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use gollm=>mira equation to amr pipeline #5851

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merged 4 commits into from
Dec 16, 2024
Merged

use gollm=>mira equation to amr pipeline #5851

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ee0bbe4
use gollm=>mira equation to amr pipeline
mwdchang Dec 16, 2024
3af5dd8
clean up
mwdchang Dec 16, 2024
6ce1407
clean up mira-endpoint
mwdchang Dec 16, 2024
8659820
Merge remote-tracking branch 'origin/main' into update-equation-to-mo…
mwdchang Dec 16, 2024
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2 changes: 1 addition & 1 deletion packages/client/hmi-client/src/temp/Equations.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ const latex2amr = async () => {
resultAmr.value.innerHTML = 'processing...';
}

const resp = await API.post('/mira/latex-to-amr', equations);
const resp = await API.post('/knowledge/equations-to-model-debug', equations);
const respData = resp.data;

if (resultCode.value) {
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128 changes: 118 additions & 10 deletions .../java/software/uncharted/terarium/hmiserver/controller/knowledge/KnowledgeController.java
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Expand Up @@ -80,6 +80,9 @@
import software.uncharted.terarium.hmiserver.service.notification.NotificationService;
import software.uncharted.terarium.hmiserver.service.tasks.EquationsCleanupResponseHandler;
import software.uncharted.terarium.hmiserver.service.tasks.LatexToAMRResponseHandler;
// latex to model chain
import software.uncharted.terarium.hmiserver.service.tasks.LatexToSympyResponseHandler;
import software.uncharted.terarium.hmiserver.service.tasks.SympyToAMRResponseHandler;
import software.uncharted.terarium.hmiserver.service.tasks.TaskService;
import software.uncharted.terarium.hmiserver.service.tasks.TaskService.TaskMode;
import software.uncharted.terarium.hmiserver.utils.ByteMultipartFile;
Expand Down Expand Up @@ -267,19 +270,35 @@ public ResponseEntity<UUID> equationsToModel(
}

if (extractionService.equals("mira")) {
final TaskRequest taskReq = new TaskRequest();
final String latex = req.get("equations").toString();
taskReq.setType(TaskType.MIRA);
try {
taskReq.setInput(latex.getBytes());
taskReq.setScript(LatexToAMRResponseHandler.NAME);
taskReq.setUserId(currentUserService.get().getId());
final TaskResponse taskResp = taskService.runTaskSync(taskReq);
final JsonNode taskResponseJSON = mapper.readValue(taskResp.getOutput(), JsonNode.class);
final TaskRequest latexToSympyRequest = new TaskRequest();
final TaskResponse latexToSympyResponse;
final TaskRequest sympyToAMRRequest = new TaskRequest();
final TaskResponse sympyToAMRResponse;

try {
// 1. LaTeX to sympy code
final String latex = req.get("equations").toString();
latexToSympyRequest.setType(TaskType.GOLLM);
latexToSympyRequest.setInput(latex.getBytes());
latexToSympyRequest.setScript(LatexToSympyResponseHandler.NAME);
latexToSympyRequest.setUserId(currentUserService.get().getId());
latexToSympyResponse = taskService.runTaskSync(latexToSympyRequest);

// 2. hand off
final JsonNode node = mapper.readValue(latexToSympyResponse.getOutput(), JsonNode.class);
final String code = node.get("response").asText();

// 3. sympy code string to amr json
sympyToAMRRequest.setType(TaskType.MIRA);
sympyToAMRRequest.setInput(code.getBytes());
sympyToAMRRequest.setScript(SympyToAMRResponseHandler.NAME);
sympyToAMRRequest.setUserId(currentUserService.get().getId());
sympyToAMRResponse = taskService.runTaskSync(sympyToAMRRequest);

final JsonNode taskResponseJSON = mapper.readValue(sympyToAMRResponse.getOutput(), JsonNode.class);
final ObjectNode amrNode = taskResponseJSON.get("response").get("amr").deepCopy();
responseAMR = mapper.convertValue(amrNode, Model.class);
} catch (Exception e) {
} catch (final Exception e) {
log.error("failed to convert LaTeX equations to AMR", e);
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, "failed to convert latex equations to AMR");
}
Expand Down Expand Up @@ -868,6 +887,95 @@ public ResponseEntity<Void> pdfExtractions(
return ResponseEntity.accepted().build();
}

@PostMapping("/equations-to-model-debug")
@Secured(Roles.USER)
@Operation(summary = "Generate AMR from latex ODE equations, DEBUGGING only")
@ApiResponses(
value = {
@ApiResponse(
responseCode = "200",
description = "Dispatched successfully",
content = @Content(
mediaType = "application/json",
schema = @io.swagger.v3.oas.annotations.media.Schema(implementation = TaskResponse.class)
)
),
@ApiResponse(responseCode = "500", description = "There was an issue dispatching the request", content = @Content)
}
)
/**
* This is similiar to /equations-to-model endpoint, but rather than
* directly creating a model asset it returns artifact at different intersections
* and handoff for debugging
**/
public ResponseEntity<JsonNode> latexToAMR(@RequestBody final String latex) {
////////////////////////////////////////////////////////////////////////////////
// 1. Convert latex string to python sympy code string
//
// Note this is a gollm string => string task
////////////////////////////////////////////////////////////////////////////////
final TaskRequest latexToSympyRequest = new TaskRequest();
final TaskResponse latexToSympyResponse;
String code = null;

try {
latexToSympyRequest.setType(TaskType.GOLLM);
latexToSympyRequest.setInput(latex.getBytes());
latexToSympyRequest.setScript(LatexToSympyResponseHandler.NAME);
latexToSympyRequest.setUserId(currentUserService.get().getId());
latexToSympyResponse = taskService.runTaskSync(latexToSympyRequest);

final JsonNode node = mapper.readValue(latexToSympyResponse.getOutput(), JsonNode.class);
code = node.get("response").asText();
} catch (final TimeoutException e) {
log.warn("Timeout while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.SERVICE_UNAVAILABLE, messages.get("task.gollm.timeout"));
} catch (final InterruptedException e) {
log.warn("Interrupted while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("task.gollm.interrupted"));
} catch (final ExecutionException e) {
log.error("Error while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("task.gollm.execution-failure"));
} catch (final Exception e) {
log.error("Unexpected error", e);
}

if (code == null) {
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("task.gollm.execution-failure"));
}

////////////////////////////////////////////////////////////////////////////////
// 2. Convert python sympy code string to amr
//
// This returns the AMR json, and intermediate data representations for debugging
////////////////////////////////////////////////////////////////////////////////
final TaskRequest sympyToAMRRequest = new TaskRequest();
final TaskResponse sympyToAMRResponse;
final JsonNode response;

try {
sympyToAMRRequest.setType(TaskType.MIRA);
sympyToAMRRequest.setInput(code.getBytes());
sympyToAMRRequest.setScript(SympyToAMRResponseHandler.NAME);
sympyToAMRRequest.setUserId(currentUserService.get().getId());
sympyToAMRResponse = taskService.runTaskSync(sympyToAMRRequest);
response = mapper.readValue(sympyToAMRResponse.getOutput(), JsonNode.class);
return ResponseEntity.ok().body(response);
} catch (final TimeoutException e) {
log.warn("Timeout while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.SERVICE_UNAVAILABLE, messages.get("task.mira.timeout"));
} catch (final InterruptedException e) {
log.warn("Interrupted while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("task.mira.interrupted"));
} catch (final ExecutionException e) {
log.error("Error while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("task.mira.execution-failure"));
} catch (final Exception e) {
log.error("Unexpected error", e);
}
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("generic.io-error.read"));
}

private ResponseStatusException handleSkemaFeignException(final FeignException e) {
final HttpStatus statusCode = HttpStatus.resolve(e.status());
if (statusCode != null && statusCode.is4xxClientError()) {
Expand Down
86 changes: 0 additions & 86 deletions ...r/src/main/java/software/uncharted/terarium/hmiserver/controller/mira/MiraController.java
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Expand Up @@ -49,11 +49,9 @@
import software.uncharted.terarium.hmiserver.service.tasks.AMRToMMTResponseHandler;
import software.uncharted.terarium.hmiserver.service.tasks.GenerateModelLatexResponseHandler;
import software.uncharted.terarium.hmiserver.service.tasks.LatexToAMRResponseHandler;
import software.uncharted.terarium.hmiserver.service.tasks.LatexToSympyResponseHandler;
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.SympyToAMRResponseHandler;
import software.uncharted.terarium.hmiserver.service.tasks.TaskService;
import software.uncharted.terarium.hmiserver.utils.Messages;
import software.uncharted.terarium.hmiserver.utils.rebac.Schema;
Expand Down Expand Up @@ -254,90 +252,6 @@ public ResponseEntity<JsonNode> generateModelLatex(@RequestBody final JsonNode m
return ResponseEntity.ok().body(latexResponse);
}

@PostMapping("/latex-to-amr")
@Secured(Roles.USER)
@Operation(summary = "Generate AMR from latex ODE equations")
@ApiResponses(
value = {
@ApiResponse(
responseCode = "200",
description = "Dispatched successfully",
content = @Content(
mediaType = "application/json",
schema = @io.swagger.v3.oas.annotations.media.Schema(implementation = TaskResponse.class)
)
),
@ApiResponse(responseCode = "500", description = "There was an issue dispatching the request", content = @Content)
}
)
public ResponseEntity<JsonNode> latexToAMR(@RequestBody final String latex) {
////////////////////////////////////////////////////////////////////////////////
// 1. Convert latex string to python sympy code string
//
// Note this is a gollm string => string task
////////////////////////////////////////////////////////////////////////////////
final TaskRequest latexToSympyRequest = new TaskRequest();
final TaskResponse latexToSympyResponse;
String code = null;

try {
latexToSympyRequest.setType(TaskType.GOLLM);
latexToSympyRequest.setInput(latex.getBytes());
latexToSympyRequest.setScript(LatexToSympyResponseHandler.NAME);
latexToSympyRequest.setUserId(currentUserService.get().getId());
latexToSympyResponse = taskService.runTaskSync(latexToSympyRequest);

final JsonNode node = objectMapper.readValue(latexToSympyResponse.getOutput(), JsonNode.class);
code = node.get("response").asText();
} catch (final TimeoutException e) {
log.warn("Timeout while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.SERVICE_UNAVAILABLE, messages.get("task.gollm.timeout"));
} catch (final InterruptedException e) {
log.warn("Interrupted while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("task.gollm.interrupted"));
} catch (final ExecutionException e) {
log.error("Error while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("task.gollm.execution-failure"));
} catch (final Exception e) {
log.error("Unexpected error", e);
}

if (code == null) {
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("task.gollm.execution-failure"));
}

////////////////////////////////////////////////////////////////////////////////
// 2. Convert python sympy code string to amr
//
// This returns the AMR json, and intermediate data representations for debugging
////////////////////////////////////////////////////////////////////////////////
final TaskRequest sympyToAMRRequest = new TaskRequest();
final TaskResponse sympyToAMRResponse;
final JsonNode response;

try {
sympyToAMRRequest.setType(TaskType.MIRA);
sympyToAMRRequest.setInput(code.getBytes());
sympyToAMRRequest.setScript(SympyToAMRResponseHandler.NAME);
sympyToAMRRequest.setUserId(currentUserService.get().getId());
sympyToAMRResponse = taskService.runTaskSync(sympyToAMRRequest);
response = objectMapper.readValue(sympyToAMRResponse.getOutput(), JsonNode.class);
return ResponseEntity.ok().body(response);
} catch (final TimeoutException e) {
log.warn("Timeout while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.SERVICE_UNAVAILABLE, messages.get("task.mira.timeout"));
} catch (final InterruptedException e) {
log.warn("Interrupted while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("task.mira.interrupted"));
} catch (final ExecutionException e) {
log.error("Error while waiting for task response", e);
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("task.mira.execution-failure"));
} catch (final Exception e) {
log.error("Unexpected error", e);
}
throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, messages.get("generic.io-error.read"));
}

@PostMapping("/convert-and-create-model")
@Secured(Roles.USER)
@Operation(summary = "Dispatch a MIRA conversion task")
Expand Down