feat(dispatch): require configuration of academic use for commercial …

…solvers
biosimulations · Sep 28, 2021 · 6c5307c · 6c5307c
1 parent a696fbc
commit 6c5307c
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Showing 17 changed files with 81 additions and 1 deletion.
diff --git a/apps/api/src/simulation-run/simulation-run.controller.ts b/apps/api/src/simulation-run/simulation-run.controller.ts
@@ -179,6 +179,7 @@ export class SimulationRunController {
       memory: run.memory,
       maxTime: run.maxTime,
       envVars: run.envVars,
+      academicUse: run.academicUse,
       isPublic: run.public,
     };
     const sim = await this.dispatchQueue.add(message);
@@ -223,6 +224,7 @@ export class SimulationRunController {
       run.memory,
       run.maxTime,
       run.envVars,
+      run.academicUse,
       run.submitted,
       run.updated,
       run.public,

diff --git a/apps/api/src/simulation-run/simulation-run.model.ts b/apps/api/src/simulation-run/simulation-run.model.ts
@@ -150,6 +150,9 @@ export class SimulationRunModel extends Document {
   })
   envVars!: EnvironmentVariable[];
 
+  @Prop({ type: Boolean, required: false, default: false })
+  academicUse!: boolean;
+
   @Prop()
   submitted!: Date;
 
@@ -178,6 +181,7 @@ export type SimulationRunModelType = Pick<
   | 'memory'
   | 'maxTime'
   | 'envVars'
+  | 'academicUse'
   | 'refreshCount'
   | 'submitted'
   | 'updated'

diff --git a/apps/dispatch-service/src/app/services/hpc/hpc.service.ts b/apps/dispatch-service/src/app/services/hpc/hpc.service.ts
@@ -32,6 +32,7 @@ export class HpcService {
     memory: number,
     maxTime: number,
     envVars: EnvironmentVariable[],
+    academicUse: boolean,
     fileName: string,
   ): Promise<{
     stdout: string;
@@ -49,6 +50,7 @@ export class HpcService {
       memory,
       maxTime,
       envVars,
+      academicUse,
       fileName,
       endpoint,
       id,

diff --git a/apps/dispatch-service/src/app/services/sbatch/sbatch.service.ts b/apps/dispatch-service/src/app/services/sbatch/sbatch.service.ts
@@ -13,6 +13,7 @@ export class SbatchService {
     memory: number,
     maxTime: number,
     envVars: EnvironmentVariable[],
+    academicUse: boolean,
     omexName: string,
     apiDomain: string,
     simId: string,
@@ -41,7 +42,10 @@ export class SbatchService {
       apiDomain = 'https://run.api.biosimulations.dev/';
     }
 
-    const singularityRunEnvVars = this.configService.get('singularity.envVars');
+    let singularityRunEnvVars = this.configService.get('singularity.envVarAll');
+    if (academicUse) {
+      singularityRunEnvVars = singularityRunEnvVars.concat(this.configService.get('singularity.envVarAcademic'));
+    }
 
     const allEnvVars = envVars.concat(singularityRunEnvVars);
 

diff --git a/apps/dispatch-service/src/app/submission/dispatch.proccessor.ts b/apps/dispatch-service/src/app/submission/dispatch.proccessor.ts
@@ -36,6 +36,7 @@ export class DispatchProcessor {
       data.memory,
       data.maxTime,
       data.envVars,
+      data.academicUse,
       data.fileName,
     );
 

diff --git a/apps/dispatch/src/app/components/run/dispatch/dispatch.component.html b/apps/dispatch/src/app/components/run/dispatch/dispatch.component.html
@@ -355,6 +355,39 @@
       </div>
     </div>
 
+    <div class="form-section">
+      <div class="form-section-head">
+        <div class="mat-form-field-prefix">
+          <biosimulations-icon icon="simulator"></biosimulations-icon>
+        </div>
+        <div class="form-section-head-title-subtitle">
+          <div class="form-section-title">Commercial solvers</div>
+          <div class="form-section-subtitle">
+            Optional: To execute the simulation with a commercial solver, confirm the purpose of the simulation is academic research or education.
+          </div>
+        </div>
+      </div>
+
+      <div class="form-section-body">
+        <div class="form-field-group">
+          <mat-checkbox
+            formControlName="academicUse"
+            [disableRipple]="true"
+            color="primary"
+          >
+            The purpose of this simulation is academic research or education.
+          </mat-checkbox>
+          <mat-hint>
+            <p>Some simulation tools, such as COBRApy and RBApy, can optionally execute simulations using commercial solvers such as Gurobi <a href="https://www.gurobi.com/products/gurobi-optimizer/" target="_blank"><biosimulations-icon icon="link"></biosimulations-icon></a>. These commercial solvers are often more accurate and more performant. However, these commercial solvers are not required to execute any of the available simulation tools. All of the available simulation tools can be run with freely available solvers.</p>
+
+            <p>Optionally, users can use these commercial solvers for academic research and education. To use these commercial solvers, check the box above to confirm that you are using runBioSimulations for academic research or education.</p>
+
+            <p>Non-academic users can execute simulations with commercial solvers by (a) running simulations through runBioSimulations' API and providing license keys through environment variables or (b) using the Docker images, command-line programs, or Python APIs for simulation tools on their own machines with their own license key environment variables or license files.</p>
+          </mat-hint>
+        </div>
+      </div>
+    </div>
+
     <div class="form-section">
       <div class="form-section-head">
         <div class="mat-form-field-prefix">

diff --git a/apps/dispatch/src/app/components/run/dispatch/dispatch.component.ts b/apps/dispatch/src/app/components/run/dispatch/dispatch.component.ts
@@ -148,6 +148,7 @@ export class DispatchComponent implements OnInit, OnDestroy {
         ],
         simulator: ['', [Validators.required]],
         simulatorVersion: ['', [Validators.required]],
+        academicUse: [false],
         cpus: [
           1,
           [
@@ -732,6 +733,7 @@ export class DispatchComponent implements OnInit, OnDestroy {
     const memory: number = this.formGroup.value.memory; // in GB
     const maxTime: number = this.formGroup.value.maxTime; // in min
     const envVars: EnvironmentVariable[] = [];
+    const academicUse: boolean = this.formGroup.value.academicUse;
     const name: string = this.formGroup.value.name;
     const email: string | null = this.formGroup.value.email || null;
 
@@ -747,6 +749,7 @@ export class DispatchComponent implements OnInit, OnDestroy {
         memory,
         maxTime,
         envVars,
+        academicUse,
         name,
         email,
       );
@@ -760,6 +763,7 @@ export class DispatchComponent implements OnInit, OnDestroy {
         memory,
         maxTime,
         envVars,
+        academicUse,
         name,
         email,
       );
@@ -774,6 +778,7 @@ export class DispatchComponent implements OnInit, OnDestroy {
         memory,
         maxTime,
         envVars,
+        academicUse,
         email,
       ),
     );
@@ -789,6 +794,7 @@ export class DispatchComponent implements OnInit, OnDestroy {
     memory: number, // in GB
     maxTime: number, // min min
     envVars: EnvironmentVariable[],
+    academicUse: boolean,
     email: string | null,
   ): void {
     const simulationId = data['id'];
@@ -803,6 +809,7 @@ export class DispatchComponent implements OnInit, OnDestroy {
       memory: memory,
       maxTime: maxTime,
       envVars: envVars,
+      academicUse: academicUse,
       submittedLocally: true,
       status: SimulationRunStatus.QUEUED,
       runtime: undefined,

diff --git a/apps/dispatch/src/app/components/simulations/view/view.model.ts b/apps/dispatch/src/app/components/simulations/view/view.model.ts
@@ -16,6 +16,7 @@ export interface FormattedSimulation {
   memory: number; // GB
   maxTime: number; // min
   envVars: EnvironmentVariable[];
+  academicUse: boolean;
   status: SimulationRunStatus;
   statusRunning: boolean;
   statusSucceeded: boolean;

diff --git a/apps/dispatch/src/app/components/simulations/view/view.service.ts b/apps/dispatch/src/app/components/simulations/view/view.service.ts
@@ -91,6 +91,7 @@ export class ViewService {
       memory: simulation.memory || 8,
       maxTime: simulation.maxTime || 20,
       envVars: simulation.envVars || [],
+      academicUse: simulation.academicUse || false,
       status: simulation.status,
       statusRunning: statusRunning,
       statusSucceeded: statusSucceeded,

diff --git a/apps/dispatch/src/app/datamodel.ts b/apps/dispatch/src/app/datamodel.ts
@@ -14,6 +14,7 @@ export interface UnknownSimulation {
   memory?: null; // GB
   maxTime?: null; // min
   envVars?: null;
+  academicUse?: null;
   status?: null;
   runtime?: null;
   submitted?: null;
@@ -33,6 +34,7 @@ export interface Simulation {
   memory: number; // GB
   maxTime: number; // min
   envVars: EnvironmentVariable[];
+  academicUse: boolean;
   status: SimulationRunStatus;
   runtime?: number;
   submitted: Date;

diff --git a/apps/dispatch/src/app/services/dispatch/dispatch.service.ts b/apps/dispatch/src/app/services/dispatch/dispatch.service.ts
@@ -93,6 +93,7 @@ export class DispatchService {
     memory: number, // in GB
     maxTime: number, // in minutes
     envVars: EnvironmentVariable[],
+    academicUse: boolean,
     name: string,
     email: string | null,
   ): Observable<SimulationRun> {
@@ -106,6 +107,7 @@ export class DispatchService {
       memory,
       maxTime,
       envVars,
+      academicUse,
       public: false,
     };
     return this.http.post<SimulationRun>(this.endpoint, body, {
@@ -121,6 +123,7 @@ export class DispatchService {
     memory: number, // in GB
     maxTime: number, // in minutes
     envVars: EnvironmentVariable[],
+    academicUse: boolean,
     name: string,
     email: string | null,
   ): Observable<SimulationRun> {
@@ -135,6 +138,7 @@ export class DispatchService {
       memory,
       maxTime,
       envVars,
+      academicUse,
       public: false,
     };
     formData.append('file', fileToUpload, fileToUpload.name);

diff --git a/apps/dispatch/src/app/services/simulation/simulation.service.ts b/apps/dispatch/src/app/services/simulation/simulation.service.ts
@@ -247,6 +247,7 @@ export class SimulationService {
               memory: dispatchSimulation.memory,
               maxTime: dispatchSimulation.maxTime,
               envVars: dispatchSimulation.envVars,
+              academicUse: dispatchSimulation.academicUse,
               updated: new Date(dispatchSimulation.updated),
               resultsSize: dispatchSimulation.resultsSize,
               projectSize: dispatchSimulation.projectSize,

diff --git a/libs/dispatch/api-models/src/lib/simulationRun.ts b/libs/dispatch/api-models/src/lib/simulationRun.ts
@@ -83,6 +83,14 @@ export class SimulationRun {
   })
   envVars: EnvironmentVariable[];
 
+  @ApiPropertyOptional({
+    type: Boolean,
+    description: 'Whether use of commercial solvers is permitted because the purpose of the simulation is academic research or education',
+    required: false,
+    default: false,
+  })
+  academicUse: boolean;
+
   @ApiPropertyOptional({
     type: String,
     format: 'email',
@@ -123,6 +131,7 @@ export class SimulationRun {
     memory: number,
     maxTime: number,
     envVars: EnvironmentVariable[],
+    academicUse: boolean,
     submitted: Date,
     updated: Date,
     isPublic?: boolean,
@@ -141,6 +150,7 @@ export class SimulationRun {
     this.memory = memory || 8;
     this.maxTime = maxTime || 20;
     this.envVars = envVars || [];
+    this.academicUse = academicUse || false;
     this.status = status || SimulationRunStatus.CREATED;
     this.public = isPublic || false;
     this.submitted = submitted;
@@ -163,6 +173,7 @@ export class UploadSimulationRun extends PickType(SimulationRun, [
   'memory',
   'maxTime',
   'envVars',
+  'academicUse',
   'public',
 ]) {}
 

diff --git a/libs/messages/messages/src/lib/dispatch.ts b/libs/messages/messages/src/lib/dispatch.ts
@@ -49,6 +49,7 @@ export class DispatchCreatedPayload extends DispatchPayload {
   memory: number;
   maxTime: number;
   envVars: EnvironmentVariable[];
+  academicUse: boolean;
 
   constructor(
     id: string,
@@ -59,6 +60,7 @@ export class DispatchCreatedPayload extends DispatchPayload {
     memory: number,
     maxTime: number,
     envVars: EnvironmentVariable[],
+    academicUse: boolean,
   ) {
     super(id);
     this.fileName = fileName;
@@ -68,6 +70,7 @@ export class DispatchCreatedPayload extends DispatchPayload {
     this.memory = memory;
     this.maxTime = maxTime;
     this.envVars = envVars;
+    this.academicUse = academicUse;
   }
 }
 

diff --git a/libs/messages/messages/src/lib/queues.ts b/libs/messages/messages/src/lib/queues.ts
@@ -27,6 +27,7 @@ export class DispatchJob {
   memory!: number;
   maxTime!: number;
   envVars!: EnvironmentVariable[];
+  academicUse!: boolean;
   isPublic!: boolean;
 }
 

diff --git a/tools/scripts/createSimulationRun.sh b/tools/scripts/createSimulationRun.sh
@@ -11,6 +11,7 @@
   "memory": 8,
   "maxTime": 20,
   "envVars": [],
+  "academicUse": true,
   "email": "info@biosimulations.org",
   "public": false,
   "url": "https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex"

diff --git a/tools/submit-example-simulation-runs b/tools/submit-example-simulation-runs
@@ -141,6 +141,7 @@ def main(runbiosimulations_api='dev', biosimulators_api='org',
                                           "memory": 8,
                                           "maxTime": 20,
                                           "envVars": [],
+                                          "academicUse": True,
                                           "email": None,
                                           "public": True,
                                           "url": url,
@@ -177,6 +178,7 @@ def main(runbiosimulations_api='dev', biosimulators_api='org',
             "memory": 8,
             "maxTime": 20,
             "envVars": [],
+            "academicUse": True,
             "submittedLocally": False,
             "status": "CREATED",
             "submitted": simulation_run['submitted'],