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fixed broken concepts for datasets and models #2964

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merged 2 commits into from
Mar 9, 2024
Merged

fixed broken concepts for datasets and models #2964

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ffaee43
fixed broken concepts for datasets and models
dgauldie Mar 8, 2024
5724e3b
added round back in
dgauldie Mar 8, 2024
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1 change: 0 additions & 1 deletion packages/client/hmi-client/src/components/dataset/tera-dataset-overview-table.vue
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Expand Up @@ -88,7 +88,6 @@ const conceptSearchTerm = ref({
name: ''
});
const curies = ref<DKG[]>([]);

const nameOfCurieCache = ref(new Map<string, string>());

const formattedData = computed(() => {
Expand Down
10 changes: 5 additions & 5 deletions packages/client/hmi-client/src/components/model/petrinet/tera-petrinet-tables.vue
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Expand Up @@ -214,7 +214,7 @@

<script setup lang="ts">
import type { DKG, Model, ModelConfiguration } from '@/types/Types';
import { cloneDeep, groupBy, isEmpty, round } from 'lodash';
import { cloneDeep, groupBy, isEmpty } from 'lodash';
import Accordion from 'primevue/accordion';
import AccordionTab from 'primevue/accordiontab';
import { computed, ref } from 'vue';
Expand All @@ -225,10 +225,10 @@ import {
} from '@/model-representation/petrinet/petrinet-service';
import { logger } from '@/utils/logger';
import {
searchCuriesEntities,
getNameOfCurieCached,
getCurieFromGroudingIdentifier,
getCurieUrl,
getNameOfCurieCached,
searchCuriesEntities,
parseCurie
} from '@/services/concept';
import DataTable from 'primevue/datatable';
Expand All @@ -253,13 +253,13 @@ interface ModelTableTypes {

const isRowEditable = ref<string | null>();
const transientTableValue = ref<ModelTableTypes | null>(null);
const nameOfCurieCache = ref(new Map<string, string>());

const curies = ref<DKG[]>([]);
const conceptSearchTerm = ref({
curie: '',
name: ''
});
const curies = ref<DKG[]>([]);
const nameOfCurieCache = ref(new Map<string, string>());

const parameters = computed(() => props.model?.semantics?.ode.parameters ?? []);
const observables = computed(() => props.model?.semantics?.ode?.observables ?? []);
Expand Down
4 changes: 2 additions & 2 deletions packages/client/hmi-client/src/services/concept.ts
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Expand Up @@ -56,7 +56,7 @@ async function getFacets(type: AssetType, curies?: ClauseValue[]): Promise<Conce
*/
async function getCuriesEntities(curies: Array<string>): Promise<Array<DKG> | null> {
try {
const response = await API.get(`/mira/${curies.toString()}`);
const response = await API.get(`/mira/currie/${curies.toString()}`);
if (response?.status !== 200) return null;
return response?.data ?? null;
} catch (error) {
Expand Down Expand Up @@ -111,7 +111,7 @@ async function getEntitySimilarity(
targets: string[]
): Promise<Array<EntitySimilarityResult> | null> {
try {
const response = await API.post('/mira/entity_similarity', { sources, targets } as Curies);
const response = await API.post('/mira/entity-similarity', { sources, targets } as Curies);
if (response?.status !== 200) return null;
return response?.data ?? null;
} catch (error) {
Expand Down
1 change: 1 addition & 0 deletions packages/client/hmi-client/src/services/goLLM.ts
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Expand Up @@ -22,6 +22,7 @@ export async function modelCard(documentId: string): Promise<void> {
await handleTaskById(taskId, {
ondata(data, closeConnection) {
if (data?.status === TaskStatus.Failed) {
closeConnection();
throw new FatalError('Task failed');
}
if (data.status === TaskStatus.Success) {
Expand Down
2 changes: 1 addition & 1 deletion packages/client/hmi-client/src/services/model.ts
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Expand Up @@ -76,7 +76,7 @@ export async function getModelConfigurations(modelId: Model['id']): Promise<Mode
* @deprecated moving to mira-stratify
*/
export async function reconstructAMR(amr: any) {
const response = await API.post('/mira/reconstruct_ode_semantics', amr);
const response = await API.post('/mira/reconstruct-ode-semantics', amr);
return response?.data;
}

Expand Down
8 changes: 5 additions & 3 deletions packages/client/hmi-client/src/workflow/ops/model-config/tera-model-config.vue
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Expand Up @@ -247,7 +247,7 @@

<script setup lang="ts">
import { cloneDeep, isEmpty } from 'lodash';
import { computed, ref, watch, onUnmounted, onMounted } from 'vue';
import { computed, onMounted, onUnmounted, ref, watch } from 'vue';
import Button from 'primevue/button';
import InputText from 'primevue/inputtext';
import Textarea from 'primevue/textarea';
Expand All @@ -256,7 +256,8 @@ import TeraDrilldown from '@/components/drilldown/tera-drilldown.vue';
import TeraDrilldownSection from '@/components/drilldown/tera-drilldown-section.vue';
import { getModel, getModelConfigurations, getModelType } from '@/services/model';
import { createModelConfiguration } from '@/services/model-configurations';
import type { Model, ModelConfiguration, Initial, ModelParameter } from '@/types/Types';
import type { Initial, Model, ModelConfiguration, ModelParameter } from '@/types/Types';
import { TaskStatus } from '@/types/Types';
import { AMRSchemaNames, ModelConfigTableData, ParamType } from '@/types/common';
import { getStratificationType } from '@/model-representation/petrinet/petrinet-service';
import {
Expand All @@ -281,7 +282,6 @@ import '@/ace-config';
import LoadingWateringCan from '@/assets/images/lottie-loading-wateringCan.json';
import { Vue3Lottie } from 'vue3-lottie';
import TeraModelSemanticTables from '@/components/model/petrinet/tera-model-semantic-tables.vue';
import { TaskStatus } from '@/types/Types';
import { FatalError } from '@/api/api';
import { formatTimestamp } from '@/utils/date';
import TeraOperatorAnnotation from '@/components/operator/tera-operator-annotation.vue';
Expand Down Expand Up @@ -431,6 +431,7 @@ const extractConfigurationsFromInputs = async () => {
{
ondata(data, closeConnection) {
if (data?.status === TaskStatus.Failed) {
closeConnection();
throw new FatalError('Configs from document - Task failed');
}
if (data.status === TaskStatus.Success) {
Expand All @@ -453,6 +454,7 @@ const extractConfigurationsFromInputs = async () => {
{
ondata(data, closeConnection) {
if (data?.status === TaskStatus.Failed) {
closeConnection();
throw new FatalError('Configs from datasets - Task failed');
}
if (data.status === TaskStatus.Success) {
Expand Down
97 changes: 79 additions & 18 deletions ...r/src/main/java/software/uncharted/terarium/hmiserver/controller/mira/MiraController.java
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@@ -1,23 +1,8 @@
package software.uncharted.terarium.hmiserver.controller.mira;

import java.util.List;
import java.util.Optional;
import java.util.UUID;

import org.springframework.http.ResponseEntity;
import org.springframework.security.access.annotation.Secured;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.PutMapping;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RestController;
import org.springframework.web.server.ResponseStatusException;
import org.springframework.web.servlet.mvc.method.annotation.SseEmitter;

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;

import feign.FeignException;
import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
Expand All @@ -26,19 +11,33 @@
import lombok.Data;
import lombok.RequiredArgsConstructor;
import lombok.extern.slf4j.Slf4j;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.annotation.Secured;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.server.ResponseStatusException;
import org.springframework.web.servlet.mvc.method.annotation.SseEmitter;
import software.uncharted.terarium.hmiserver.annotations.IgnoreRequestLogging;
import software.uncharted.terarium.hmiserver.models.dataservice.Artifact;
import software.uncharted.terarium.hmiserver.models.dataservice.model.Model;
import software.uncharted.terarium.hmiserver.models.mira.Curies;
import software.uncharted.terarium.hmiserver.models.mira.DKG;
import software.uncharted.terarium.hmiserver.models.mira.EntitySimilarityResult;
import software.uncharted.terarium.hmiserver.models.task.TaskRequest;
import software.uncharted.terarium.hmiserver.models.task.TaskRequest.TaskType;
import software.uncharted.terarium.hmiserver.models.task.TaskResponse;
import software.uncharted.terarium.hmiserver.proxies.mira.MIRAProxy;
import software.uncharted.terarium.hmiserver.security.Roles;
import software.uncharted.terarium.hmiserver.service.data.ArtifactService;
import software.uncharted.terarium.hmiserver.service.tasks.MdlToStockflowResponseHandler;
import software.uncharted.terarium.hmiserver.service.tasks.SbmlToPetrinetResponseHandler;
import software.uncharted.terarium.hmiserver.service.tasks.StellaToStockflowResponseHandler;
import software.uncharted.terarium.hmiserver.service.tasks.TaskService;

import java.util.List;
import java.util.Optional;
import java.util.UUID;

@RequestMapping("/mira")
@RestController
@Slf4j
Expand All @@ -49,6 +48,9 @@ public class MiraController {
final private ArtifactService artifactService;
final private TaskService taskService;

@Autowired
MIRAProxy proxy;

@Data
static public class ModelConversionRequest {
public UUID artifactId;
Expand All @@ -59,7 +61,7 @@ static public class ModelConversionResponse {
public Model response;
}

private boolean endsWith(final String filename, final List<String> suffixes) {
private static boolean endsWith(final String filename, final List<String> suffixes) {
for (final String suffix : suffixes) {
if (filename.endsWith(suffix)) {
return true;
Expand Down Expand Up @@ -164,4 +166,63 @@ public ResponseEntity<Void> cancelTask(@PathVariable("task-id") final UUID taskI
public SseEmitter subscribe(@PathVariable("task-id") final UUID taskId) {
return taskService.subscribe(taskId);
}

@GetMapping("/currie/{curies}")
@Secured(Roles.USER)
public ResponseEntity<List<DKG>> searchConcept(
@PathVariable("curies") final String curies) {
try {
final ResponseEntity<List<DKG>> response = proxy.getEntities(curies);
if (response.getStatusCode().is2xxSuccessful()) {
return ResponseEntity.ok(response.getBody());
}
return ResponseEntity.internalServerError().build();
} catch (final FeignException.NotFound e) { // Handle 404 errors
log.info("Could not find resource in the DKG", e);
return ResponseEntity.notFound().build();
} catch (final Exception e) {
log.error("Unable to fetch DKG", e);
return ResponseEntity.internalServerError().build();
}
}

@GetMapping("/search")
@Secured(Roles.USER)
public ResponseEntity<List<DKG>> search(
@RequestParam("q") final String q,
@RequestParam(required = false, name = "limit", defaultValue = "10") final Integer limit,
@RequestParam(required = false, name = "offset", defaultValue = "0") final Integer offset) {
try {
final ResponseEntity<List<DKG>> response = proxy.search(q, limit, offset);
if (response.getStatusCode().is2xxSuccessful()) {
return ResponseEntity.ok(response.getBody());
}
return ResponseEntity.internalServerError().build();
} catch (final FeignException.NotFound e) { // Handle 404 errors
log.info("Could not find resource in the DKG", e);
return ResponseEntity.notFound().build();
} catch (final Exception e) {
log.error("Unable to fetch DKG", e);
return ResponseEntity.internalServerError().build();
}
}

// This rebuilds the semantics ODE via MIRA
// 1. Send AMR to MIRA => MIRANet
// 2. Send MIRANet to MIRA to convert back to AMR Petrinet
// 3. Send AMR back
@PostMapping("/reconstruct-ode-semantics")
@Secured(Roles.USER)
public ResponseEntity<JsonNode> reconstructODESemantics(
final Object amr) {
return ResponseEntity.ok(proxy.reconstructODESemantics(amr).getBody());

}

@PostMapping("/entity-similarity")
@Secured(Roles.USER)
public ResponseEntity<List<EntitySimilarityResult>> entitySimilarity(
@RequestBody final Curies obj) {
return ResponseEntity.ok(proxy.entitySimilarity(obj).getBody());
}
}
91 changes: 0 additions & 91 deletions ...ain/java/software/uncharted/terarium/hmiserver/controller/miraservice/MIRAController.java
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