Merge branch 'main' into abcdj

datalad_catalog/catalog/assets/app_component_contexttab.js

@@ -0,0 +1,33 @@
+// Component definition: an "additional tab" with context
+Vue.component('context-tab-body', function (resolve, reject) {
+  url = template_dir + "/context-tab-template.html"
+  fetch(url).
+    then(response => {
+        return response.text();
+    }).
+    then(text => {
+        resolve(
+          {
+            template: text,
+            props: {
+              tabby: Object,
+            },
+            data: function () {
+              return {
+                context_tab_ready: false,
+              };
+            },
+            computed: {},
+            methods: {
+              toUpperString(str_in) {
+                return str_in.charAt(0).toUpperCase() + str_in.slice(1)
+              }
+            },
+            async created() {
+              this.context_tab_ready = true;
+              // console.log(new_tab)
+            }
+          }
+        )
+    });
+});

datalad_catalog/catalog/index.html

@@ -20,8 +20,8 @@
     <link type="text/css" rel="stylesheet" href="assets/bootstrap-vue.2.21.2.min.css"/>
 
     <!-- Required scripts -->
-    <!-- <script src="https://unpkg.com/[email protected]/dist/vue.js"></script> -->
-    <script src="assets/vue.2.6.14.min.js"></script>
+    <script src="https://unpkg.com/[email protected]/dist/vue.js"></script>
+    <!-- <script src="assets/vue.2.6.14.min.js"></script> -->
     <script src="assets/bootstrap-vue.2.21.2.min.js"></script>
     <script src="assets/vue-router.3.5.3.min.js"></script>
     <script src="assets/md5-2.3.0.js"></script>
@@ -72,6 +72,7 @@
     <!-- Run the Vue app scripts - DO NOT CHANGE ORDER -->
     <script src="assets/app_globals.js"></script>
     <script src="assets/app_component_item.js"></script>
+    <script src="assets/app_component_contexttab.js"></script>
     <script src="assets/app_component_dataset.js"></script>
     <script src="assets/app_component_about.js"></script>
     <script src="assets/app_component_notfound.js"></script>

datalad_catalog/catalog/metadata/c475969b-2919-57b1-a3e6-71770acaa222/0.1.0/aa1/11b599c3a81615b29b99b1d87a7db.json

@@ -0,0 +1 @@
+{"type": "directory", "dataset_id": "c475969b-2919-57b1-a3e6-71770acaa222", "dataset_version": "0.1.0", "children": [{"type": "file", "dataset_id": "c475969b-2919-57b1-a3e6-71770acaa222", "dataset_version": "0.1.0", "metadata_sources": {"key_source_map": {}, "sources": [{"source_name": "tabby", "source_version": "0.1.0", "source_parameter": {}, "source_time": 1702323824.80198, "agent_name": "Stephan Heunis", "agent_email": "[email protected]"}]}, "path": "raw/adelie.csv", "contentbytesize": 23755, "url": "https://portal.edirepository.org/nis/dataviewer?packageid=knb-lter-pal.219.3&entityid=002f3893385f710df69eeebe893144ff", "name": "adelie.csv"}, {"type": "file", "dataset_id": "c475969b-2919-57b1-a3e6-71770acaa222", "dataset_version": "0.1.0", "metadata_sources": {"key_source_map": {}, "sources": [{"source_name": "tabby", "source_version": "0.1.0", "source_parameter": {}, "source_time": 1702323824.80198, "agent_name": "Stephan Heunis", "agent_email": "[email protected]"}]}, "path": "raw/gentoo.csv", "contentbytesize": 11263, "url": "https://portal.edirepository.org/nis/dataviewer?packageid=knb-lter-pal.220.3&entityid=e03b43c924f226486f2f0ab6709d2381", "name": "gentoo.csv"}, {"type": "file", "dataset_id": "c475969b-2919-57b1-a3e6-71770acaa222", "dataset_version": "0.1.0", "metadata_sources": {"key_source_map": {}, "sources": [{"source_name": "tabby", "source_version": "0.1.0", "source_parameter": {}, "source_time": 1702323824.80198, "agent_name": "Stephan Heunis", "agent_email": "[email protected]"}]}, "path": "raw/chinstrap.csv", "contentbytesize": 18872, "url": "https://portal.edirepository.org/nis/dataviewer?packageid=knb-lter-pal.221.2&entityid=fe853aa8f7a59aa84cdd3197619ef462", "name": "chinstrap.csv"}], "path": "raw", "name": "raw"}

datalad_catalog/catalog/metadata/c475969b-2919-57b1-a3e6-71770acaa222/0.1.0/cad/486b905182ab9d7cee7d80ea1173d.json

@@ -0,0 +1,196 @@
+{
+    "type": "dataset",
+    "dataset_id": "c475969b-2919-57b1-a3e6-71770acaa222",
+    "dataset_version": "0.1.0",
+    "children": [
+        {
+            "type": "directory",
+            "name": "raw",
+            "path": "raw",
+            "dataset_id": "c475969b-2919-57b1-a3e6-71770acaa222",
+            "dataset_version": "0.1.0"
+        }
+    ],
+    "metadata_sources": {
+        "key_source_map": {
+            "license": [
+                "tabby"
+            ],
+            "doi": [
+                "tabby"
+            ],
+            "authors": [
+                "tabby"
+            ],
+            "keywords": [
+                "tabby"
+            ],
+            "funding": [
+                "tabby"
+            ],
+            "publications": [
+                "tabby"
+            ],
+            "access_request_contact": [
+                "tabby"
+            ],
+            "additional_display": [
+                "tabby"
+            ]
+        },
+        "sources": [
+            {
+                "source_name": "tabby",
+                "source_version": "0.1.0",
+                "source_parameter": {},
+                "source_time": 1702323824.737152,
+                "agent_name": "Stephan Heunis",
+                "agent_email": "[email protected]"
+            }
+        ]
+    },
+    "name": null,
+    "license": {
+        "name": "https://creativecommons.org/publicdomain/zero/1.0/",
+        "url": "https://creativecommons.org/publicdomain/zero/1.0/"
+    },
+    "description": null,
+    "doi": "https://doi.org/10.5281/zenodo.3960218",
+    "authors": [
+        {
+            "email": "[email protected]",
+            "name": "Allison Horst",
+            "identifiers": [
+                {
+                    "name": "ORCID",
+                    "identifier": "0000-0002-6047-5564"
+                }
+            ]
+        },
+        {
+            "email": "[email protected]",
+            "name": "Alison Hill",
+            "identifiers": [
+                {
+                    "name": "ORCID",
+                    "identifier": "0000-0002-8082-1890"
+                }
+            ]
+        },
+        {
+            "email": "[email protected]",
+            "name": "Kristen Gorman",
+            "identifiers": [
+                {
+                    "name": "ORCID",
+                    "identifier": "0000-0002-0258-9264"
+                }
+            ]
+        }
+    ],
+    "keywords": [
+        "penguins",
+        "sea ice",
+        "foraging",
+        "ecological niches",
+        "islands",
+        "antarctica",
+        "animal sexual behavior",
+        "isotopes"
+    ],
+    "funding": [
+        {
+            "@type": "schema:Grant",
+            "name": "DFG",
+            "identifier": "431549029-INF",
+            "schema:url": "https://gepris.dfg.de/gepris/projekt/431549029?context=projekt&task=showDetail&id=431549029&"
+        },
+        {
+            "@type": "schema:Grant",
+            "name": "NSF-OPP",
+            "identifier": "#0217282",
+            "schema:url": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0217282&HistoricalAwards=false"
+        },
+        {
+            "@type": "schema:Grant",
+            "name": "NSF-OPP",
+            "identifier": "#0823101",
+            "schema:url": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0823101&HistoricalAwards=false"
+        },
+        {
+            "@type": "schema:Grant",
+            "name": "NSF-OPP",
+            "identifier": "#0741351",
+            "schema:url": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0741351&HistoricalAwards=false"
+        }
+    ],
+    "publications": [
+        {
+            "@type": "schema:CreativeWork",
+            "datePublished": "2014",
+            "doi": "https://doi.org/10.1371/journal.pone.0090081",
+            "title": "Gorman KB, Williams TD, Fraser WR (2014) Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis). PLoS ONE 9(3): e90081.",
+            "authors": []
+        }
+    ],
+    "access_request_contact": {
+        "givenName": "Allison",
+        "familyName": "Horst",
+        "email": "[email protected]"
+    },
+    "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"
+                },
+                "sample (organism)": [
+                    {
+                        "@type": "https://openminds.ebrains.eu/controlledTerms/Species",
+                        "name": "Pygoscelis adeliae",
+                        "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/NCBITaxon_9238",
+                        "synonym": "Adelie penguin"
+                    },
+                    {
+                        "@type": "https://openminds.ebrains.eu/controlledTerms/Species",
+                        "name": "Pygoscelis papua",
+                        "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/NCBITaxon_30457",
+                        "synonym": "Gentoo penguin"
+                    },
+                    {
+                        "@type": "https://openminds.ebrains.eu/controlledTerms/Species",
+                        "name": "Pygoscelis antarcticus",
+                        "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/NCBITaxon_79643",
+                        "synonym": "chinstrap penguin"
+                    }
+                ],
+                "sample (organism part)": {
+                    "@type": "https://openminds.ebrains.eu/controlledTerms/UBERONParcellation",
+                    "name": "body proper",
+                    "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/UBERON_0013702"
+                },
+                "homepage": {
+                    "@type": "https://schema.org/URL",
+                    "@value": "https://github.com/allisonhorst/palmerpenguins"
+                },
+                "data controller": {
+                    "@type": "https://schema.org/Person",
+                    "email": "[email protected]",
+                    "name": "Allison Horst"
+                },
+                "used for": {
+                    "@type": "https://schema.org/Thing",
+                    "name": "Testing effort for DBI backends",
+                    "url": "https://dbitest.r-dbi.org/",
+                    "description": "The dataset is used as example data for testing data base backend features in automated tests"
+                }
+            }
+        }
+    ]
+}

datalad_catalog/catalog/templates/context-tab-template.html

@@ -0,0 +1,70 @@
+<tbody v-if="context_tab_ready">
+<tr v-for="content_key in Object.keys(tabby.content).filter((k) => !k.startsWith('@'))">
+    <!-- PROPERTY NAME -->
+    <td width="30%">
+      <strong>
+        <!-- name -->
+        <span :id="tabby.name + '_' + content_key">{{ toUpperString(content_key) }}</span>
+        <!-- popover -->
+        <span v-if="tabby.content?.['@context']?.[content_key]">
+          &nbsp;<sup><i :id="tabby.name + '_' + content_key + '_info'" class="fas fa-circle-info"></i></sup>
+          <b-popover triggers="hover" :target="tabby.name + '_' + content_key + '_info'" placement="topleft">
+            <a :href="tabby.content?.['@context']?.[content_key]">{{ tabby.content?.['@context']?.[content_key] }}</a>
+          </b-popover>
+        </span>
+      </strong>
+    </td>
+    <!-- PROPERTY VALUE -->
+    <td>
+      <!-- Always work with an array; if single value given create a one-element array out of it -->
+      <span v-for="(val, idx) in Array.isArray(tabby.content[content_key]) ? tabby.content[content_key] : Array.of(tabby.content[content_key])">
+        <template v-if="typeof val === 'object'">
+          <!-- URL -->
+          <template v-if="val?.['@type'] == 'https://schema.org/URL'">
+            <a :href="val['@value']"> {{val['@value']}}</a><br>
+          </template>
+          <!-- Person -->
+          <template v-else-if="val?.['@type'] == 'https://schema.org/Person'">
+            <template v-if="Object.hasOwn(val, 'email')">
+              <!-- with e-mail -->
+              <a :href="'mailto:' + val.email"> {{val.name}}</a><br>
+            </template>
+            <template v-else>
+              <!-- without e-mail -->
+              {{val.name}}
+            </template>
+          </template>
+          <!-- Thing (name, url, description) -->
+          <template v-else-if="val?.['@type'] == 'https://schema.org/Thing'">
+            <template v-if="Object.hasOwn(val, 'name') && Object.hasOwn(val, 'url')">
+              <!-- with url -->
+              <a :href="val.url">{{val.name}}</a> {{val?.description}}
+            </template>
+            <template v-else>
+              <!-- without url -->
+              {{val?.name}} {{val?.description}}
+            </template>
+          </template>
+          <!-- OpenMINDS Species -->
+          <template v-else-if="val?.['@type'] == 'https://openminds.ebrains.eu/controlledTerms/Species'">
+            <a :href="val.preferredOntologyIdentifier">{{val.name}} ({{val?.synonym}})</a><br>
+          </template>
+          <!-- OpenMINDS UBERONParcellation -->
+          <template v-else-if="val?.['@type'] == 'https://openminds.ebrains.eu/controlledTerms/UBERONParcellation'">
+            <a :href="val.preferredOntologyIdentifier">{{val.name}}</a><br>
+          </template>
+          <!-- Anything else - type unknown or not declared -->
+          <template v-else>
+            {{val}}
+          </template>
+        </template>
+
+        <template v-else>
+          <!-- Primitive value, presumably text or number but we take any -->
+          {{val}}
+        </template>
+
+      </span>
+    </td>
+  </tr>
+</tbody>

datalad_catalog/catalog/templates/dataset-template.html

@@ -466,7 +466,7 @@ <h5><span v-if="fund.name">{{fund.name}}</span><span v-else><em>(fund name not s
           </span>
           <!-- EXTRA TABS -->
           <span v-if="selectedDataset.additional_display && selectedDataset.additional_display.length">
-            <span v-for="new_tab in selectedDataset.additional_display">
+            <span v-for="(new_tab, index) in selectedDataset.additional_display">
               <b-tab :key="new_tab.name" ref="tabelement">
                 <template v-slot:title>
                   <span v-if="new_tab.icon"><i :class="new_tab.icon"></i></span><span v-else><i class="fas fa-bars"></i></span> {{new_tab.name}}
@@ -480,7 +480,10 @@ <h5><span v-if="fund.name">{{fund.name}}</span><span v-else><em>(fund name not s
                         <th>Value(s)</th>
                       </tr>
                     </thead>
-                    <tbody>
+                    <!-- If the tab has @context, treat it as a semantic tab and try to look up each object's @type for custom rendering -->
+                    <context-tab-body v-if="new_tab.content?.['@context']" :tabby="new_tab" ></context-tab-body>
+                    <!-- If the tab has NO @context: standard additional tab rendering with no customizations -->
+                    <tbody v-else>
                       <tr v-for="content_key in Object.keys(new_tab.content)">
                          <td><strong>{{ content_key.charAt(0).toUpperCase() + content_key.slice(1) }}</strong></td> 
                          <td>
@@ -494,9 +497,9 @@ <h5><span v-if="fund.name">{{fund.name}}</span><span v-else><em>(fund name not s
                             </span>
                           </span>
                           <span v-else>{{ new_tab.content[content_key] }}</span>
-                         </td>
+                         </td>  
                       </tr>
-                     </tbody>
+                    </tbody>
                   </table>
                 </span>
               </b-tab>

datalad_catalog/constraints.py

@@ -22,6 +22,10 @@
     WithDescription,
 )
 
+from datalad_next.constraints.basic import (
+    EnsureDType,
+)
+
 __docformat__ = "restructuredtext"
 
 
@@ -31,6 +35,10 @@
 # - a JSON serialized string
 metadata_constraint = WithDescription(
     AnyOf(
+        WithDescription(
+            EnsureDType(dict),
+            error_message="not a valid Python dictionary",
+        ),
         WithDescription(
             EnsureJSON(),
             error_message="not valid JSON content",