def getAllSOPs():
projectId = request.args.get('projectId')
if (projectDAO.getProjectById(projectId)):
sops = artefactDAO.getAllArtefacts(projectId)
return jsonify(sops), status.HTTP_200_OK
else:
return 'Project with id does not exist.', status.HTTP_404_NOT_FOUND
def getProjectById():
id = request.args.get('id')
project = projectDAO.getProjectById(id)
if project:
return jsonify(project), status.HTTP_200_OK
else:
return 'Project with id does not exist.', status.HTTP_404_NOT_FOUND
def getSOPsByType():
projectId = request.args.get('projectId')
artefactClass = request.args.get('sopType')
if (projectDAO.getProjectById(projectId)):
sops = artefactDAO.getArtefactsByType(projectId, artefactClass)
return jsonify(sops), status.HTTP_200_OK
else:
return 'Project with id does not exist.', status.HTTP_404_NOT_FOUND
def getAllClinicalSamples():
projectId = request.args.get('projectId')
if (projectDAO.getProjectById(projectId)):
samples = clinicalSampleDAO.getClinicalSamplesByProject(projectId)
return jsonify(samples), status.HTTP_200_OK
else:
return 'Project with id does not exist.', status.HTTP_404_NOT_FOUND
def getMaxCounter():
projectId = request.args.get('projectId')
if (projectDAO.getProjectById(projectId)):
maxCounter = clinicalSampleDAO.getMaxCounter(projectId)
return jsonify({"maxCounter": maxCounter}), status.HTTP_200_OK
else:
return 'Project with id does not exist.', status.HTTP_404_NOT_FOUND
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 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 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 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