def getAllSpectralLibraries():
projectId = request.args.get('projectId')
if (projectDAO.getProjectById(projectId)):
spec_libs = spectralLibraryDAO.getAllLibrariesForProject(projectId)
for s in spec_libs:
augmentedClinicalSamples = clinicalSampleDAO.augmentClinicalSampleNames(
s['clinicalSamples'])
augmentedMSRuns = MSRunDAO.augmentMSRunNames(s['msRunIds'])
s['clinicalSamples'] = augmentedClinicalSamples
s['msRunIds'] = augmentedMSRuns
return jsonify(spec_libs), status.HTTP_200_OK
else:
return 'Project with id does not exist.', status.HTTP_404_NOT_FOUND
def getMSRunById():
id = ObjectId(request.args.get('id'))
msrun = MSRunDAO.getMsRun(id)
if(msrun):
msrun = msrun.dump()
augmentedClinicalSamples = clinicalSampleDAO.augmentClinicalSampleNames(
msrun['clinicalSamples'])
msReadySampleName = msReadySamplesDAO.getMSReadySampleName(
msrun['msReadySampleId'])
msrun['clinicalSamples'] = augmentedClinicalSamples
msrun['msReadySampleName'] = msReadySampleName
return jsonify(msrun), status.HTTP_200_OK
else:
return 'MS Run with id does not exist.', status.HTTP_404_NOT_FOUND
def getMSRunsByProjectId():
projectId = request.args.get('projectId')
if (projectDAO.getProjectById(projectId)):
msruns = MSRunDAO.getAllMSRunsByProjectId(projectId)
for msrun in msruns:
augmentedClinicalSamples = clinicalSampleDAO.augmentClinicalSampleNames(
msrun['clinicalSamples'])
msReadySampleName = msReadySamplesDAO.getMSReadySampleName(
msrun['msReadySampleId'])
msrun['clinicalSamples'] = augmentedClinicalSamples
msrun['msReadySampleName'] = msReadySampleName
return jsonify(msruns), status.HTTP_200_OK
else:
return 'Project with id does not exist.', status.HTTP_404_NOT_FOUND
def getAllSwathAnalysis():
projectId = request.args.get('projectId')
if (projectDAO.getProjectById(projectId)):
swath_analysis = swathAnalysisDAO.getSWATHByProject(projectId)
for s in swath_analysis:
augmentedClinicalSamples = clinicalSampleDAO.augmentClinicalSampleNames(
s['clinicalSamples'])
augmentedMSRuns = MSRunDAO.augmentMSRunNames(
s['msRunIds'])
s['clinicalSamples'] = augmentedClinicalSamples
s['msRunIds'] = augmentedMSRuns
return jsonify(swath_analysis), status.HTTP_200_OK
else:
return 'Project with id does not exist.', status.HTTP_404_NOT_FOUND
def getMsReadySamplesByClinicalSampleId():
clinicalSampleId = ObjectId(request.args.get('id'))
if clinicalSampleDAO.getClinicalSampleById(clinicalSampleId):
samples = msReadySamplesDAO.getMSReadySamplesByClinicalSampleId(
clinicalSampleId)
for s in samples:
augmentedClinicalSamples = clinicalSampleDAO.augmentClinicalSampleNames(
s['clinicalSamples'])
intermediateSampleName = intermediateSampleDAO.getIntermediateSampleName(
s['intermediateSampleId'])
s['clinicalSamples'] = augmentedClinicalSamples
s['intermediateSampleName'] = intermediateSampleName
return jsonify(samples), status.HTTP_200_OK
else:
return 'Clinical Sample with id does not exist.', status.HTTP_404_NOT_FOUND
def getMsReadySamplesById():
id = ObjectId(request.args.get('id'))
sample = msReadySamplesDAO.getMSReadySampleById(id)
if (sample):
s = sample.dump()
augmentedClinicalSamples = clinicalSampleDAO.augmentClinicalSampleNames(
s['clinicalSamples'])
intermediateSampleName = intermediateSampleDAO.getIntermediateSampleName(
s['intermediateSampleId'])
s['clinicalSamples'] = augmentedClinicalSamples
s['intermediateSampleName'] = intermediateSampleName
return jsonify(s), status.HTTP_200_OK
else:
return 'Ms Ready Sample with id does not exist.', status.HTTP_404_NOT_FOUND
def getMsReadySamplesByProject():
projectId = request.args.get('projectId')
if (projectDAO.getProjectById(projectId)):
samples = msReadySamplesDAO.getMsReadySamplesByProject(projectId)
for s in samples:
augmentedClinicalSamples = clinicalSampleDAO.augmentClinicalSampleNames(
s['clinicalSamples'])
intermediateSampleName = intermediateSampleDAO.getIntermediateSampleName(
s['intermediateSampleId'])
s['clinicalSamples'] = augmentedClinicalSamples
s['intermediateSampleName'] = intermediateSampleName
return jsonify(samples), status.HTTP_200_OK
else:
return 'Project with id does not exist.', status.HTTP_404_NOT_FOUND
def getMsRunsByClinicalSampleId():
clinicalSampleId = ObjectId(request.args.get('id'))
if clinicalSampleDAO.getClinicalSampleById(clinicalSampleId):
msruns = MSRunDAO.getMsRunsByClinicalSampleId(
clinicalSampleId)
for ms_run in msruns:
augmentedClinicalSamples = clinicalSampleDAO.augmentClinicalSampleNames(
ms_run['clinicalSamples'])
msReadySampleName = msReadySamplesDAO.getMSReadySampleName(
ms_run['msReadySampleId'])
ms_run['clinicalSamples'] = augmentedClinicalSamples
ms_run['msReadySampleName'] = msReadySampleName
return jsonify(msruns), status.HTTP_200_OK
else:
return 'Clinical Sample with id does not exist.', status.HTTP_404_NOT_FOUND
def getIntermediateSampleById():
id = ObjectId(request.args.get('id'))
s = intermediateSampleDAO.getIntermediateSampleById(id)
if (s):
s = s.dump()
augmentedClinicalSamples = clinicalSampleDAO.augmentClinicalSampleNames(
s['clinicalSamples'])
# if('parentSamples' in s):
# augmentedIntermediateSamples = intermediateSampleDAO.augmentIntermediateSampleNames(
# s['parentSamples'])
# s['parentSamples'] = augmentedIntermediateSamples
s['clinicalSamples'] = augmentedClinicalSamples
return jsonify(s), status.HTTP_200_OK
else:
return 'Intermediate Sample with id does not exist.', status.HTTP_404_NOT_FOUND
def getIntermediateSamplesByProject():
projectId = request.args.get('projectId')
if (projectDAO.getProjectById(projectId)):
samples = intermediateSampleDAO.getIntermediateSamplesByProject(
projectId)
for s in samples:
augmentedClinicalSamples = clinicalSampleDAO.augmentClinicalSampleNames(
s['clinicalSamples'])
# if('parentSamples' in s):
# augmentedIntermediateSamples = intermediateSampleDAO.augmentIntermediateSampleNames(
# s['parentSamples'])
# s['parentSamples'] = augmentedIntermediateSamples
s['clinicalSamples'] = augmentedClinicalSamples
return jsonify(samples), status.HTTP_200_OK
else:
return 'Project with id does not exist.', status.HTTP_404_NOT_FOUND