a simple HTTP server.
+Since this site is self-contained and static, no further build processes or access to content delivery networks (CDNs) are necessary in order to serve the content. All that is needed is a simple HTTP server with one specific addition - a custom redirect. This is required because the application makes use of [Vue Router's history mode](https://v3.router.vuejs.org/guide/essentials/history-mode.html#html5-history-mode), which requires a server-side redirect configuration to deal with the fact that a VueJS application is actually a single-page app.
 
-This can be achieved locally, for example using Python:
+For serving the content locally, this is already taken care of in `datalad-catalog`, and you can simply run the following:
 
 ```bash
 cd path/to/catalog/directory
-python3 -m http.server
+datalad catalog-serve -c .
 ```
 
-The content can also be hosted and served online. A straightforward and free way to achieve this is via GitHub and [GitHub Pages](https://pages.github.com/). After publishing this content as a GitHub repository, you can activate GitHub Pages in the repository's settings. See detailed instructions [here](https://docs.github.com/en/pages/getting-started-with-github-pages/creating-a-github-pages-site).
+The content can also be hosted and served online. A straightforward way to achieve this, and one which has a free tier, is via [Netlify](https://www.netlify.com/) (the common alternative, [GitHub Pages](https://pages.github.com/), does not currently support server-side redirects). After publishing this content, e.g. as a GitHub repository, you can link that repository to a site on Netlify. [See here](https://docs.netlify.com/routing/redirects/) how to set up redirects with Netlify. Of course, the site can also be served from your preferred server setup, as long as page redirects can be supported.
 
 ## Maintaining content
 

catalog/assets/app.js

@@ -22,25 +22,9 @@ var datacat = new Vue({
     gotoExternal(dest) {
       window.open(dest);
     },
-    async load() {
-      // Load templates
-      await Promise.all(
-        Object.keys(template_paths).map(async (key, index) => {
-          url = template_dir + "/" + template_paths[key]
-          fetch(url).
-          then(response => {
-              return response.text();
-          }).
-          then(text => {
-              console.log('template loaded: '+key)
-              console.log(text)
-              document.getElementById(key).innerHTML = text;
-          });
-        })
-      )
-    }
   },
   beforeCreate() {
+    console.debug("Executing lifecycle hook: beforeCreate")
     fetch(config_file)
       .then((response) => {
         if (response.ok) {
@@ -54,6 +38,13 @@ var datacat = new Vue({
       })
       .then((responseJson) => {
         obj = responseJson;
+        // first ensure that the config has all required fields;
+        // if some are missing, fill them in from default_config
+        for (const [key, value] of Object.entries(default_config)) {
+          if (!obj.hasOwnProperty(key) ) {
+            obj[key] = value;
+          }
+        }
         // set social links
         this.social_links = obj.social_links
         // set dataset options

catalog/assets/app_globals.js

@@ -15,10 +15,10 @@ const default_config = {
   logo_path: "/artwork/catalog_logo.svg",
   social_links: {
     about: null,
-    documentation: null,
-    github: null,
-    mastodon: null,
-    x: null
+    documentation: "https://docs.datalad.org/projects/catalog/en/latest/",
+    github: "https://github.com/datalad/datalad-catalog",
+    mastodon: "https://fosstodon.org/@datalad",
+    x: "https://x.com/datalad"
   },
   dataset_options: {
     include_metadata_export: true,
@@ -56,15 +56,24 @@ async function grabSubDatasets(app) {
 function getFilePath(dataset_id, dataset_version, path, ext = ".json") {
   // Get node file location from  dataset id, dataset version, and node path
   // using a file system structure similar to RIA stores
-  file = metadata_dir + "/" + dataset_id + "/" + dataset_version;
-  blob = dataset_id + "-" + dataset_version;
-  if (path) {
-    blob = blob + "-" + path;
+  // - dataset_id is required, all the other parameters are optional
+  // - dataset_id could either be an actual dataset ID or an alias
+  file = metadata_dir + "/" + dataset_id
+  blob = dataset_id
+  if (dataset_version) {
+    file = file + "/" + dataset_version;
+    blob = blob + "-" + dataset_version;
+    // path to file only makes sense with the context of a dataset id AND version
+    if (path) {
+      blob = blob + "-" + path;
+    }
+    blob = md5(blob);
+    blob_parts = [blob.substring(0, SPLIT_INDEX), blob.substring(SPLIT_INDEX)];
+    return file + "/" + blob_parts[0] + "/" + blob_parts[1] + ext;
+  } else {
+    blob = md5(blob);
+    return file + "/" + blob + ext;
   }
-  blob = md5(blob);
-  blob_parts = [blob.substring(0, SPLIT_INDEX), blob.substring(SPLIT_INDEX)];
-  file = file + "/" + blob_parts[0] + "/" + blob_parts[1] + ext;
-  return file;
 }
 
 function getRelativeFilePath(dataset_id, dataset_version, path) {

catalog/assets/app_router.js

@@ -8,6 +8,7 @@ const routes = [
     path: "/",
     name: "home",
     beforeEnter: (to, from, next) => {
+      console.debug("Executing navigation guard: beforeEnter - route '/')")
       const superfile = metadata_dir + "/super.json";
       // https://www.dummies.com/programming/php/using-xmlhttprequest-class-properties/
       var rawFile = new XMLHttpRequest();
@@ -22,6 +23,7 @@ const routes = [
                 dataset_id: superds["dataset_id"],
                 dataset_version: superds["dataset_version"],
               },
+              query: to.query,
             });
             next();
           } else if (rawFile.status === 404) {
@@ -36,7 +38,7 @@ const routes = [
     },
   },
   {
-    path: "/dataset/:dataset_id/:dataset_version/:tab_name?",
+    path: "/dataset/:dataset_id/:dataset_version?",
     component: datasetView,
     name: "dataset",
   },
@@ -45,7 +47,7 @@ const routes = [
     path: '/:catchAll(.*)', 
     component: notFound,
     name: '404'
-  }
+  },
 ];
 
 // Create router

catalog/metadata/0036b2c6-f131-4660-9ef9-945087ad02d3/7b4cda8de84b041cad5ccee1fc751bc1.json

@@ -0,0 +1 @@
+{"type": "redirect", "dataset_id": "0036b2c6-f131-4660-9ef9-945087ad02d3", "dataset_version": "1139b4c82d7ecd0d9ab25bf4c00ec2c06461d6da"}

catalog/metadata/1015ed7c-0a3d-4dfc-9c4f-11fe71673a41/656a74dd70558c5eb834d79f80db5884ff8caeb7/7c9/b81b743373903e24e43d49662d4ee.json

@@ -1 +1 @@
-{"type": "dataset", "dataset_id": "1015ed7c-0a3d-4dfc-9c4f-11fe71673a41", "dataset_version": "656a74dd70558c5eb834d79f80db5884ff8caeb7", "children": [{"type": "directory", "name": "FZJ", "path": "FZJ"}, {"type": "directory", "name": "UKD", "path": "UKD"}], "metadata_sources": {"key_source_map": {"type": ["catalog_core"], "dataset_id": ["catalog_core"], "dataset_version": ["catalog_core"], "url": ["catalog_core", "tabby"], "authors": ["tabby"], "name": ["tabby"], "description": ["tabby"], "keywords": ["tabby"], "funding": ["tabby"], "subdatasets": ["tabby"], "additional_display": ["tabby"]}, "sources": [{"source_name": "catalog_core", "source_version": "1", "source_parameter": {}, "source_time": 1713263552.4326751, "agent_email": "t.heunis@fz-juelich.de", "agent_name": "Tosca Heunis"}, {"source_name": "tabby", "source_version": "0.1.0", "source_parameter": {}, "source_time": 1713263552.470434, "agent_name": "Tosca Heunis", "agent_email": "t.heunis@fz-juelich.de"}]}, "url": ["ssh://git@github.com/~/abcd-j/data.git", "https://www.abcd-j.de/", "https://github.com/abcd-j/data.git"], "authors": [{"name": "ABCD-J Research Consortium"}], "name": "The ABCD-J Data Catalog", "description": "This data catalog contains datasets from the ABCD-J research community project, officially titled \u201cVerbundprojekt: Accessing Behavior for Clinical Data and Joint usage (ABCD-J) - Eine Plattform f\u00fcr Verhaltensmarker der digitalen Neuromedizin in NRW\u201d. This project is a collaboration between five research institutions in the German state of North Rhine-Westphalia: University Clinic RWTH Aachen, University Clinic Bonn, University Clinic K\u00f6ln, University Clinic D\u00fcsseldorf and Research Centre J\u00fclich. The overarching goal of ABCD-J is to elevate existing technical solutions for research practice adoption. From the social perspective, the ABCD-J project aims to promote and facilitate collaboration between multiple research centres, while from the technical perspective the project will accelerate research through homogenization of workflows and processes, with particular emphasis on digital biomarker development.", "keywords": ["Aachen", "Bonn", "Cologne", "D\u00fcsseldorf", "J\u00fclich", "Collaboration", "Research", "Open data", "FAIR", "Biomarker", "Clinical", "Behaviour"], "funding": [{"@type": "schema:Grant", "name": "MKW-NRW: Ministerium f\u00fcr Kultur und Wissenschaft des Landes Nordrhein-Westfalen", "identifier": "Kooperationsplattformen 2022: KP22-106A", "schema:url": "https://www.mkw.nrw/"}], "subdatasets": [{"dataset_id": "3f8a45c0-08fc-479c-b561-cb6f744d2b5c", "dataset_version": "32f3303308c89b037fe1700547348470539a30cb", "dataset_path": "FZJ/jumax", "dataset_url": null, "dirs_from_path": ["FZJ", "jumax"]}, {"dataset_id": "0036b2c6-f131-4660-9ef9-945087ad02d3", "dataset_version": "1139b4c82d7ecd0d9ab25bf4c00ec2c06461d6da", "dataset_path": "FZJ/movies", "dataset_url": null, "dirs_from_path": ["FZJ", "movies"]}, {"dataset_id": "db7592d0-6206-5684-a29c-8059a6033241", "dataset_version": "0.1.0", "dataset_path": "UKD/ocr-PIRA-cohort", "dataset_url": null, "dirs_from_path": ["UKD", "ocr-PIRA-cohort"]}, {"dataset_id": "372e66b3-e654-4a0f-ba4c-6394bf314f2f", "dataset_version": "d468e9a9455b38b959db34bc5335fd66e42b2884", "dataset_path": "FZJ/EMA_Pilot", "dataset_url": null, "dirs_from_path": ["FZJ", "EMA_Pilot"]}, {"dataset_id": "d72933c1-a660-5970-8bfd-48fcdac59dc5", "dataset_version": "latest", "dataset_path": "UKD/Gliem-Pavic", "dataset_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167274", "dirs_from_path": ["UKD", "Gliem-Pavic"]}, {"dataset_id": "c0ebe952-528e-40c8-a44f-4a80bff28ffb", "dataset_version": "4f5d78d24e6be85d26e22fbc088b2d8469163758", "dataset_path": "FZJ/SpEx", "dataset_url": "https://data.fz-juelich.de/dataset.xhtml?persistentId=doi:10.26165/JUELICH-DATA/CHWZDZ", "dirs_from_path": ["FZJ", "SpEx"]}], "additional_display": [{"name": "ABCD-J", "icon": "fa-solid fa-graduation-cap", "content": {"@context": {"homepage": "https://schema.org/mainEntityOfPage", "data controller": "https://w3id.org/dpv#hasDataController", "sample (organism)": "https://openminds.ebrains.eu/controlledTerms/Species", "sample (organism part)": "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation", "used for": "http://www.w3.org/ns/prov#hadUsage"}, "homepage": {"@type": "https://schema.org/URL", "@value": "https://www.abcd-j.de/"}}}]}
+{"type": "dataset", "dataset_id": "1015ed7c-0a3d-4dfc-9c4f-11fe71673a41", "dataset_version": "656a74dd70558c5eb834d79f80db5884ff8caeb7", "children": [{"type": "directory", "name": "FZJ", "path": "FZJ"}, {"type": "directory", "name": "UKD", "path": "UKD"}], "metadata_sources": {"key_source_map": {"type": ["catalog_core"], "dataset_id": ["catalog_core"], "dataset_version": ["catalog_core"], "url": ["catalog_core", "tabby"], "authors": ["tabby"], "name": ["tabby"], "description": ["tabby"], "keywords": ["tabby"], "funding": ["tabby"], "subdatasets": ["tabby"], "additional_display": ["tabby"], "alias": ["automated_alias_entry"]}, "sources": [{"source_name": "catalog_core", "source_version": "1", "source_parameter": {}, "source_time": 1713263552.4326751, "agent_email": "t.heunis@fz-juelich.de", "agent_name": "Tosca Heunis"}, {"source_name": "tabby", "source_version": "0.1.0", "source_parameter": {}, "source_time": 1713263552.470434, "agent_name": "Tosca Heunis", "agent_email": "t.heunis@fz-juelich.de"}, {"source_name": "automated_alias_entry", "source_version": "0.1.0", "source_parameter": {}, "source_time": 1714298033.906975, "agent_name": "Stephan Heunis", "agent_email": "s.heunis@fz-juelich.de"}]}, "url": ["ssh://git@github.com/~/abcd-j/data.git", "https://www.abcd-j.de/", "https://github.com/abcd-j/data.git"], "authors": [{"name": "ABCD-J Research Consortium"}], "name": "The ABCD-J Data Catalog", "description": "This data catalog contains datasets from the ABCD-J research community project, officially titled \u201cVerbundprojekt: Accessing Behavior for Clinical Data and Joint usage (ABCD-J) - Eine Plattform f\u00fcr Verhaltensmarker der digitalen Neuromedizin in NRW\u201d. This project is a collaboration between five research institutions in the German state of North Rhine-Westphalia: University Clinic RWTH Aachen, University Clinic Bonn, University Clinic K\u00f6ln, University Clinic D\u00fcsseldorf and Research Centre J\u00fclich. The overarching goal of ABCD-J is to elevate existing technical solutions for research practice adoption. From the social perspective, the ABCD-J project aims to promote and facilitate collaboration between multiple research centres, while from the technical perspective the project will accelerate research through homogenization of workflows and processes, with particular emphasis on digital biomarker development.", "keywords": ["Aachen", "Bonn", "Cologne", "D\u00fcsseldorf", "J\u00fclich", "Collaboration", "Research", "Open data", "FAIR", "Biomarker", "Clinical", "Behaviour"], "funding": [{"@type": "schema:Grant", "name": "MKW-NRW: Ministerium f\u00fcr Kultur und Wissenschaft des Landes Nordrhein-Westfalen", "identifier": "Kooperationsplattformen 2022: KP22-106A", "schema:url": "https://www.mkw.nrw/"}], "subdatasets": [{"dataset_id": "3f8a45c0-08fc-479c-b561-cb6f744d2b5c", "dataset_version": "32f3303308c89b037fe1700547348470539a30cb", "dataset_path": "FZJ/jumax", "dataset_url": null, "dirs_from_path": ["FZJ", "jumax"]}, {"dataset_id": "0036b2c6-f131-4660-9ef9-945087ad02d3", "dataset_version": "1139b4c82d7ecd0d9ab25bf4c00ec2c06461d6da", "dataset_path": "FZJ/movies", "dataset_url": null, "dirs_from_path": ["FZJ", "movies"]}, {"dataset_id": "db7592d0-6206-5684-a29c-8059a6033241", "dataset_version": "0.1.0", "dataset_path": "UKD/ocr-PIRA-cohort", "dataset_url": null, "dirs_from_path": ["UKD", "ocr-PIRA-cohort"]}, {"dataset_id": "372e66b3-e654-4a0f-ba4c-6394bf314f2f", "dataset_version": "d468e9a9455b38b959db34bc5335fd66e42b2884", "dataset_path": "FZJ/EMA_Pilot", "dataset_url": null, "dirs_from_path": ["FZJ", "EMA_Pilot"]}, {"dataset_id": "d72933c1-a660-5970-8bfd-48fcdac59dc5", "dataset_version": "latest", "dataset_path": "UKD/Gliem-Pavic", "dataset_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167274", "dirs_from_path": ["UKD", "Gliem-Pavic"]}, {"dataset_id": "c0ebe952-528e-40c8-a44f-4a80bff28ffb", "dataset_version": "4f5d78d24e6be85d26e22fbc088b2d8469163758", "dataset_path": "FZJ/SpEx", "dataset_url": "https://data.fz-juelich.de/dataset.xhtml?persistentId=doi:10.26165/JUELICH-DATA/CHWZDZ", "dirs_from_path": ["FZJ", "SpEx"]}], "additional_display": [{"name": "ABCD-J", "icon": "fa-solid fa-graduation-cap", "content": {"@context": {"homepage": "https://schema.org/mainEntityOfPage", "data controller": "https://w3id.org/dpv#hasDataController", "sample (organism)": "https://openminds.ebrains.eu/controlledTerms/Species", "sample (organism part)": "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation", "used for": "http://www.w3.org/ns/prov#hadUsage"}, "homepage": {"@type": "https://schema.org/URL", "@value": "https://www.abcd-j.de/"}}}], "alias": "abcdj"}

catalog/metadata/1015ed7c-0a3d-4dfc-9c4f-11fe71673a41/90eb6d77d0622afac1fae8130ee50b58.json

@@ -0,0 +1 @@
+{"type": "redirect", "dataset_id": "1015ed7c-0a3d-4dfc-9c4f-11fe71673a41", "dataset_version": "656a74dd70558c5eb834d79f80db5884ff8caeb7"}

catalog/metadata/372e66b3-e654-4a0f-ba4c-6394bf314f2f/350504699dc1a6306b65fd26ee0175e5.json

@@ -0,0 +1 @@
+{"type": "redirect", "dataset_id": "372e66b3-e654-4a0f-ba4c-6394bf314f2f", "dataset_version": "d468e9a9455b38b959db34bc5335fd66e42b2884"}