@abi-software/simulationvuer 3.0.1 → 3.0.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/simulationvuer",
-  "version": "3.0.1",
+  "version": "3.0.2",
   "private": false,
   "scripts": {
     "serve": "vite serve --host --force",
@@ -18,9 +18,10 @@
   },
   "dependencies": {
     "@abi-software/plotvuer": "1.0.7",
-    "@opencor/opencor": "^0.20251112.0",
+    "@opencor/opencor": "^0.20251205.0",
     "element-plus": "2.8.4",
     "jsonschema": "^1.4.0",
+    "mathjs": "^15.1.0",
     "unplugin-vue-components": "^0.26.0",
     "vue": "^3.4.21"
   },

package/src/components/SimulationVuer.vue

@@ -3,9 +3,9 @@
     <div class="container" v-if="opencorOmexFile === null">
       <p v-if="!hasValidSimulationUiInfo && !showUserMessage" class="default error"><span class="error">Error:</span> {{ errorMessage }}.</p>
       <div class="main" v-if="hasValidSimulationUiInfo">
-        <div class="main-left" :class="{'with-buttons': !libopencorSet || uuid}">
-          <p class="default name" v-if="!libopencorSet">{{ name }}</p>
-          <el-divider v-if="!libopencorSet"></el-divider>
+        <div class="main-left" :class="{'with-buttons': uuid}">
+          <p class="default name">{{ name }}</p>
+          <el-divider></el-divider>
           <p class="default input-parameters">Input parameters</p>
           <div class="input scrollbar">
             <SimulationVuerInput v-for="(input, index) in simulationUiInfo.input"
@@ -20,18 +20,15 @@
             />
           </div>
           <div class="buttons-container">
-            <div class="primary-button" v-if="!libopencorSet">
+            <div class="primary-button">
               <el-button type="primary" size="small" @click="startSimulation()">Run Simulation</el-button>
             </div>
             <div class="secondary-button" v-if="uuid">
               <el-button size="small" @click="runOnOsparc()">Run on oSPARC</el-button>
             </div>
-            <div class="secondary-button" v-if="!libopencorSet">
+            <div class="secondary-button">
               <el-button size="small" @click="viewDataset()">View Dataset</el-button>
             </div>
-            <div class="secondary-button" v-if="libopencorSet && idType === 'pmr_path'">
-              <el-button size="small" @click="viewWorkspace()">View Workspace</el-button>
-            </div>
             <p class="default note" v-if="uuid">Additional parameters are available on oSPARC</p>
           </div>
         </div>
@@ -63,7 +60,6 @@ import SimulationVuerInput from "./SimulationVuerInput.vue";
 import { ElButton, ElDivider, ElLoading } from "element-plus";
 import { evaluateValue, finaliseUi, OPENCOR_SOLVER_NAME } from "./common.js";
 import { validJson } from "./json.js";
-import libOpenCOR from "https://mapcore-demo.org/current/opencor-wasm/0.0.3/libopencor.js";
 import { markRaw } from "vue";
 import { create, all } from "mathjs";
 import OpenCOR from '@opencor/opencor';
@@ -157,8 +153,6 @@ export default {
       isMounted: false,
       isSimulationValid: true,
       layout: [],
-      libopencor: undefined,
-      libopencorSet: false,
       model: undefined,
       name: null,
       opencorBasedSimulation: true,
@@ -193,150 +187,6 @@ export default {
         },
       };
     },
-    /**
-     * @public
-     * Manage the file associated with the given `url` and `fileContents`.
-     * @arg `url`
-     * @arg `fileContents`
-     */
-    manageFile(url, fileContents) {
-      let file = this.fileManager.file(url);
-
-      if (file === null) {
-        file = new this.libopencor.File(url);
-      }
-
-      const fileContentsPtr = this.libopencor._malloc(fileContents.length);
-      const mem = new Uint8Array(this.libopencor.HEAPU8.buffer, fileContentsPtr, fileContents.length);
-
-      mem.set(fileContents);
-
-      file.setContents(fileContentsPtr, fileContents.length);
-
-      this.libopencor._free(fileContentsPtr);
-
-      return file;
-    },
-    /**
-     * @public
-     * Run a PMR-based COMBINE archive using libOpenCOR.
-     */
-    runSimulation() {
-      if (this.instance === undefined) {
-        // Retrieve an instance of the model.
-
-        const document = new this.libopencor.SedDocument(this.fileManager.file(PMR_URL + this.id));
-
-        this.model = markRaw(document.model());
-        this.instance = markRaw(document.instantiate());
-
-        document.delete();
-      }
-
-      // Run the simulation after passing some changes, if any, to the model.
-
-      this.model.removeAllChanges();
-
-      for (const [parameter, value] of Object.entries(this.parametersData())) {
-        const parameterParts = parameter.split("/")
-
-        this.model.addChange(new this.libopencor.SedChangeAttribute(parameterParts[0], parameterParts[1], value.toString()));
-      }
-
-      this.instance.run();
-
-      // Retrieve the simulation results.
-
-      const res = {};
-      const instanceTask = this.instance.task(0);
-      let foundAllOutputs = true;
-      let foundOutput;
-
-      for (const output of this.outputData()) {
-        foundOutput = false;
-
-        if (output === instanceTask.voiName) {
-          res[output] = instanceTask.voiAsArray;
-
-          foundOutput = true;
-        }
-
-        if (res[output] === undefined) {
-          for (let i = 0; i < instanceTask.stateCount; ++i) {
-            if (output === instanceTask.stateName(i)) {
-              res[output] = instanceTask.stateAsArray(i);
-
-              foundOutput = true;
-
-              break;
-            }
-          }
-        }
-
-        if (res[output] === undefined) {
-          for (let i = 0; i < instanceTask.rateCount; ++i) {
-            if (output === instanceTask.rateName(i)) {
-              res[output] = instanceTask.rateAsArray(i);
-
-              foundOutput = true;
-
-              break;
-            }
-          }
-        }
-
-        if (res[output] === undefined) {
-          for (let i = 0; i < instanceTask.constantCount; ++i) {
-            if (output === instanceTask.constantName(i)) {
-              res[output] = instanceTask.constantAsArray(i);
-
-              foundOutput = true;
-
-              break;
-            }
-          }
-        }
-
-        if (res[output] === undefined) {
-          for (let i = 0; i < instanceTask.computedConstantCount; ++i) {
-            if (output === instanceTask.computedConstantName(i)) {
-              res[output] = instanceTask.computedConstantAsArray(i);
-
-              foundOutput = true;
-
-              break;
-            }
-          }
-        }
-
-        if (res[output] === undefined) {
-          for (let i = 0; i < instanceTask.algebraicCount; ++i) {
-            if (output === instanceTask.algebraicName(i)) {
-              res[output] = instanceTask.algebraicAsArray(i);
-
-              foundOutput = true;
-
-              break;
-            }
-          }
-        }
-
-        if (!foundOutput) {
-          console.warn("SIMULATION: output '" + output + "' could not be found.");
-
-          foundAllOutputs = false;
-        }
-      }
-
-      if (foundAllOutputs) {
-        this.processSimulationResults(res);
-      } else {
-        this.hasValidSimulationUiInfo = false;
-        this.errorMessage = "some outputs could not be found";
-      }
-
-      this.showUserMessage = false;
-    },
     /**
      * @public
      * Build the simulation UI using `simulationUiInfo`, a JSON object that describes the contents of the simulation UI.
@@ -349,7 +199,7 @@ export default {
 
       // Make sure that the simulation UI information is valid.
 
-      this.hasValidSimulationUiInfo = validJson(this.simulationUiInfo, this.libopencor === undefined);
+      this.hasValidSimulationUiInfo = validJson(this.simulationUiInfo);
 
       if (!this.hasValidSimulationUiInfo) {
         this.errorMessage = "the simulation.json file is malformed";
@@ -357,26 +207,23 @@ export default {
         return;
       }
 
-      // Retrieve and keep track of the solver to be used for the simulation, if
-      // needed.
-
-      if (this.libopencor === undefined) {
-        this.simulationUiInfo.simulation.solvers.forEach((solver) => {
-          if ((solver.if === undefined) || evaluateValue(this, solver.if)) {
-            this.solver = solver;
-          }
-        });
-
-        if (this.solver === undefined) {
-          this.hasValidSimulationUiInfo = false;
-          this.errorMessage = "no solver name and/or solver version specified";
+      // Retrieve and keep track of the solver to be used for the simulation.
 
-          return;
+      this.simulationUiInfo.simulation.solvers.forEach((solver) => {
+        if ((solver.if === undefined) || evaluateValue(this, solver.if)) {
+          this.solver = solver;
         }
+      });
 
-        this.opencorBasedSimulation = this.solver.name === OPENCOR_SOLVER_NAME;
+      if (this.solver === undefined) {
+        this.hasValidSimulationUiInfo = false;
+        this.errorMessage = "no solver name and/or solver version specified";
+
+        return;
       }
 
+      this.opencorBasedSimulation = this.solver.name === OPENCOR_SOLVER_NAME;
+
       // Initialise our UI.
 
       this.simulationUiInfo.output.data.forEach((data) => {
@@ -433,40 +280,6 @@ export default {
         finaliseUi(this);
       });
     },
-    /**
-     * @public
-     * Extract the simulation UI JSON file from the given file contents and build the simulation UI.
-     * @arg `libopencor`
-     * @arg `fileContents`
-     */
-    extractAndBuildSimulationUi(libopencor, fileContents) {
-      this.libopencor = markRaw(libopencor);
-      this.libopencorSet = true;
-      this.fileManager = markRaw(this.libopencor.FileManager.instance());
-
-      const file = this.manageFile(PMR_URL + this.id, fileContents);
-
-      if (file.type.value !== libopencor.File.Type.COMBINE_ARCHIVE.value) {
-        this.showUserMessage = false;
-      } else {
-        const decoder = new TextDecoder();
-        const simulationJson = file.childFileFromFileName("simulation.json");
-
-        if (simulationJson === null) {
-          this.errorMessage = "no simulation JSON file could be found";
-
-          this.showUserMessage = false;
-        } else {
-          const simulationUiInfo = JSON.parse(decoder.decode(simulationJson.contents()));
-
-          this.showUserMessage = false;
-
-          this.$nextTick(() => {
-            this.buildSimulationUi(simulationUiInfo);
-          });
-        }
-      }
-    },
     /**
      * @public
      * Run the simulation-based dataset directly on oSPARC. Not all simulation-based datasets can be run directly on
@@ -749,18 +562,8 @@ export default {
       this.opencorOmexFile = this.id;
     } else if (this.idType === IdType.PMR_PATH) {
       this.opencorOmexFile = PMR_URL + this.id;
-    } else {
-      // Extract the simulation UI JSON file from the COMBINE archive and build
-      // the simulation UI.
-
-      this.userMessage = "Retrieving COMBINE archive...";
-      this.showUserMessage = true;
-
-      this.$nextTick(() => {
-        libOpenCOR().then((libopencor) => {
-          this.extractAndBuildSimulationUi(libopencor, this.id);
-        });
-      });
+    } else { // IdType.RAW_COMBINE_ARCHIVE
+      this.opencorOmexFile = this.id;
     }
   },
   mounted: function () {

package/src/components/common.js

@@ -28,15 +28,6 @@ export function updateUi(parent) {
 
       parent.$refs.simInput[index].visible = (input.visible === undefined) ? true : evaluateValue(parent, input.visible);
     });
-
-    if (parent.libopencor !== undefined) {
-      parent.userMessage = "Running the model...";
-      parent.showUserMessage = true;
-
-      parent.$nextTick(() => {
-        parent.runSimulation();
-      });
-    }
   });
 }
 

package/src/components/json.js

@@ -1,7 +1,7 @@
 import { Validator } from "jsonschema";
 import { OPENCOR_SOLVER_NAME } from "./common.js";
 
-export function validJson(json, simulationInfoNeeded) {
+export function validJson(json) {
   // Check the JSON against our schema.
 
   const validator = new Validator();
@@ -214,7 +214,7 @@ export function validJson(json, simulationInfoNeeded) {
             type: "array",
           },
         },
-        required: simulationInfoNeeded,
+        required: true,
         type: "object",
       },
     },
@@ -436,87 +436,85 @@ export function validJson(json, simulationInfoNeeded) {
 
   // Make sure that the simulation information makes sense.
 
-  if (simulationInfoNeeded) {
-    let needOpencorSettings = false;
-
-    if (!json.simulation.solvers.every((solver) => {
-      if (solver.if !== undefined) {
-        if (solver.if === "") {
-          console.warn("JSON: a simulation solver if must not be empty.");
-
-          return false;
-        }
-      }
-
-      if (solver.input !== undefined) {
-        if (solver.input.name === "") {
-          console.warn("JSON: a simulation solver input name must not be empty.");
-
-          return false;
-        }
+  let needOpencorSettings = false;
 
-        if (solver.input.value === "") {
-          console.warn("JSON: a simulation solver input value must not be empty.");
+  if (!json.simulation.solvers.every((solver) => {
+    if (solver.if !== undefined) {
+      if (solver.if === "") {
+        console.warn("JSON: a simulation solver if must not be empty.");
 
-          return false;
-        }
+        return false;
       }
+    }
 
-      if (solver.name === "") {
-        console.warn("JSON: a simulation solver name must not be empty.");
+    if (solver.input !== undefined) {
+      if (solver.input.name === "") {
+        console.warn("JSON: a simulation solver input name must not be empty.");
 
         return false;
       }
 
-      needOpencorSettings = needOpencorSettings || (solver.name === OPENCOR_SOLVER_NAME);
-
-      if (solver.version === "") {
-        console.warn("JSON: a simulation solver version must not be empty.");
+      if (solver.input.value === "") {
+        console.warn("JSON: a simulation solver input value must not be empty.");
 
         return false;
       }
+    }
+
+    if (solver.name === "") {
+      console.warn("JSON: a simulation solver name must not be empty.");
 
-      return true;
-    })) {
       return false;
     }
 
-    if (needOpencorSettings && (json.simulation.opencor === undefined)) {
-      console.warn("JSON: the simulation solver for OpenCOR is specified so simulation OpenCOR settings must also be specified.");
+    needOpencorSettings = needOpencorSettings || (solver.name === OPENCOR_SOLVER_NAME);
+
+    if (solver.version === "") {
+      console.warn("JSON: a simulation solver version must not be empty.");
 
       return false;
     }
 
-    if (json.simulation.opencor !== undefined) {
-      if (json.simulation.opencor.resource === "") {
-        console.warn("JSON: the simulation OpenCOR resource must not be empty.");
+    return true;
+  })) {
+    return false;
+  }
 
-        return false;
-      }
+  if (needOpencorSettings && (json.simulation.opencor === undefined)) {
+    console.warn("JSON: the simulation solver for OpenCOR is specified so simulation OpenCOR settings must also be specified.");
 
-      if (json.simulation.opencor.endingPoint !== undefined) {
-        if (json.simulation.opencor.pointInterval !== undefined) {
-          if (json.simulation.opencor.endingPoint <= 0.0) {
-            console.warn("JSON: the simulation OpenCOR ending point (" + json.simulation.opencor.endingPoint + ") must be greater than zero.");
+    return false;
+  }
 
-            return false;
-          }
+  if (json.simulation.opencor !== undefined) {
+    if (json.simulation.opencor.resource === "") {
+      console.warn("JSON: the simulation OpenCOR resource must not be empty.");
 
-          if (json.simulation.opencor.pointInterval <= 0.0) {
-            console.warn("JSON: the simulation OpenCOR point interval (" + json.simulation.opencor.pointInterval + ") must be greater than zero.");
+      return false;
+    }
+
+    if (json.simulation.opencor.endingPoint !== undefined) {
+      if (json.simulation.opencor.pointInterval !== undefined) {
+        if (json.simulation.opencor.endingPoint <= 0.0) {
+          console.warn("JSON: the simulation OpenCOR ending point (" + json.simulation.opencor.endingPoint + ") must be greater than zero.");
+
+          return false;
+        }
 
-            return false;
-          }
-        } else {
-          console.warn("JSON: a simulation OpenCOR ending point is specified so a simulation OpenCOR point interval must also be specified.");
+        if (json.simulation.opencor.pointInterval <= 0.0) {
+          console.warn("JSON: the simulation OpenCOR point interval (" + json.simulation.opencor.pointInterval + ") must be greater than zero.");
 
           return false;
         }
-      } else if (json.simulation.opencor.pointInterval !== undefined) {
-        console.warn("JSON: a simulation OpenCOR point interval is specified so a simulation OpenCOR ending point must also be specified.");
+      } else {
+        console.warn("JSON: a simulation OpenCOR ending point is specified so a simulation OpenCOR point interval must also be specified.");
 
         return false;
       }
+    } else if (json.simulation.opencor.pointInterval !== undefined) {
+      console.warn("JSON: a simulation OpenCOR point interval is specified so a simulation OpenCOR ending point must also be specified.");
+
+      return false;
     }
   }