Merging for v2.1.0

CHANGELOG.md

@@ -7,6 +7,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [2.1.0] - 2025-09-25
+
+### Added
+
+- Screencast for the Onto-DESIDE use case (#228).
+- Presentation as presented during the SemDev Workhop co-located with SEMANTiCS 2025 (#234).
+
+### Fixed
+
+- Link in table result header is no longer arbitrary if more than one predicate has the same object (#230.)
+- Avoided "Error getting variable options..." in templated queries with indirect sources to which the user has no read access (#231).
+- Corrected fetch status in templated queries with indirect sources to which the user has no read access (#232).
+
 ## [2.0.0] - 2025-05-29
 
 ### Added
@@ -270,4 +283,5 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 [1.6.0]: https://github.com/SolidLabResearch/miravi-a-linked-data-viewer/releases/tag/v1.6.0
 [1.7.0]: https://github.com/SolidLabResearch/miravi-a-linked-data-viewer/releases/tag/v1.7.0
 [2.0.0]: https://github.com/SolidLabResearch/miravi-a-linked-data-viewer/releases/tag/v2.0.0
-[Unreleased]: https://github.com/SolidLabResearch/miravi-a-linked-data-viewer/compare/v2.0.0...HEAD
+[2.1.0]: https://github.com/SolidLabResearch/miravi-a-linked-data-viewer/releases/tag/v2.1.0
+[Unreleased]: https://github.com/SolidLabResearch/miravi-a-linked-data-viewer/compare/v2.1.0...HEAD

README.md

@@ -8,6 +8,13 @@ Rooted in the Latin *mirari* ("to look with wonder"), it turns fragmented knowle
 
 <img src="./doc/miravi.png" width="200">
 
+Miravi is fully configurable. In the illustration below, [this configuration](./main/configs/onto-deside/config.json) is at work.
+
+![A screencast about configs/onto-deside](doc/screencast-onto-deside.gif)
+
+For a more complete presentation of Miravi and description of the design choices, please have a look at our
+[presentation as presented during the SemDev Workhop co-located with SEMANTiCS 2025](./doc/slides-miravi-semdev-2025.pdf).
+
 Table of contents:
 
 * [Preface](#preface)
@@ -27,9 +34,10 @@ Table of contents:
 * [Custom queries](#custom-queries)
 * [Representation Mapper](#representation-mapper)
 * [Advanced topics](#advanced-topics)
+  * [Adding your own configuration](#adding-your-own-configuration)
   * [Converting custom queries into common queries](#converting-custom-queries-into-common-queries)
+* [Illustrations](#illustrations)
 * [For developers](#for-developers)
-  * [Adding your own configuration](#adding-your-own-configuration)
   * [Testing](#testing)
     * [Additional prerequisites](#additional-prerequisites)
     * [Testing the production version](#testing-the-production-version)
@@ -366,6 +374,18 @@ They've already got styling matching that of `react-admin` and are easy to use.
 
 ## Advanced topics
 
+### Adding your own configuration
+
+The easiest way to add your own configuration is:
+
+1. Get inspired by the configuration in `main/configs/demo`.
+2. Choose your `<your-config>`: a string obeying regex `[a-z0-9-]+`; directory `main/configs/<your-config>` should not yet be in use.
+3. Add your own queries in the `main/configs/<your-config>/public/queries` directory and in general, your own resources in the `main/configs/<your-config>/public` directory.
+4. Add your own additional resources in `main/configs/<your-config>/public`, if the defaults you'll get from `main/config-defaults/public` are not satisfactory for you.
+5. Write your own `main/configs/<your-config>/config.json` file, following the [configuration file documentation above](#configuration-file).
+6. Run or build as documented above for the `demo` configuration, of course now using `<your-config>`.
+7. Consider a pull request to add your configuration to this repo.
+
 ### Converting custom queries into common queries
 
 Once you have your basic configuration working, you may extend it with custom queries interactively with the query editor
@@ -384,19 +404,12 @@ Follow these steps to get started:
 5. **Adapt any other properties** according to your preferences.
 6. **Save `main/configs/<your-config>/config.json`**, rerun or rebuild and refresh your browser to test.
 
-## For developers
+## Illustrations
 
-### Adding your own configuration
+* [A screencast about configs/onto-deside](doc/screencast-onto-deside.gif)
+* [Presentation as presented during the SemDev Workhop co-located with SEMANTiCS 2025](./doc/slides-miravi-semdev-2025.pdf)
 
-The easiest way to add your own configuration is:
-
-1. Get inspired by the configuration in `main/configs/demo`.
-2. Choose your `<your-config>`: a string obeying regex `[a-z0-9-]+`; directory `main/configs/<your-config>` should not yet be in use.
-3. Add your own queries in the `main/configs/<your-config>/public/queries` directory and in general, your own resources in the `main/configs/<your-config>/public` directory.
-4. Add your own additional resources in `main/configs/<your-config>/public`, if the defaults you'll get from `main/config-defaults/public` are not satisfactory for you.
-5. Write your own `main/configs/<your-config>/config.json` file, following the [configuration file documentation above](#configuration-file).
-6. Run or build as documented above for the `demo` configuration, of course now using `<your-config>`.
-7. Consider a pull request to add your configuration to this repo.
+## For developers
 
 ### Testing
 

main/configs/test/config.json

@@ -444,6 +444,38 @@
         "queryLocation": "/sourceQueries/index_example_common_lt.rq"
       }
     },
+    {
+      "id": "9081",
+      "queryGroupId": "gr-test",
+      "queryLocation": "component_material_one_variable.rq",
+      "name": "Component and materials - 1 variable (indirect source & indirect variables; one unauthorized source)",
+      "description": "Query components (including details about materials) with the sources obtained from index files and variables from the sources. One unauthorized indirect source, to check lenient while getting variable options.",
+      "indirectVariables": {
+        "queryLocations": [
+          "variableQueries/components_name_variable.rq"
+        ]
+      },
+      "sourcesIndex": {
+        "url": "http://localhost:8080/example/index-example-with-unauthorized-source-lt",
+        "queryLocation": "/sourceQueries/index_example_common_lt.rq"
+      }
+    },
+    {
+      "id": "9082",
+      "queryGroupId": "gr-test",
+      "queryLocation": "component_material_one_variable.rq",
+      "name": "Component and materials - 1 variable (indirect source & indirect variables; no indirect sources found)",
+      "description": "Query components (including details about materials) with zero sources obtained from index files and variables from the sources.",
+      "indirectVariables": {
+        "queryLocations": [
+          "variableQueries/components_name_variable.rq"
+        ]
+      },
+      "sourcesIndex": {
+        "url": "http://localhost:8080/example/index-example-texon-only-lt",
+        "queryLocation": "/sourceQueries/index_example_common_lt_bad.rq"
+      }
+    },
     {
       "id": "9090",
       "queryGroupId": "gr-test",
@@ -549,6 +581,32 @@
           "http://localhost:8080/example/favourite-musicians-file-does-not-exist"
         ]
       }
+    },
+    {
+      "id": "9200",
+      "queryGroupId": "gr-test",
+      "queryLocation": "schema_name.rq",
+      "name": "A query that looks for names that are the object of predicate schema:name",
+      "description": "Tests a single link in the 'name' column header.",
+      "comunicaContext": {
+        "sources": [
+          "http://localhost:8080/example/names-labels"
+        ],
+        "lenient": true
+      }
+    },
+    {
+      "id": "9201",
+      "queryGroupId": "gr-test",
+      "queryLocation": "schema_name_rdfs_label.rq",
+      "name": "A query that looks for names that are both the objects of predicates schema:name and rdfs:label",
+      "description": "Tests two links in the 'name' column header.",
+      "comunicaContext": {
+        "sources": [
+          "http://localhost:8080/example/names-labels"
+        ],
+        "lenient": true
+      }
     }
   ]
 }

main/configs/test/public/queries/schema_name.rq

@@ -0,0 +1,6 @@
+PREFIX schema: <http://schema.org/>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT ?name WHERE {
+  ?s schema:name ?name.
+}

main/configs/test/public/queries/schema_name_rdfs_label.rq

@@ -0,0 +1,7 @@
+PREFIX schema: <http://schema.org/>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT ?name WHERE {
+  ?s schema:name ?name.
+  ?s rdfs:label ?name.
+}

main/configs/test/public/queries/sourceQueries/index_example_common_lt_bad.rq

@@ -0,0 +1,5 @@
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?source WHERE {
+  ?s rdfs:seeAlso_hihihahahoho ?source.
+}

main/src/components/ActionBar/SourceFetchStatusIcon/SourceFetchStatusIcon.jsx

@@ -1,3 +1,4 @@
+import PendingIcon from '@mui/icons-material/Pending';
 import CheckIcon from '@mui/icons-material/Check';
 import CancelIcon from "@mui/icons-material/Cancel";
 import RemoveCircleOutlineIcon from '@mui/icons-material/RemoveCircleOutline';
@@ -14,7 +15,13 @@ import comunicaEngineWrapper from '../../../comunicaEngineWrapper/comunicaEngine
 function SourceFetchStatusIcon({ source }) {
   const status = comunicaEngineWrapper.getFetchStatusNumber(source);
 
-  if (comunicaEngineWrapper.getFetchSuccess(source)) {
+  if (comunicaEngineWrapper.getFetchSuccess(source) === undefined) {
+    return (
+      <Tooltip title="Not fetched">
+        <PendingIcon size="small" />
+      </Tooltip>
+    );
+  } else if (comunicaEngineWrapper.getFetchSuccess(source)) {
     return (
       <Tooltip title="Fetch was successful">
         <CheckIcon size="small" />

main/src/components/ListResultTable/QueryResultList/TableHeader/TableHeader.jsx

@@ -60,16 +60,18 @@ function TableHeader({ children }) {
                 </span>
               </Tooltip>}
               {!!variableOntology && variableOntology[child.props.source] && (
-                <Link
-                  target="_blank"
-                  href={variableOntology[child.props.source]}
-                  sx={{ height: "100%", margin: "0 5px", "& > *": { verticalAlign: "middle" } }}
-                >
-                  <LinkIcon
-                    fontSize="small"
-                    sx={{ height: "100%", color: "gray" }}
-                  />
-                </Link>
+                variableOntology[child.props.source].map((link) => (
+                  <Link
+                    target="_blank"
+                    href={link}
+                    sx={{ height: "100%", margin: "0 0 0 5px", "& > *": { verticalAlign: "middle" } }}
+                  >
+                    <LinkIcon
+                      fontSize="small"
+                      sx={{ height: "100%", color: "gray" }}
+                    />
+                  </Link>
+                ))
               )}
               {sort.field === child.props.source && (
                 <>

main/src/comunicaEngineWrapper/comunicaEngineWrapper.js

@@ -36,6 +36,7 @@ class ComunicaEngineWrapper {
     this._fetchSuccess = {};
     this._fetchStatusNumber = {};
     this._underlyingFetchFunction = undefined;
+    // LOG console.log(`Comunica engines reset`);
   }
 
   getFetchSuccess(arg) {
@@ -168,13 +169,14 @@ class ComunicaEngineWrapper {
    * @param {array} httpProxies - array of httpProxy definitions
    */
   _prepareQuery(context, httpProxies) {
-    // avoid faulty fetch status for sources cached in Comunica
-    for (const source of context.sources) {
-      this._fetchSuccess[source] = true;
-    }
-    this._underlyingFetchFunction = fetch;
+    // note: there is no need to preset this._fetchSuccess[source] here;
+    // if Comunica caches, we still have the previous value
     if (getDefaultSession().info.isLoggedIn) {
       this._underlyingFetchFunction = authFetch;
+      // LOG console.log(`Using authFetch as underlying fetch function`);
+    } else {
+      this._underlyingFetchFunction = fetch;
+      // LOG console.log(`Using fetch as underlying fetch function`);
     }
     context.fetch = ComunicaEngineWrapper._getWrappedFetchFunction(this._underlyingFetchFunction, httpProxies, this);
   }

main/src/dataProvider/SparqlDataProvider.js

@@ -189,10 +189,10 @@ function replaceVariables(rawText, variableValues) {
 }
 
 /**
- * Given a query and an object, this function returns the predicate of the object in the query.
+ * Given a query and an object, this function returns the predicates of the object in the query.
  * 
  * @param {object} query - the parsed query in which the predicate is to be looked for.
- * @returns {object} an object with the variable as key and the predicate as value.
+ * @returns {object} an object with the variable as key and as value an array of predicates.
  */
 function findPredicates(query) {
   const ontologyMapper = {};
@@ -204,7 +204,11 @@ function findPredicates(query) {
       if (part.triples) {
         for (const triple of part.triples) {
           if (triple.predicate.termType !== "Variable") {
-            ontologyMapper[triple.object.value] = triple.predicate.value;
+            if (!ontologyMapper[triple.object.value]) {
+              ontologyMapper[triple.object.value] = [triple.predicate.value];
+            } else if (!ontologyMapper[triple.object.value].includes(triple.predicate.value)) {
+              ontologyMapper[triple.object.value].push(triple.predicate.value);
+            }
           }
         }
       }
@@ -293,22 +297,19 @@ async function getSourcesFromSourcesIndex(sourcesIndex, httpProxies) {
 
     const bindingsStream = await comunicaEngineWrapper.queryBindings(queryStringIndexSource,
       { lenient: true, sources: [sourcesIndex.url] }, httpProxies, { engine: "link-traversal" });
-    await new Promise((resolve, reject) => {
-      bindingsStream.on('data', (bindings) => {
-        // LOG console.log(`getSourcesFromSourcesIndex bindings: ${bindings.toString()}`);
-        for (const term of bindings.values()) {  // check for 1st value
-          const source = term.value;
-          if (!sourcesList.includes(source)) {
-            // LOG console.log(`getSourcesFromSourcesIndex adding source: ${source}`);
-            sourcesList.push(source);
-          }
-          // we only want the first term, whatever the variable's name is (note: a for ... of loop seems the only way to access it)
-          break;
+    const bindingsArray = await bindingsStream.toArray();
+    for (const bindings of bindingsArray) {
+      // LOG console.log(`getSourcesFromSourcesIndex bindings: ${bindings.toString()}`);
+      for (const term of bindings.values()) {  // check for 1st value
+        const source = term.value;
+        if (!sourcesList.includes(source)) {
+          // LOG console.log(`getSourcesFromSourcesIndex adding source: ${source}`);
+          sourcesList.push(source);
         }
-      });
-      bindingsStream.on('end', resolve);
-      bindingsStream.on('error', reject);
-    });
+        // we only want the first term, whatever the variable's name is (note: a for ... of loop seems the only way to access it)
+        break;
+      }
+    }
   }
   catch (error) {
     throw new Error(`Error adding sources from index: ${error.message}`);
@@ -380,6 +381,9 @@ async function getVariableOptions(query) {
   }
   // END duplicated chunk of code
 
+  if (query.comunicaContext.sources.length === 0) {
+    throw new Error(`Error getting variable options... No sources found.`);
+  }
 
   let variableOptions;
   let queryStringList = [];
@@ -417,35 +421,35 @@ async function getVariableOptions(query) {
 
   try {
     for (const queryString of queryStringList) {
+      // queryBindings with lenient true to avoid errors with unauthorized sources
       const bindingsStream = await comunicaEngineWrapper.queryBindings(queryString,
-        { sources: query.comunicaContext.sources }, query.httpProxies);
-      await new Promise((resolve, reject) => {
-        bindingsStream.on('data', (bindings) => {
-          // LOG console.log(`getVariableOptions bindings: ${bindings.toString()}`);
-          for (const [variable, term] of bindings) {
-            const name = variable.value;
-            if (!variableOptions[name]) {
-              variableOptions[name] = [];
-            }
-            const variableValue = termToSparqlCompatibleString(term);
-            if (variableValue && !variableOptions[name].includes(variableValue)) {
-              // LOG console.log(`getVariableOptions adding variable option for '${name}': ${variableValue}`);
-              variableOptions[name].push(variableValue);
-            }
+        { lenient: true, sources: query.comunicaContext.sources }, query.httpProxies);
+      // convert stream to array (works when no bindings found - handling events 'data', 'end' and 'error' does not work when no bindints found)
+      const bindingsArray = await bindingsStream.toArray();
+      for (const bindings of bindingsArray) {
+        // LOG console.log(`getVariableOptions bindings: ${bindings.toString()}`);
+        for (const [variable, term] of bindings) {
+          const name = variable.value;
+          if (!variableOptions[name]) {
+            variableOptions[name] = [];
           }
-        });
-        bindingsStream.on('end', resolve);
-        bindingsStream.on('error', reject);
-      });
+          const variableValue = termToSparqlCompatibleString(term);
+          if (variableValue && !variableOptions[name].includes(variableValue)) {
+            // LOG console.log(`getVariableOptions adding variable option for '${name}': ${variableValue}`);
+            variableOptions[name].push(variableValue);
+          }
+        }
+      }
     }
   }
   catch (error) {
     throw new Error(`Error getting variable options... ${error.message}`);
   }
 
-  if (variableOptions == {}) {
-    throw new Error(`Error getting variable options... The variable options are empty`);
+  if (Object.keys(variableOptions).length === 0) {
+    throw new Error(`Error getting variable options... No variable options found.`);
   }
+
   return variableOptions;
 }