def update_project(self, database):
"""Fetch project info and update project in the database."""
opended_after_140630 = comp_dates('2014-06-30', self.ordered_opened)
try:
LOG.info('Handeling {proj}'.format(proj = self.name))
project = database.ProjectDB(lims, self.id, self.samp_db)
key = find_proj_from_view(self.proj_db, self.name)
project.obj['_id'] = find_or_make_key(key)
if not opended_after_140630:
project.obj = load_status_from_google_docs.get(self.name, project.obj)
if self.upload_data:
info = save_couchdb_obj(self.proj_db, project.obj)
else:
info = self.print_couchdb_obj_to_file(project.obj)
return "project {name} is handled and {info}: _id = {id}".format(
name=self.name, info=info, id=project.obj['_id'])
except:
return ('Issues geting info for {name}. The "Application" udf might'
' be missing'.format(name = self.name))
def update_project(self, database):
"""Fetch project info and update project in the database."""
opended_after_140630 = comp_dates('2014-06-30', self.ordered_opened)
try:
LOG.info('Handeling {proj}'.format(proj=self.name))
project = database.ProjectDB(lims, self.id, self.samp_db)
key = find_proj_from_view(self.proj_db, self.name)
project.obj['_id'] = find_or_make_key(key)
if not opended_after_140630:
project.obj = load_status_from_google_docs.get(
self.name, project.obj)
if self.upload_data:
info = save_couchdb_obj(self.proj_db, project.obj)
else:
info = self.print_couchdb_obj_to_file(project.obj)
return "project {name} is handled and {info}: _id = {id}".format(
name=self.name, info=info, id=project.obj['_id'])
except:
return (
'Issues geting info for {name}. The "Application" udf might'
' be missing'.format(name=self.name))
def __init__(self, lims_instance, project_id, samp_db):
self.lims = lims_instance
self.samp_db = samp_db
self.lims_project = Project(self.lims,id = project_id)
self.preps = ProcessInfo(self.lims , self.lims.get_processes(projectname = self.lims_project.name, type = AGRLIBVAL.values()))
runs = self.lims.get_processes(projectname = self.lims_project.name, type = SEQUENCING.values())
self.runs = ProcessInfo(self.lims, runs)
project_summary = self.lims.get_processes(projectname = self.lims_project.name, type = SUMMARY.values())
self.project = {'source' : 'lims',
'application' : None,
'samples':{},
'open_date' : self.lims_project.open_date,
'close_date' : self.lims_project.close_date,
'entity_type' : 'project_summary',
'contact' : self.lims_project.researcher.email,
'project_name' : self.lims_project.name,
'project_id' : self.lims_project.id}
self.project = get_udfs('details', self.project, self.lims_project.udf.items(), PROJ_UDF_EXCEPTIONS)
if dict(self.lims_project.researcher.lab.udf.items()).has_key('Affiliation'):
self.project['affiliation'] = dict(self.lims_project.researcher.lab.udf.items())['Affiliation']
if len(project_summary) == 1:
self.project = get_udfs('project_summary', self.project, project_summary[0].udf.items())
elif len(project_summary) > 1:
print 'Warning. project summary process run more than once'
#################Temporary solution untill 20158 implemented in lims >>>>>>>>>>>>>>>>>>>>>>>
## can be reooved when all project opened before 2014-01-27 have been closed for more than 60 days
## then we also need to block old projects so that they are not overwriten in case of someone manualy
## updating it with the -p flagg
opened = self.lims_project.open_date
googledocs_status = {}
if opened:
try:
googledocs_status = load_status_from_google_docs.get(self.lims_project.name)
except:
print 'issues finding status from 20158'
pass
## Finish Date = last seq date if proj closed. Will be removed and feched from lims.
seq_finished = None
if self.lims_project.close_date and len(runs) > 0:
d = '2000-10-10'
for run in runs:
try:
new_date = dict(run.udf.items())['Finish Date'].isoformat()
if comp_dates(d,new_date):
d = new_date
seq_finished = d
except:
pass
self.project['sequencing_finished'] = seq_finished
#Temporary solution untill 20158 implemented in lims <<<<<<<<<<<<<<<<<<<<<<<
## Getting sample info
samples = self.lims.get_samples(projectlimsid = self.lims_project.id)
self.project['no_of_samples'] = len(samples)
if len(samples) > 0:
processes_per_artifact = self.build_processes_per_artifact(self.lims, self.lims_project.name)
self.project['first_initial_qc'] = '3000-10-10'
for samp in samples:
sampDB = SampleDB(self.lims,
samp.id,
self.project['project_name'],
self.samp_db,
self.project['application'],
self.preps.info,
self.runs.info,
googledocs_status,#googledocs_status Temporary solution untill 20158 implemented in lims!!
processes_per_artifact = processes_per_artifact)
self.project['samples'][sampDB.name] = sampDB.obj
##### initial qc fixa
try:
initial_qc_start_date = self.project['samples'][sampDB.name]['initial_qc']['start_date']
if comp_dates(initial_qc_start_date,self.project['first_initial_qc']):
self.project['first_initial_qc'] = initial_qc_start_date
except:
pass
self.project = delete_Nones(self.project)
