def get_container_from_id(flowcell):
if flowcell[7:].startswith('00000000'):
#Miseq
proc = lims.get_processes(type='MiSeq Run (MiSeq) 4.0',
udf={'Flow Cell ID': flowcell[7:]})[0]
c = lims.get_containers(name=proc.udf['Reagent Cartridge ID'])[0]
else:
#NovaSeq (S1, S2, S4 and SP),HiSeq2500 (Illumina Flow Cell) and HiSeqX (Patterned Flow Cell)
if lims.get_containers(name=flowcell[8:],
type=[
'S1', 'S2', 'S4', 'SP',
'Illumina Flow Cell', 'Patterned Flow Cell'
]):
c = lims.get_containers(name=flowcell[8:])[0]
else:
try:
#NextSeq500
proc = lims.get_processes(
type='Illumina Sequencing (NextSeq) v1.0',
udf={'Flow Cell ID': flowcell[8:]})[0]
except IndexError:
#NextSeq2000
proc = lims.get_processes(
type='Illumina Sequencing (NextSeq) v1.0',
udf={'Flow Cell ID': flowcell.split('_')[1]})[0]
c = lims.get_containers(name=proc.udf['Reagent Cartridge ID'])[0]
return c
def post(self):
project_id = self.get_argument('project_id', '')
responsible = self.get_argument('responsible', '')
if not project_id or not responsible:
self.set_status(400)
self.write('no project_id or bioinfo_responsible')
return
lims_project = LIMSProject(lims, id=project_id)
if not lims_project:
self.set_status(400)
self.write('lims project not found: {}'.format(project_id))
return
project_name = lims_project.name
stepname=['Project Summary 1.3']
processes=lims.get_processes(type=stepname, projectname=project_name)
if processes == []:
error = "{} for {} is not available in LIMS.".format(stepname, limsproject)
self.set_status(400)
self.write(error)
return
for process in processes:
process.get(force=True)
process.udf['Bioinfo responsible'] = responsible
try:
process.put()
except Exception, e:
# still try to update everything
# but will print error anyway
self.set_status(400)
self.write(e.message)
continue
def post(self):
project_id = self.get_argument('project_id', '')
responsible = self.get_argument('responsible', '')
if not project_id or not responsible:
self.set_status(400)
self.write('no project_id or bioinfo_responsible')
return
lims_project = LIMSProject(lims, id=project_id)
if not lims_project:
self.set_status(400)
self.write('lims project not found: {}'.format(project_id))
return
project_name = lims_project.name
stepname=['Project Summary 1.3']
process=lims.get_processes(type=stepname, projectname=project_name)
if process == []:
error = "{} for {} is not available in LIMS.".format(stepname, limsproject)
self.set_status(400)
self.write(error)
return
process = process[0]
process.udf['Bioinfo responsible'] = responsible
try:
process.put()
except Exception, e:
self.set_status(400)
self.write(e.message)
return
def post(self):
project_id = self.get_argument('project_id', '')
responsible = self.get_argument('responsible', '')
if not project_id or not responsible:
self.set_status(400)
self.write('no project_id or bioinfo_responsible')
return
lims_project = LIMSProject(lims, id=project_id)
if not lims_project:
self.set_status(400)
self.write('lims project not found: {}'.format(project_id))
return
project_name = lims_project.name
stepname=['Project Summary 1.3']
processes=lims.get_processes(type=stepname, projectname=project_name)
if processes == []:
error = "{} for {} is not available in LIMS.".format(stepname, limsproject)
self.set_status(400)
self.write(error)
return
for process in processes:
process.get(force=True)
process.udf['Bioinfo responsible'] = responsible
try:
process.put()
except Exception, e:
# still try to update everything
# but will print error anyway
self.set_status(400)
self.write(e.message)
continue
def get_container_from_id(flowcell):
if flowcell[7:].startswith('00000000'):
#Miseq
proc=lims.get_processes(type='MiSeq Run (MiSeq) 4.0',udf={'Flow Cell ID': flowcell[7:]})[0]
c = lims.get_containers(name=proc.udf['Reagent Cartridge ID'])[0]
else:
#Hiseq
c = lims.get_containers(name=flowcell[8:])[0]
return c
def post(self):
project_id = self.get_argument('project_id', '')
responsible = self.get_argument('responsible', '')
if not project_id or not responsible:
self.set_status(400)
self.write('no project_id or bioinfo_responsible')
return
lims_project = LIMSProject(lims, id=project_id)
if not lims_project:
self.set_status(400)
self.write('lims project not found: {}'.format(project_id))
return
project_name = lims_project.name
stepname = ['Project Summary 1.3']
processes = lims.get_processes(type=stepname, projectname=project_name)
if processes == []:
error = "{} for {} is not available in LIMS.".format(
stepname, project_name)
self.set_status(400)
self.write(error)
return
for process in processes:
process.get(force=True)
process.udf['Bioinfo responsible'] = responsible
try:
process.put()
except Exception as e:
# still try to update everything
# but will print error anyway
self.set_status(400)
self.write(e.message)
continue
# update status db
# if lims was not updated, after a while this change will be discarded
doc_id = None
view = self.application.projects_db.view("project/project_id")
for row in view[project_id]:
doc_id = row.value
break
if doc_id == None:
self.set_status(400)
self.write('Status DB has not been updated: project not found')
return
doc = self.application.projects_db.get(doc_id)
doc['project_summary'][
'bioinfo_responsible'] = responsible if responsible != 'unassigned' else None
try:
self.application.projects_db.save(doc)
except Exception as e:
self.set_status(400)
self.write(e.message)
self.set_status(201)
self.write({'success': 'success!!'})
def get_container_from_id(flowcell):
if flowcell[7:].startswith('00000000'):
#Miseq
proc = lims.get_processes(type='MiSeq Run (MiSeq) 4.0',
udf={'Flow Cell ID': flowcell[7:]})[0]
c = lims.get_containers(name=proc.udf['Reagent Cartridge ID'])[0]
else:
#Hiseq
c = lims.get_containers(name=flowcell[8:])[0]
return c
def post(self):
project_id = self.get_argument('project_id', '')
responsible = self.get_argument('responsible', '')
if not project_id or not responsible:
self.set_status(400)
self.write('no project_id or bioinfo_responsible')
return
lims_project = LIMSProject(lims, id=project_id)
if not lims_project:
self.set_status(400)
self.write('lims project not found: {}'.format(project_id))
return
project_name = lims_project.name
stepname=['Project Summary 1.3']
processes=lims.get_processes(type=stepname, projectname=project_name)
if processes == []:
error = "{} for {} is not available in LIMS.".format(stepname, project_name)
self.set_status(400)
self.write(error)
return
for process in processes:
process.get(force=True)
process.udf['Bioinfo responsible'] = responsible
try:
process.put()
except Exception as e:
# still try to update everything
# but will print error anyway
self.set_status(400)
self.write(e.message)
continue
# update status db
# if lims was not updated, after a while this change will be discarded
doc_id = None
view = self.application.projects_db.view("project/project_id")
for row in view[project_id]:
doc_id = row.value
break
if doc_id == None:
self.set_status(400)
self.write('Status DB has not been updated: project not found')
return
doc=self.application.projects_db.get(doc_id)
doc['project_summary']['bioinfo_responsible'] = responsible if responsible != 'unassigned' else None
try:
self.application.projects_db.save(doc)
except Exception as e:
self.set_status(400)
self.write(e.message)
self.set_status(201)
self.write({'success': 'success!!'})
def get(self, project_id):
project=Project(lims, id=project_id)
processes=lims.get_processes(projectname=project.name, type='Project Summary 1.3')
samples=lims.get_samples(projectname=project.name)
self.getProjectSummaryFields(lims)
t = self.application.loader.load("project_summary.html")
self.write(t.generate(gs_globals=self.application.gs_globals,
project_id=project_id,
processes=processes,
samples=samples,
step_fields=self.step_fields,
sample_fields=self.sample_fields))
def get(self, project_id):
project=Project(lims, id=project_id)
processes=lims.get_processes(projectname=project.name, type='Project Summary 1.3')
samples=lims.get_samples(projectname=project.name)
self.getProjectSummaryFields(lims)
t = self.application.loader.load("project_summary.html")
self.write(t.generate(gs_globals=self.application.gs_globals,
project_id=project_id,
processes=processes,
samples=samples,
step_fields=self.step_fields,
sample_fields=self.sample_fields))
