Initial implementation of a stand-alone phenotype similarity scoring service #259
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…service. - service is @ /rest/patients/matching-notification/compute-score - service accepts POST requests and has two POST parameters, `referencePatient` and `matchPatient` (both should be JSON strings in the Phenotips JSON format) - `referencePatient` and `matchPatient` are interchangeable - service only scores phenotypes, disorders and genes are ignored
sdumitriu
requested changes
Mar 21, 2019
| * @return result JSON | ||
| */ | ||
| @POST | ||
| @Consumes(MediaType.APPLICATION_JSON) |
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This doesn't really consume json, since it manually parses jsons from an x-www-form-encoded list of parameters.
| this.slf4Jlogger.error("Can't convert JSON to a patient: [{}]", ex.getMessage()); | ||
| return null; | ||
| } | ||
| final Patient patient = this.repository.create(); |
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This actually creates a patient, so it is not suitable for use in production.
Some alternatives:
- Make sure you delete the patient at the end (preferably skipping the document trash), although this will create some churn
- Although using internal classes is discouraged, in this case it would be better to manually create a PhenoTipsPatient on a new XWikiDocument in a temporary space, and later delete that document
- Implement the
Patientinterface like it's done inorg.phenotips.data.script.PatientSpecificityScriptService.FakePatient, with no actual persistence and only implementing the methods the score cares about - Make that an actual public implementation,
TransientPatientImplthat other services can use for temporary storage; it could extendPhenoTipsPatientand override methods so that they never actually save the underlyingXWikiDocument, but otherwise it would behave just like a real patient
| @@ -27,7 +27,7 @@ | |||
| </parent> | |||
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| <properties> | |||
| <coverage.instructionRatio>0.59</coverage.instructionRatio> | |||
| <coverage.instructionRatio>0.54</coverage.instructionRatio> | |||
| import javax.inject.Singleton; | ||
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| /** | ||
| * For Arun. |
| public interface PatientSimilarityScorer | ||
| { | ||
| /** | ||
| * Returns phenotype similarity score. |
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The name of the class suggests that this is a generic similarity scorer, not one that only looks at phenotypes. Either:
- keep the API to return just a single score, but then modify the javadoc to be more generic, and write different implementations for different score aspects
- modify the API to return more than one score, possibly as a map (
{"phenotype":0.6, "genotype": 1.0, "disease":0,"overall":0.8})
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Do not merge, this PR is for convenience of monitoring changes only