Kerbearasaurus/use-phenoml-ts-sdk #10
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![cursor[bot]](https://avatars.githubusercontent.com/in/1210556?s=60&v=4){kind=small}
| username: email, | ||
| password, | ||
| baseUrl: 'https://experiment.app.pheno.ml', | ||
| }); |
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Inconsistent baseUrl configuration across PhenoML client instances
Medium Severity
The new phenoml-workflow.ts bot explicitly sets baseUrl: 'https://experiment.app.pheno.ml' when creating the PhenoMLClient, but the converted bots (lang2fhir-create.ts, lang2fhir-document.ts, phenoml-cohort.ts) omit this configuration and rely on the SDK's default. The original code in all these bots explicitly used PHENOML_API_URL = "https://experiment.app.pheno.ml". If the SDK's default baseUrl differs from this experiment endpoint, the converted bots will connect to the wrong API environment, causing failures or unexpected behavior.
Additional Locations (2)
| throw new Error(`Authentication failed: ${authResponse.status} ${authResponse.statusText}`); | ||
| } | ||
| // Initialize PhenoML client with automatic auth handling | ||
| const phenomlClient = new PhenoMLClient({ username: email, password }); |
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Inconsistent baseUrl configuration in PhenoML client initialization
Medium Severity
The refactored bots (lang2fhir-create.ts, lang2fhir-document.ts, phenoml-cohort.ts) initialize PhenoMLClient without a baseUrl, while the new bots (phenoml-workflow.ts, phenoml-ips-summary.ts) explicitly set baseUrl: 'https://experiment.app.pheno.ml'. The old code being replaced explicitly used this URL via PHENOML_API_URL. If the SDK's default differs from this experiment URL, the refactored bots will fail or hit an incorrect endpoint while the new bots work correctly.
Additional Locations (2)
| const content = Buffer.from(arrayBuffer).toString('base64'); | ||
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| const contentType = inputDocRef.content?.[0].attachment?.contentType || 'application/pdf'; | ||
| const fileType = FILE_TYPE_MAP[contentType] || 'application/pdf'; |
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Unsupported file types silently misrepresented as PDF
Medium Severity
When a document has a content type not in FILE_TYPE_MAP (e.g., 'image/gif', 'image/tiff', 'application/msword'), the code silently falls back to 'application/pdf'. This sends the actual file bytes to the SDK while claiming it's a PDF, which will cause incorrect processing or confusing parsing errors. The old code would pass the actual content type, letting the API validate and reject unsupported types with a clear error. Missing validation for unsupported file types before calling the SDK.
| const content = Buffer.from(arrayBuffer).toString('base64'); | ||
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| const contentType = inputDocRef.content?.[0].attachment?.contentType || 'application/pdf'; | ||
| const fileType = FILE_TYPE_MAP[contentType] || 'application/pdf'; |
There was a problem hiding this comment.
Unsupported file types silently misrepresented as PDF
Medium Severity
When a document has a content type not in FILE_TYPE_MAP (e.g., 'image/gif', 'image/tiff', 'application/msword'), the code silently falls back to 'application/pdf'. This sends the actual file bytes to the SDK while claiming it's a PDF, which will cause incorrect processing or confusing parsing errors. The old code would pass the actual content type, letting the API validate and reject unsupported types with a clear error. Missing validation for unsupported file types before calling the SDK.
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Brillante! @kerbearasaurus como siempre...! "A Medplum Bot that generates International Patient Summary (IPS) using PhenoML" Felicitaciones, porque siempre están pensado en construir "cosas" "herramientas" que las Personas y los Profesionales necesitan y usarán! :) |
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use phenoml ts SDK for all bots
Note
Integrates PhenoML TS SDK and adds new automation bots
lang2fhir-createandlang2fhir-documentfor generating FHIR resources from text/documentsphenoml-cohortto analyze natural language into FHIR queries and createGroupcohortsphenoml-ips-summaryto produce IPS narrative from a patient bundle or fetched resourcesphenoml-workflowto execute PhenoML workflows by ID with input dataPHENOML_EMAIL,PHENOML_PASSWORD.build-bots.mjsbundles SDK (esbuild) and outputs todist/deploy-bots.tsregisters all new bots and their compiled artifacts (Lambda runtime)phenoml(and@huggingface/transformers) dependencies and retains existing scripts withbuild:botspipeline.Written by Cursor Bugbot for commit 2517f4d. This will update automatically on new commits. Configure here.