def setUpClass(cls):
# Temporarily add new sample for use in exclusion tests
s_con = SampleRunMetricsConnection(dbname="samples-test",
username="******",
password="******")
s = s_con.get_entry("1_121015_BB002BBBXX_TGACCA")
kw = copy.deepcopy(s)
del kw["_id"]
new_s = SampleRunMetricsDocument(**kw)
new_s["sequence"] = "AGTTGA"
new_s["name"] = "1_121015_BB002BBBXX_AGTTGA"
s_con.save(new_s)
kw = copy.deepcopy(s)
del kw["_id"]
new_s = SampleRunMetricsDocument(**kw)
new_s["sample_prj"] = "j-doe_00_01"
new_s["sequence"] = "CGAACG"
new_s["name"] = "1_121015_BB002BBBXX_CGAACG"
s_con.save(new_s)
s = s_con.get_entry("3_120924_AC003CCCXX_ACAGTG")
kw = copy.deepcopy(s)
del kw["_id"]
new_s = SampleRunMetricsDocument(**kw)
new_s["sample_prj"] = "j-doe_00_02"
new_s["sequence"] = "GGAAGG"
new_s["name"] = "3_120924_AC003CCCXX_GGAAGG"
s_con.save(new_s)
def tearDownClass(cls):
s_con = SampleRunMetricsConnection(dbname="samples-test",
username="******",
password="******")
s = s_con.get_entry("1_121015_BB002BBBXX_AGTTGA")
doc = s_con.db.get(s["_id"])
s_con.db.delete(doc)
s = s_con.get_entry("1_121015_BB002BBBXX_CGAACG")
doc = s_con.db.get(s["_id"])
s_con.db.delete(doc)
s = s_con.get_entry("3_120924_AC003CCCXX_GGAAGG")
doc = s_con.db.get(s["_id"])
s_con.db.delete(doc)
def test_get_flowcell(self):
"""Test getting a flowcell for a given sample"""
sample_con = SampleRunMetricsConnection(
dbname="samples-test", username=self.user, password=self.pw, url=self.url
)
fc = sample_con.get_entry(self.examples["sample"], "flowcell")
self.assertEqual(str(fc), self.examples["flowcell"])
def test_dbcon(self):
"""Test database connection and that we get expected values."""
s_con = SampleRunMetricsConnection(dbname="samples-test", username="******", password="******")
samples = [s_con.get_entry(x) for x in s_con.name_view]
samples_d = {x["name"]: x for x in samples}
self.assertEqual(samples_d["1_120924_AC003CCCXX_TGACCA"]["date"], "120924")
self.assertEqual(samples_d["1_121015_BB002BBBXX_TGACCA"]["flowcell"], "BB002BBBXX")
self.assertEqual(samples_d["2_120924_AC003CCCXX_ACAGTG"]["entity_type"], "sample_run_metrics")
self.assertEqual(samples_d["3_120924_AC003CCCXX_ACAGTG"]["lane"], "3")
self.assertEqual(samples_d["4_120924_AC003CCCXX_CGTTAA"]["sequence"], "CGTTAA")
self.assertEqual(samples_d["2_121015_BB002BBBXX_TGACCA"]["project_id"], "P002")
fc_con = FlowcellRunMetricsConnection(dbname="flowcells-test", username="******", password="******")
flowcells = [fc_con.get_entry(x) for x in fc_con.name_view]
flowcells_d = {x["name"]: x for x in flowcells}
self.assertEqual(flowcells_d["120924_AC003CCCXX"]["name"], "120924_AC003CCCXX")
self.assertEqual(flowcells_d["121015_BB002BBBXX"]["name"], "121015_BB002BBBXX")
self.assertEqual(flowcells_d["120924_AC003CCCXX"]["entity_type"], "flowcell_run_metrics")
p_con = ProjectSummaryConnection(dbname="projects-test", username="******", password="******")
projects = [p_con.get_entry(x) for x in p_con.name_view]
projects_d = {x["project_name"]: x for x in projects}
self.assertEqual(projects_d["J.Doe_00_01"]["min_m_reads_per_sample_ordered"], 0.1)
self.assertEqual(projects_d["J.Doe_00_01"]["no_of_samples"], 2)
self.assertEqual(
set(projects_d["J.Doe_00_01"]["samples"].keys()), set(["P001_101_index3", "P001_102", "P001_103"])
)
self.assertEqual(projects_d["J.Doe_00_01"]["customer_reference"], "GnuGenome")
self.assertEqual(projects_d["J.Doe_00_02"]["min_m_reads_per_sample_ordered"], 0.2)
self.assertEqual(projects_d["J.Doe_00_03"]["samples"].keys(), ["3_index6"])
self.assertIn("A", projects_d["J.Doe_00_03"]["samples"]["3_index6"]["library_prep"])
def test_2_make_note(self):
"""Make a note subset by example flowcell and project"""
s_con = SampleRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
fc_con = FlowcellRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
p_con = ProjectSummaryConnection(username=self.user, password=self.pw, url=self.url)
paragraphs = sample_note_paragraphs()
headers = sample_note_headers()
samples = s_con.get_samples(self.examples["flowcell"], self.examples["project"])
project = p_con.get_entry(self.examples["project"])
samples = p_con.map_srm_to_name(self.examples["project"], fc_id=self.examples["flowcell"], use_bc_map=True)
for k,v in samples.items():
s_param = parameters
s = s_con.get_entry(k)
s_param.update({key:s[srm_to_parameter[key]] for key in srm_to_parameter.keys()})
fc = "{}_{}".format(s["date"], s["flowcell"])
s_param["phix_error_rate"] = fc_con.get_phix_error_rate(str(fc), s["lane"])
s_param['avg_quality_score'] = s_con.calc_avg_qv(s["name"])
s_param['rounded_read_count'] = round(float(s_param['rounded_read_count'])/1e6,1) if s_param['rounded_read_count'] else None
s_param['customer_name'] = project['samples'][v["sample"]].get('customer_name', None)
if project:
s_param['ordered_amount'] = p_con.get_ordered_amount(self.examples["project"])
s_param['customer_reference'] = s_param.get('customer_reference', project['customer_reference'])
s_param['uppnex_project_id'] = s_param.get('uppnex_project_id', project['uppnex_id'])
s_param['success'] = sequencing_success(s_param, cutoffs)
s_param.update({k:"N/A" for k in s_param.keys() if s_param[k] is None})
make_note("{}.pdf".format(s["barcode_name"]), headers, paragraphs, **s_param)
def test_get_flowcell(self):
"""Test getting a flowcell for a given sample"""
sample_con = SampleRunMetricsConnection(dbname="samples-test",
username=self.user,
password=self.pw,
url=self.url)
fc = sample_con.get_entry(self.examples["sample"], "flowcell")
self.assertEqual(str(fc), self.examples["flowcell"])
def test_dbcon(self):
"""Test database connection and that we get expected values."""
s_con = SampleRunMetricsConnection(dbname="samples-test",
username="******",
password="******")
samples = [s_con.get_entry(x) for x in s_con.name_view]
samples_d = {x["name"]: x for x in samples}
self.assertEqual(samples_d["1_120924_AC003CCCXX_TGACCA"]["date"],
"120924")
self.assertEqual(samples_d["1_121015_BB002BBBXX_TGACCA"]["flowcell"],
"BB002BBBXX")
self.assertEqual(
samples_d["2_120924_AC003CCCXX_ACAGTG"]["entity_type"],
"sample_run_metrics")
self.assertEqual(samples_d["3_120924_AC003CCCXX_ACAGTG"]["lane"], "3")
self.assertEqual(samples_d["4_120924_AC003CCCXX_CGTTAA"]["sequence"],
"CGTTAA")
self.assertEqual(samples_d["2_121015_BB002BBBXX_TGACCA"]["project_id"],
"P002")
fc_con = FlowcellRunMetricsConnection(dbname="flowcells-test",
username="******",
password="******")
flowcells = [fc_con.get_entry(x) for x in fc_con.name_view]
flowcells_d = {x["name"]: x for x in flowcells}
self.assertEqual(flowcells_d["120924_AC003CCCXX"]["name"],
"120924_AC003CCCXX")
self.assertEqual(flowcells_d["121015_BB002BBBXX"]["name"],
"121015_BB002BBBXX")
self.assertEqual(flowcells_d["120924_AC003CCCXX"]["entity_type"],
"flowcell_run_metrics")
p_con = ProjectSummaryConnection(dbname="projects-test",
username="******",
password="******")
projects = [p_con.get_entry(x) for x in p_con.name_view]
projects_d = {x["project_name"]: x for x in projects}
self.assertEqual(
projects_d["J.Doe_00_01"]["min_m_reads_per_sample_ordered"], 0.1)
self.assertEqual(projects_d["J.Doe_00_01"]["no_of_samples"], 2)
self.assertEqual(set(projects_d["J.Doe_00_01"]["samples"].keys()),
set(["P001_101_index3", "P001_102", "P001_103"]))
self.assertEqual(projects_d["J.Doe_00_01"]["customer_reference"],
"GnuGenome")
self.assertEqual(
projects_d["J.Doe_00_02"]["min_m_reads_per_sample_ordered"], 0.2)
self.assertEqual(projects_d["J.Doe_00_03"]["samples"].keys(),
["3_index6"])
self.assertIn(
"A",
projects_d["J.Doe_00_03"]["samples"]["3_index6"]["library_prep"])
def test_2_make_project_note(self):
"""Make a project note subset by flowcell and project"""
s_con = SampleRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
fc_con = FlowcellRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
p_con = ProjectSummaryConnection(username=self.user, password=self.pw, url=self.url)
paragraphs = project_note_paragraphs()
headers = project_note_headers()
param = parameters
project = p_con.get_entry(self.examples["project"])
if not project:
print "No project named {}".format(self.examples["project"])
return
if project:
ordered_amount = p_con.get_ordered_amount(self.examples["project"])
else:
return
ordered_amount = self.pargs.ordered_million_reads
## Start collecting the data
sample_table = []
sample_list = project['samples']
param.update({key:project.get(ps_to_parameter[key], None) for key in ps_to_parameter.keys()})
samples = p_con.map_name_to_srm(self.examples["project"], check_consistency=True, use_bc_map=True)
all_passed = True
for k,v in samples.items():
if k=="Unexpected":
continue
project_sample = sample_list[k]
vals = {x:project_sample.get(prjs_to_table[x], None) for x in prjs_to_table.keys()}
vals['MOrdered'] = ordered_amount
vals['BarcodeSeq'] = s_con.get_entry(v.keys()[0], "sequence")
## Set status
vals['Status'] = set_status(vals) if vals['Status'] is None else vals['Status']
vals.update({k:"N/A" for k in vals.keys() if vals[k] is None})
if vals['Status']=="N/A" or vals['Status']=="NP": all_passed = False
sample_table.append([vals[k] for k in table_keys])
if all_passed: param["finished"] = 'Project finished.'
sample_table.sort()
sample_table = list(sample_table for sample_table,_ in itertools.groupby(sample_table))
sample_table.insert(0, ['ScilifeID', 'CustomerID', 'BarcodeSeq', 'MSequenced', 'MOrdered', 'Status'])
paragraphs["Samples"]["tpl"] = make_sample_table(sample_table)
make_note("{}.pdf".format(self.examples["project"]), headers, paragraphs, **param)
def _project_status_note_table(project_name=None,
username=None,
password=None,
url=None,
use_ps_map=True,
use_bc_map=False,
check_consistency=False,
ordered_million_reads=None,
uppnex_id=None,
customer_reference=None,
exclude_sample_ids={},
project_alias=None,
sample_aliases={},
projectdb="projects",
samplesdb="samples",
flowcelldb="flowcells",
include_all_samples=False,
param={},
**kw):
# mapping project_summary to parameter keys
ps_to_parameter = {
"scilife_name": "scilife_name",
"customer_name": "customer_name",
"project_name": "project_name"
}
# mapping project sample to table
table_keys = [
'ScilifeID', 'SubmittedID', 'BarcodeSeq', 'MSequenced', 'MOrdered'
]
output_data = {
'stdout': StringIO(),
'stderr': StringIO(),
'debug': StringIO()
}
# Connect and run
s_con = SampleRunMetricsConnection(dbname=samplesdb,
username=username,
password=password,
url=url)
fc_con = FlowcellRunMetricsConnection(dbname=flowcelldb,
username=username,
password=password,
url=url)
p_con = ProjectSummaryConnection(dbname=projectdb,
username=username,
password=password,
url=url)
#Get the information source for this project
source = p_con.get_info_source(project_name)
# Get project summary from project database
sample_aliases = _literal_eval_option(sample_aliases, default={})
prj_summary = p_con.get_entry(project_name)
if not prj_summary:
LOG.warn("No such project '{}'".format(project_name))
return
LOG.debug("Working on project '{}'.".format(project_name))
# Determine if project is finished by getting all samples sequenced date
try:
all_samples_sequenced = prj_summary['project_summary'][
'all_samples_sequenced']
except (TypeError, KeyError):
all_samples_sequenced = False
# Get sample run list and loop samples to make mapping sample -> {sampleruns}
sample_run_list = _set_sample_run_list(project_name,
flowcell=None,
project_alias=project_alias,
s_con=s_con)
samples = {}
for s in sample_run_list:
prj_sample = p_con.get_project_sample(
project_name, s.get("project_sample_name", None))
if prj_sample:
sample_name = prj_sample['project_sample'].get(
"scilife_name", None)
s_d = {s["name"]: {'sample': sample_name, 'id': s["_id"]}}
samples.update(s_d)
else:
if s["barcode_name"] in sample_aliases:
s_d = {
sample_aliases[s["barcode_name"]]: {
'sample': sample_aliases[s["barcode_name"]],
'id': s["_id"]
}
}
samples.update(s_d)
else:
s_d = {
s["name"]: {
'sample': s["name"],
'id': s["_id"],
'barcode_name': s["barcode_name"]
}
}
LOG.warn(
"No mapping found for sample run:\n '{}'".format(s_d))
# Convert to mapping from desired sample name to list of aliases
# Less important for the moment; one solution is to update the
# Google docs summary table to use the P names
sample_dict = prj_summary['samples']
param.update({
key: prj_summary.get(ps_to_parameter[key], None)
for key in ps_to_parameter.keys()
})
param["ordered_amount"] = param.get(
"ordered_amount",
p_con.get_ordered_amount(project_name, samples=sample_dict))
if not param.get('customer_reference'):
try:
param['customer_reference'] = prj_summary['details'][
'customer_project_reference']
except (TypeError, KeyError):
param['customer_reference'] = prj_summary.get('customer_reference')
param['uppnex_project_id'] = param.get('uppnex_project_id',
prj_summary.get('uppnex_id'))
# Override database values if options passed at command line
if uppnex_id:
param["uppnex_project_id"] = uppnex_id
if customer_reference:
param["customer_reference"] = customer_reference
# Process options
ordered_million_reads = _literal_eval_option(ordered_million_reads)
exclude_sample_ids = _literal_eval_option(exclude_sample_ids, default={})
## Start collecting the data
sample_table = []
samples_excluded = []
last_library_preps = p_con.get_latest_library_prep(project_name)
last_library_preps_srm = [
x for l in last_library_preps.values() for x in l
]
LOG.debug(
"Looping through sample map that maps project sample names to sample run metrics ids"
)
for k, v in samples.items():
LOG.debug("project sample '{}' maps to '{}'".format(k, v))
if not include_all_samples:
if v['sample'] not in last_library_preps.keys():
LOG.info(
"No library prep information for sample {}; keeping in report"
.format(v['sample']))
else:
if k not in last_library_preps_srm:
LOG.info(
"Sample run {} ('{}') is not latest library prep ({}) for project sample {}: excluding from report"
.format(
k, v["id"], ",".join(
list(
set(last_library_preps[
v['sample']].values()))), v['sample']))
continue
else:
pass
if re.search("Unexpected", k):
continue
barcode_seq = s_con.get_entry(k, "sequence")
# Exclude sample id?
if _exclude_sample_id(exclude_sample_ids, v['sample'], barcode_seq):
samples_excluded.append(v['sample'])
continue
# Get the project sample name from the sample run and set table values
project_sample = sample_dict[v['sample']]
vals = _set_sample_table_values(v['sample'], project_sample,
barcode_seq, ordered_million_reads,
param)
sample_table.append([vals[k] for k in table_keys])
# Loop through samples in sample_dict for which there is no sample run information
samples_in_table_or_excluded = list(set([x[0] for x in sample_table
])) + samples_excluded
samples_not_in_table = list(
set(sample_dict.keys()) - set(samples_in_table_or_excluded))
for sample in samples_not_in_table:
if re.search("Unexpected", sample):
continue
project_sample = sample_dict[sample]
# Set project_sample_d: a dictionary mapping from sample run metrics name to sample run metrics database id
project_sample_d = _set_project_sample_dict(project_sample, source)
if project_sample_d:
for k, v in project_sample_d.iteritems():
barcode_seq = s_con.get_entry(k, "sequence")
vals = _set_sample_table_values(sample, project_sample,
barcode_seq,
ordered_million_reads, param)
sample_table.append([vals[k] for k in table_keys])
else:
barcode_seq = None
vals = _set_sample_table_values(sample, project_sample,
barcode_seq, ordered_million_reads,
param)
sample_table.append([vals[k] for k in table_keys])
if all_samples_sequenced:
param["finished"] = 'All samples for this project have been sequenced.'
sample_table.sort()
sample_table = list(sample_table
for sample_table, _ in itertools.groupby(sample_table))
sample_table.insert(
0,
['ScilifeID', 'SubmittedID', 'BarcodeSeq', 'MSequenced', 'MOrdered'])
return output_data, sample_table, param
def _project_status_note_table(project_name=None, username=None, password=None, url=None,
use_ps_map=True, use_bc_map=False, check_consistency=False,
ordered_million_reads=None, uppnex_id=None, customer_reference=None,
exclude_sample_ids={}, project_alias=None, sample_aliases={},
projectdb="projects", samplesdb="samples", flowcelldb="flowcells",
include_all_samples=False, param={}, **kw):
# mapping project_summary to parameter keys
ps_to_parameter = {"scilife_name":"scilife_name", "customer_name":"customer_name", "project_name":"project_name"}
# mapping project sample to table
table_keys = ['ScilifeID', 'SubmittedID', 'BarcodeSeq', 'MSequenced', 'MOrdered']
output_data = {'stdout':StringIO(), 'stderr':StringIO(), 'debug':StringIO()}
# Connect and run
s_con = SampleRunMetricsConnection(dbname=samplesdb, username=username, password=password, url=url)
fc_con = FlowcellRunMetricsConnection(dbname=flowcelldb, username=username, password=password, url=url)
p_con = ProjectSummaryConnection(dbname=projectdb, username=username, password=password, url=url)
#Get the information source for this project
source = p_con.get_info_source(project_name)
# Get project summary from project database
sample_aliases = _literal_eval_option(sample_aliases, default={})
prj_summary = p_con.get_entry(project_name)
if not prj_summary:
LOG.warn("No such project '{}'".format(project_name))
return
LOG.debug("Working on project '{}'.".format(project_name))
# Determine if project is finished by getting all samples sequenced date
try:
all_samples_sequenced = prj_summary['project_summary']['all_samples_sequenced']
except (TypeError,KeyError):
all_samples_sequenced = False
# Get sample run list and loop samples to make mapping sample -> {sampleruns}
sample_run_list = _set_sample_run_list(project_name, flowcell=None, project_alias=project_alias, s_con=s_con)
samples = {}
for s in sample_run_list:
prj_sample = p_con.get_project_sample(project_name, s.get("project_sample_name", None))
if prj_sample:
sample_name = prj_sample['project_sample'].get("scilife_name", None)
s_d = {s["name"] : {'sample':sample_name, 'id':s["_id"]}}
samples.update(s_d)
else:
if s["barcode_name"] in sample_aliases:
s_d = {sample_aliases[s["barcode_name"]] : {'sample':sample_aliases[s["barcode_name"]], 'id':s["_id"]}}
samples.update(s_d)
else:
s_d = {s["name"]:{'sample':s["name"], 'id':s["_id"], 'barcode_name':s["barcode_name"]}}
LOG.warn("No mapping found for sample run:\n '{}'".format(s_d))
# Convert to mapping from desired sample name to list of aliases
# Less important for the moment; one solution is to update the
# Google docs summary table to use the P names
sample_dict = prj_summary['samples']
param.update({key:prj_summary.get(ps_to_parameter[key], None) for key in ps_to_parameter.keys()})
param["ordered_amount"] = param.get("ordered_amount", p_con.get_ordered_amount(project_name, samples=sample_dict))
if not param.get('customer_reference') :
try:
param['customer_reference'] = prj_summary['details']['customer_project_reference']
except (TypeError,KeyError):
param['customer_reference'] = prj_summary.get('customer_reference')
param['uppnex_project_id'] = param.get('uppnex_project_id', prj_summary.get('uppnex_id'))
# Override database values if options passed at command line
if uppnex_id:
param["uppnex_project_id"] = uppnex_id
if customer_reference:
param["customer_reference"] = customer_reference
# Process options
ordered_million_reads = _literal_eval_option(ordered_million_reads)
exclude_sample_ids = _literal_eval_option(exclude_sample_ids, default={})
## Start collecting the data
sample_table = []
samples_excluded = []
last_library_preps = p_con.get_latest_library_prep(project_name)
last_library_preps_srm = [x for l in last_library_preps.values() for x in l]
LOG.debug("Looping through sample map that maps project sample names to sample run metrics ids")
for k,v in samples.items():
LOG.debug("project sample '{}' maps to '{}'".format(k, v))
if not include_all_samples:
if v['sample'] not in last_library_preps.keys():
LOG.info("No library prep information for sample {}; keeping in report".format(v['sample']))
else:
if k not in last_library_preps_srm:
LOG.info("Sample run {} ('{}') is not latest library prep ({}) for project sample {}: excluding from report".format(k, v["id"], ",".join(list(set(last_library_preps[v['sample']].values()))), v['sample']))
continue
else:
pass
if re.search("Unexpected", k):
continue
barcode_seq = s_con.get_entry(k, "sequence")
# Exclude sample id?
if _exclude_sample_id(exclude_sample_ids, v['sample'], barcode_seq):
samples_excluded.append(v['sample'])
continue
# Get the project sample name from the sample run and set table values
project_sample = sample_dict[v['sample']]
vals = _set_sample_table_values(v['sample'], project_sample, barcode_seq, ordered_million_reads, param)
sample_table.append([vals[k] for k in table_keys])
# Loop through samples in sample_dict for which there is no sample run information
samples_in_table_or_excluded = list(set([x[0] for x in sample_table])) + samples_excluded
samples_not_in_table = list(set(sample_dict.keys()) - set(samples_in_table_or_excluded))
for sample in samples_not_in_table:
if re.search("Unexpected", sample):
continue
project_sample = sample_dict[sample]
# Set project_sample_d: a dictionary mapping from sample run metrics name to sample run metrics database id
project_sample_d = _set_project_sample_dict(project_sample, source)
if project_sample_d:
for k,v in project_sample_d.iteritems():
barcode_seq = s_con.get_entry(k, "sequence")
vals = _set_sample_table_values(sample, project_sample, barcode_seq, ordered_million_reads, param)
sample_table.append([vals[k] for k in table_keys])
else:
barcode_seq = None
vals = _set_sample_table_values(sample, project_sample, barcode_seq, ordered_million_reads, param)
sample_table.append([vals[k] for k in table_keys])
if all_samples_sequenced: param["finished"] = 'All samples for this project have been sequenced.'
sample_table.sort()
sample_table = list(sample_table for sample_table,_ in itertools.groupby(sample_table))
sample_table.insert(0, ['ScilifeID', 'SubmittedID', 'BarcodeSeq', 'MSequenced', 'MOrdered'])
return output_data, sample_table, param
def project_status_note(project_name=None,
username=None,
password=None,
url=None,
use_ps_map=True,
use_bc_map=False,
check_consistency=False,
ordered_million_reads=None,
uppnex_id=None,
customer_reference=None,
exclude_sample_ids={},
project_alias=None,
sample_aliases={},
projectdb="projects",
samplesdb="samples",
flowcelldb="flowcells",
include_all_samples=False,
**kw):
"""Make a project status note. Used keywords:
:param project_name: project name
:param user: db user name
:param password: db password
:param url: db url
:param use_ps_map: use project summary mapping
:param use_bc_map: use project to barcode name mapping
:param check_consistency: check consistency between mappings
:param ordered_million_reads: number of ordered reads in millions
:param uppnex_id: the uppnex id
:param customer_reference: customer project name
:param exclude_sample_ids: exclude some sample ids from project note
:param project_alias: project alias name
:param sample_aliases: sample alias names
:param projectdb: project db name
:param samplesdb: samples db name
:param flowcelldb: flowcells db name
:param include_all_samples: include all samples in report
"""
# parameters
parameters = {
"project_name": project_name,
"finished": "Not finished, or cannot yet assess if finished.",
}
# mapping project_summary to parameter keys
ps_to_parameter = {
"scilife_name": "scilife_name",
"customer_name": "customer_name",
"project_name": "project_name"
}
# mapping project sample to table
table_keys = [
'ScilifeID', 'CustomerID', 'BarcodeSeq', 'MSequenced', 'MOrdered',
'Status'
]
output_data = {
'stdout': StringIO(),
'stderr': StringIO(),
'debug': StringIO()
}
# Connect and run
s_con = SampleRunMetricsConnection(dbname=samplesdb,
username=username,
password=password,
url=url)
fc_con = FlowcellRunMetricsConnection(dbname=flowcelldb,
username=username,
password=password,
url=url)
p_con = ProjectSummaryConnection(dbname=projectdb,
username=username,
password=password,
url=url)
# Set report paragraphs
paragraphs = project_note_paragraphs()
headers = project_note_headers()
# Set local param variable
param = parameters
# Get project summary from project database
sample_aliases = _literal_eval_option(sample_aliases, default={})
prj_summary = p_con.get_entry(project_name)
if not prj_summary:
LOG.warn("No such project '{}'".format(project_name))
return
LOG.debug("Working on project '{}'.".format(project_name))
# Get sample run list and loop samples to make mapping sample -> {sampleruns}
sample_run_list = _set_sample_run_list(project_name,
flowcell=None,
project_alias=project_alias,
s_con=s_con)
samples = {}
for s in sample_run_list:
prj_sample = p_con.get_project_sample(
project_name, s.get("project_sample_name", None))
if prj_sample:
sample_name = prj_sample['project_sample'].get(
"scilife_name", None)
s_d = {s["name"]: {'sample': sample_name, 'id': s["_id"]}}
samples.update(s_d)
else:
if s["barcode_name"] in sample_aliases:
s_d = {
sample_aliases[s["barcode_name"]]: {
'sample': sample_aliases[s["barcode_name"]],
'id': s["_id"]
}
}
samples.update(s_d)
else:
s_d = {
s["name"]: {
'sample': s["name"],
'id': s["_id"],
'barcode_name': s["barcode_name"]
}
}
LOG.warn(
"No mapping found for sample run:\n '{}'".format(s_d))
# Convert to mapping from desired sample name to list of aliases
# Less important for the moment; one solution is to update the
# Google docs summary table to use the P names
sample_dict = prj_summary['samples']
param.update({
key: prj_summary.get(ps_to_parameter[key], None)
for key in ps_to_parameter.keys()
})
param["ordered_amount"] = param.get("ordered_amount",
p_con.get_ordered_amount(project_name))
param['customer_reference'] = param.get(
'customer_reference', prj_summary.get('customer_reference'))
param['uppnex_project_id'] = param.get('uppnex_project_id',
prj_summary.get('uppnex_id'))
# Override database values if options passed at command line
if uppnex_id:
param["uppnex_project_id"] = uppnex_id
if customer_reference:
param["customer_reference"] = customer_reference
# Process options
ordered_million_reads = _literal_eval_option(ordered_million_reads)
exclude_sample_ids = _literal_eval_option(exclude_sample_ids, default={})
## Start collecting the data
sample_table = []
samples_excluded = []
all_passed = True
last_library_preps = p_con.get_latest_library_prep(project_name)
last_library_preps_srm = [
x for l in last_library_preps.values() for x in l
]
LOG.debug(
"Looping through sample map that maps project sample names to sample run metrics ids"
)
for k, v in samples.items():
LOG.debug("project sample '{}' maps to '{}'".format(k, v))
if not include_all_samples:
if v['sample'] not in last_library_preps.keys():
LOG.info(
"No library prep information for sample {}; keeping in report"
.format(v['sample']))
else:
if k not in last_library_preps_srm:
LOG.info(
"Sample run {} ('{}') is not latest library prep ({}) for project sample {}: excluding from report"
.format(k, v["id"],
last_library_preps[v['sample']].values()[0],
v['sample']))
continue
else:
pass
if re.search("Unexpected", k):
continue
barcode_seq = s_con.get_entry(k, "sequence")
# Exclude sample id?
if _exclude_sample_id(exclude_sample_ids, v['sample'], barcode_seq):
samples_excluded.append(v['sample'])
continue
# Get the project sample name from the sample run and set table values
project_sample = sample_dict[v['sample']]
vals = _set_sample_table_values(v['sample'], project_sample,
barcode_seq, ordered_million_reads,
param)
if vals['Status'] == "N/A" or vals['Status'] == "NP":
all_passed = False
sample_table.append([vals[k] for k in table_keys])
# Loop through samples in sample_dict for which there is no sample run information
samples_in_table_or_excluded = list(set([x[0] for x in sample_table
])) + samples_excluded
samples_not_in_table = list(
set(sample_dict.keys()) - set(samples_in_table_or_excluded))
for sample in samples_not_in_table:
if re.search("Unexpected", sample):
continue
project_sample = sample_dict[sample]
# Set project_sample_d: a dictionary mapping from sample run metrics name to sample run metrics database id
project_sample_d = _set_project_sample_dict(project_sample)
if project_sample_d:
for k, v in project_sample_d.iteritems():
barcode_seq = s_con.get_entry(k, "sequence")
vals = _set_sample_table_values(sample, project_sample,
barcode_seq,
ordered_million_reads, param)
if vals['Status'] == "N/A" or vals['Status'] == "NP":
all_passed = False
sample_table.append([vals[k] for k in table_keys])
else:
barcode_seq = None
vals = _set_sample_table_values(sample, project_sample,
barcode_seq, ordered_million_reads,
param)
if vals['Status'] == "N/A" or vals['Status'] == "NP":
all_passed = False
sample_table.append([vals[k] for k in table_keys])
if all_passed: param["finished"] = 'Project finished.'
sample_table.sort()
sample_table = list(sample_table
for sample_table, _ in itertools.groupby(sample_table))
sample_table.insert(0, [
'ScilifeID', 'CustomerID', 'BarcodeSeq', 'MSequenced', 'MOrdered',
'Status'
])
paragraphs["Samples"]["tpl"] = make_sample_table(sample_table)
make_note("{}_project_summary.pdf".format(project_name), headers,
paragraphs, **param)
make_rest_note("{}_project_summary.rst".format(project_name),
sample_table=sample_table,
report="project_report",
**param)
param.update(
{k: "N/A"
for k in param.keys() if param[k] is None or param[k] == ""})
output_data["debug"].write(
json.dumps({
'param': param,
'table': sample_table
}))
return output_data
def project_status_note(project_name=None, username=None, password=None, url=None,
use_ps_map=True, use_bc_map=False, check_consistency=False,
ordered_million_reads=None, uppnex_id=None, customer_reference=None,
exclude_sample_ids={}, project_alias=None, sample_aliases={},
projectdb="projects", samplesdb="samples", flowcelldb="flowcells",
include_all_samples=False, **kw):
"""Make a project status note. Used keywords:
:param project_name: project name
:param user: db user name
:param password: db password
:param url: db url
:param use_ps_map: use project summary mapping
:param use_bc_map: use project to barcode name mapping
:param check_consistency: check consistency between mappings
:param ordered_million_reads: number of ordered reads in millions
:param uppnex_id: the uppnex id
:param customer_reference: customer project name
:param exclude_sample_ids: exclude some sample ids from project note
:param project_alias: project alias name
:param sample_aliases: sample alias names
:param projectdb: project db name
:param samplesdb: samples db name
:param flowcelldb: flowcells db name
:param include_all_samples: include all samples in report
"""
# parameters
parameters = {
"project_name" : project_name,
"finished" : "Not finished, or cannot yet assess if finished.",
}
# mapping project_summary to parameter keys
ps_to_parameter = {"scilife_name":"scilife_name", "customer_name":"customer_name", "project_name":"project_name"}
# mapping project sample to table
table_keys = ['ScilifeID', 'CustomerID', 'BarcodeSeq', 'MSequenced', 'MOrdered', 'Status']
output_data = {'stdout':StringIO(), 'stderr':StringIO(), 'debug':StringIO()}
# Connect and run
s_con = SampleRunMetricsConnection(dbname=samplesdb, username=username, password=password, url=url)
fc_con = FlowcellRunMetricsConnection(dbname=flowcelldb, username=username, password=password, url=url)
p_con = ProjectSummaryConnection(dbname=projectdb, username=username, password=password, url=url)
# Set report paragraphs
paragraphs = project_note_paragraphs()
headers = project_note_headers()
# Set local param variable
param = parameters
# Get project summary from project database
sample_aliases = _literal_eval_option(sample_aliases, default={})
prj_summary = p_con.get_entry(project_name)
if not prj_summary:
LOG.warn("No such project '{}'".format(project_name))
return
LOG.debug("Working on project '{}'.".format(project_name))
# Get sample run list and loop samples to make mapping sample -> {sampleruns}
sample_run_list = _set_sample_run_list(project_name, flowcell=None, project_alias=project_alias, s_con=s_con)
samples = {}
for s in sample_run_list:
prj_sample = p_con.get_project_sample(project_name, s.get("project_sample_name", None))
if prj_sample:
sample_name = prj_sample['project_sample'].get("scilife_name", None)
s_d = {s["name"] : {'sample':sample_name, 'id':s["_id"]}}
samples.update(s_d)
else:
if s["barcode_name"] in sample_aliases:
s_d = {sample_aliases[s["barcode_name"]] : {'sample':sample_aliases[s["barcode_name"]], 'id':s["_id"]}}
samples.update(s_d)
else:
s_d = {s["name"]:{'sample':s["name"], 'id':s["_id"], 'barcode_name':s["barcode_name"]}}
LOG.warn("No mapping found for sample run:\n '{}'".format(s_d))
# Convert to mapping from desired sample name to list of aliases
# Less important for the moment; one solution is to update the
# Google docs summary table to use the P names
sample_dict = prj_summary['samples']
param.update({key:prj_summary.get(ps_to_parameter[key], None) for key in ps_to_parameter.keys()})
param["ordered_amount"] = param.get("ordered_amount", p_con.get_ordered_amount(project_name))
param['customer_reference'] = param.get('customer_reference', prj_summary.get('customer_reference'))
param['uppnex_project_id'] = param.get('uppnex_project_id', prj_summary.get('uppnex_id'))
# Override database values if options passed at command line
if uppnex_id:
param["uppnex_project_id"] = uppnex_id
if customer_reference:
param["customer_reference"] = customer_reference
# Process options
ordered_million_reads = _literal_eval_option(ordered_million_reads)
exclude_sample_ids = _literal_eval_option(exclude_sample_ids, default={})
## Start collecting the data
sample_table = []
samples_excluded = []
all_passed = True
last_library_preps = p_con.get_latest_library_prep(project_name)
last_library_preps_srm = [x for l in last_library_preps.values() for x in l]
LOG.debug("Looping through sample map that maps project sample names to sample run metrics ids")
for k,v in samples.items():
LOG.debug("project sample '{}' maps to '{}'".format(k, v))
if not include_all_samples:
if v['sample'] not in last_library_preps.keys():
LOG.info("No library prep information for sample {}; keeping in report".format(v['sample']))
else:
if k not in last_library_preps_srm:
LOG.info("Sample run {} ('{}') is not latest library prep ({}) for project sample {}: excluding from report".format(k, v["id"], last_library_preps[v['sample']].values()[0], v['sample']))
continue
else:
pass
if re.search("Unexpected", k):
continue
barcode_seq = s_con.get_entry(k, "sequence")
# Exclude sample id?
if _exclude_sample_id(exclude_sample_ids, v['sample'], barcode_seq):
samples_excluded.append(v['sample'])
continue
# Get the project sample name from the sample run and set table values
project_sample = sample_dict[v['sample']]
vals = _set_sample_table_values(v['sample'], project_sample, barcode_seq, ordered_million_reads, param)
if vals['Status']=="N/A" or vals['Status']=="NP": all_passed = False
sample_table.append([vals[k] for k in table_keys])
# Loop through samples in sample_dict for which there is no sample run information
samples_in_table_or_excluded = list(set([x[0] for x in sample_table])) + samples_excluded
samples_not_in_table = list(set(sample_dict.keys()) - set(samples_in_table_or_excluded))
for sample in samples_not_in_table:
if re.search("Unexpected", sample):
continue
project_sample = sample_dict[sample]
# Set project_sample_d: a dictionary mapping from sample run metrics name to sample run metrics database id
project_sample_d = _set_project_sample_dict(project_sample)
if project_sample_d:
for k,v in project_sample_d.iteritems():
barcode_seq = s_con.get_entry(k, "sequence")
vals = _set_sample_table_values(sample, project_sample, barcode_seq, ordered_million_reads, param)
if vals['Status']=="N/A" or vals['Status']=="NP": all_passed = False
sample_table.append([vals[k] for k in table_keys])
else:
barcode_seq = None
vals = _set_sample_table_values(sample, project_sample, barcode_seq, ordered_million_reads, param)
if vals['Status']=="N/A" or vals['Status']=="NP": all_passed = False
sample_table.append([vals[k] for k in table_keys])
if all_passed: param["finished"] = 'Project finished.'
sample_table.sort()
sample_table = list(sample_table for sample_table,_ in itertools.groupby(sample_table))
sample_table.insert(0, ['ScilifeID', 'CustomerID', 'BarcodeSeq', 'MSequenced', 'MOrdered', 'Status'])
paragraphs["Samples"]["tpl"] = make_sample_table(sample_table)
make_note("{}_project_summary.pdf".format(project_name), headers, paragraphs, **param)
make_rest_note("{}_project_summary.rst".format(project_name), sample_table=sample_table, report="project_report", **param)
param.update({k:"N/A" for k in param.keys() if param[k] is None or param[k] == ""})
output_data["debug"].write(json.dumps({'param':param, 'table':sample_table}))
return output_data
class TestQCUpload(PmFullTest):
def setUp(self):
"""FIXME: All other tests depend on data being uploaded, so
these are not real unit tests. The setup to TestQCUpload has to
be run prior to other tests, else unexpected failures will
occur."""
self.app = self.make_app(
argv=['qc', 'upload-qc', flowcells[0], '--mtime', '10000'],
extensions=[
'scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'
])
self._run_app()
self.app = self.make_app(
argv=['qc', 'upload-qc', flowcells[1], '--mtime', '10000'],
extensions=[
'scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'
])
self._run_app()
self.s_con = SampleRunMetricsConnection(dbname="samples-test",
username="******",
password="******")
self.p_con = ProjectSummaryConnection(dbname="projects-test",
username="******",
password="******")
self.fc_con = FlowcellRunMetricsConnection(dbname="flowcells-test",
username="******",
password="******")
def test_samplesheet(self):
"""Test samplesheet upload"""
fc = self.fc_con.get_entry("120924_AC003CCCXX")
self.assertEqual(fc["samplesheet_csv"][0]["Index"], "TGACCA")
self.assertEqual(fc["samplesheet_csv"][0]["Description"],
"J__Doe_00_01")
self.assertEqual(fc["samplesheet_csv"][0]["FCID"], "C003CCCXX")
self.assertEqual(fc["samplesheet_csv"][1]["SampleRef"], "hg19")
self.assertEqual(fc["samplesheet_csv"][2]["SampleID"],
"P002_101_index3")
def test_qc_upload(self):
"""Test running qc upload to server. Slightly circular testing
here - I setup the module with qc update so by definition the
test must 'work'"""
self.app = self.make_app(
argv=['qc', 'upload-qc', flowcells[1], '--mtime', '100'],
extensions=[
'scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'
])
self._run_app()
s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
self.assertIsNone(s["project_sample_name"])
self.assertEqual(s["project_id"], "P003")
def test_qc_update(self):
"""Test running qc update of a project id"""
s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
s["project_id"] = None
self.assertIsNone(s["project_id"])
self.s_con.save(s)
self.app = self.make_app(argv=[
'qc', 'update', '--sample_prj', projects[2], '--project_id',
'P003', '--debug', '--force'
],
extensions=[
'scilifelab.pm.ext.ext_qc',
'scilifelab.pm.ext.ext_couchdb'
])
self._run_app()
s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
self.assertEqual(s["project_id"], "P003")
def test_qc_update_sample_names(self):
"""Test running qc update of project sample names"""
s1 = self.s_con.get_entry("1_120924_AC003CCCXX_TGACCA")
s2 = self.s_con.get_entry("2_120924_AC003CCCXX_ACAGTG")
s1["project_sample_name"] = None
s2["project_sample_name"] = None
self.assertIsNone(s1["project_sample_name"])
self.assertIsNone(s2["project_sample_name"])
self.s_con.save(s1)
self.s_con.save(s2)
sample_map = {
'P001_101_index3': 'P001_101_index3',
'P001_102_index6': 'P001_102'
}
self.app = self.make_app(argv=[
'qc', 'update', '--sample_prj', projects[0], '--names',
"{}".format(sample_map), '--debug', '--force'
],
extensions=[
'scilifelab.pm.ext.ext_qc',
'scilifelab.pm.ext.ext_couchdb'
])
self._run_app()
s1 = self.s_con.get_entry("1_120924_AC003CCCXX_TGACCA")
s2 = self.s_con.get_entry("2_120924_AC003CCCXX_ACAGTG")
self.assertEqual(s1["project_sample_name"], "P001_101_index3")
self.assertEqual(s2["project_sample_name"], "P001_102")
class TestQCUpload(PmFullTest):
def setUp(self):
self.app = self.make_app(
argv=["qc", "upload-qc", flowcells[0], "--mtime", "10000"],
extensions=["scilifelab.pm.ext.ext_qc", "scilifelab.pm.ext.ext_couchdb"],
)
self._run_app()
self.s_con = SampleRunMetricsConnection(dbname="samples-test", username="******", password="******")
self.p_con = ProjectSummaryConnection(dbname="projects-test", username="******", password="******")
self.fc_con = FlowcellRunMetricsConnection(dbname="flowcells-test", username="******", password="******")
def test_samplesheet(self):
"""Test samplesheet upload"""
fc = self.fc_con.get_entry("120924_AC003CCCXX")
self.assertEqual(fc["samplesheet_csv"][0]["Index"], "TGACCA")
self.assertEqual(fc["samplesheet_csv"][0]["Description"], "J__Doe_00_01")
self.assertEqual(fc["samplesheet_csv"][0]["FCID"], "C003CCCXX")
self.assertEqual(fc["samplesheet_csv"][1]["SampleRef"], "hg19")
self.assertEqual(fc["samplesheet_csv"][2]["SampleID"], "P001_101_index3")
def test_qc_upload(self):
"""Test running qc upload to server"""
self.app = self.make_app(
argv=["qc", "upload-qc", flowcells[1], "--mtime", "100"],
extensions=["scilifelab.pm.ext.ext_qc", "scilifelab.pm.ext.ext_couchdb"],
)
self._run_app()
s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
self.assertIsNone(s["project_sample_name"])
self.assertEqual(s["project_id"], "P003")
def test_qc_update(self):
"""Test running qc update of a project id"""
s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
s["project_id"] = None
self.assertIsNone(s["project_id"])
self.s_con.save(s)
self.app = self.make_app(
argv=["qc", "update", "--sample_prj", projects[2], "--project_id", "P003", "--debug", "--force"],
extensions=["scilifelab.pm.ext.ext_qc", "scilifelab.pm.ext.ext_couchdb"],
)
self._run_app()
s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
self.assertEqual(s["project_id"], "P003")
def test_qc_update_sample_names(self):
"""Test running qc update of project sample names"""
s1 = self.s_con.get_entry("1_120924_AC003CCCXX_TGACCA")
s2 = self.s_con.get_entry("2_120924_AC003CCCXX_ACAGTG")
s1["project_sample_name"] = None
s2["project_sample_name"] = None
self.assertIsNone(s1["project_sample_name"])
self.assertIsNone(s2["project_sample_name"])
self.s_con.save(s1)
self.s_con.save(s2)
sample_map = {"P001_101_index3": "P001_101_index3", "P001_102_index6": "P001_102"}
self.app = self.make_app(
argv=[
"qc",
"update",
"--sample_prj",
projects[0],
"--names",
"{}".format(sample_map),
"--debug",
"--force",
],
extensions=["scilifelab.pm.ext.ext_qc", "scilifelab.pm.ext.ext_couchdb"],
)
self._run_app()
s1 = self.s_con.get_entry("1_120924_AC003CCCXX_TGACCA")
s2 = self.s_con.get_entry("2_120924_AC003CCCXX_ACAGTG")
self.assertEqual(s1["project_sample_name"], "P001_101_index3")
self.assertEqual(s2["project_sample_name"], "P001_102")
def test_2_make_project_note(self):
"""Make a project note subset by flowcell and project"""
s_con = SampleRunMetricsConnection(username=self.user,
password=self.pw,
url=self.url)
fc_con = FlowcellRunMetricsConnection(username=self.user,
password=self.pw,
url=self.url)
p_con = ProjectSummaryConnection(username=self.user,
password=self.pw,
url=self.url)
paragraphs = project_note_paragraphs()
headers = project_note_headers()
param = parameters
project = p_con.get_entry(self.examples["project"])
if not project:
print "No project named {}".format(self.examples["project"])
return
if project:
ordered_amount = p_con.get_ordered_amount(self.examples["project"])
else:
return
ordered_amount = self.pargs.ordered_million_reads
## Start collecting the data
sample_table = []
sample_list = project['samples']
param.update({
key: project.get(ps_to_parameter[key], None)
for key in ps_to_parameter.keys()
})
samples = p_con.map_name_to_srm(self.examples["project"],
check_consistency=True,
use_bc_map=True)
all_passed = True
for k, v in samples.items():
if k == "Unexpected":
continue
project_sample = sample_list[k]
vals = {
x: project_sample.get(prjs_to_table[x], None)
for x in prjs_to_table.keys()
}
vals['MOrdered'] = ordered_amount
vals['BarcodeSeq'] = s_con.get_entry(v.keys()[0], "sequence")
## Set status
vals['Status'] = set_status(
vals) if vals['Status'] is None else vals['Status']
vals.update({k: "N/A" for k in vals.keys() if vals[k] is None})
if vals['Status'] == "N/A" or vals['Status'] == "NP":
all_passed = False
sample_table.append([vals[k] for k in table_keys])
if all_passed: param["finished"] = 'Project finished.'
sample_table.sort()
sample_table = list(
sample_table
for sample_table, _ in itertools.groupby(sample_table))
sample_table.insert(0, [
'ScilifeID', 'CustomerID', 'BarcodeSeq', 'MSequenced', 'MOrdered',
'Status'
])
paragraphs["Samples"]["tpl"] = make_sample_table(sample_table)
make_note("{}.pdf".format(self.examples["project"]), headers,
paragraphs, **param)
class TestQCUpload(PmFullTest):
def setUp(self):
"""FIXME: All other tests depend on data being uploaded, so
these are not real unit tests. The setup to TestQCUpload has to
be run prior to other tests, else unexpected failures will
occur."""
self.app = self.make_app(argv = ['qc', 'upload-qc', flowcells[0], '--mtime', '10000'], extensions=['scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'])
self._run_app()
self.app = self.make_app(argv = ['qc', 'upload-qc', flowcells[1], '--mtime', '10000'], extensions=['scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'])
self._run_app()
self.s_con = SampleRunMetricsConnection(dbname="samples-test", username="******", password="******")
self.p_con = ProjectSummaryConnection(dbname="projects-test", username="******", password="******")
self.fc_con = FlowcellRunMetricsConnection(dbname="flowcells-test", username="******", password="******")
def test_samplesheet(self):
"""Test samplesheet upload"""
fc = self.fc_con.get_entry("120924_AC003CCCXX")
self.assertEqual(fc["samplesheet_csv"][0]["Index"], "TGACCA")
self.assertEqual(fc["samplesheet_csv"][0]["Description"], "J__Doe_00_01")
self.assertEqual(fc["samplesheet_csv"][0]["FCID"], "C003CCCXX")
self.assertEqual(fc["samplesheet_csv"][1]["SampleRef"], "hg19")
self.assertEqual(fc["samplesheet_csv"][2]["SampleID"], "P002_101_index3")
def test_qc_upload(self):
"""Test running qc upload to server. Slightly circular testing
here - I setup the module with qc update so by definition the
test must 'work'"""
self.app = self.make_app(argv = ['qc', 'upload-qc', flowcells[1], '--mtime', '100'], extensions=['scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'])
self._run_app()
s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
self.assertIsNone(s["project_sample_name"])
self.assertEqual(s["project_id"], "P003")
def test_qc_update(self):
"""Test running qc update of a project id"""
s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
s["project_id"]= None
self.assertIsNone(s["project_id"])
self.s_con.save(s)
self.app = self.make_app(argv = ['qc', 'update', '--sample_prj', projects[2], '--project_id', 'P003', '--debug', '--force'], extensions=['scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'])
self._run_app()
s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
self.assertEqual(s["project_id"], "P003")
def test_qc_update_sample_names(self):
"""Test running qc update of project sample names"""
s1 = self.s_con.get_entry("1_120924_AC003CCCXX_TGACCA")
s2 = self.s_con.get_entry("2_120924_AC003CCCXX_ACAGTG")
s1["project_sample_name"] = None
s2["project_sample_name"] = None
self.assertIsNone(s1["project_sample_name"])
self.assertIsNone(s2["project_sample_name"])
self.s_con.save(s1)
self.s_con.save(s2)
sample_map = {'P001_101_index3': 'P001_101_index3', 'P001_102_index6':'P001_102'}
self.app = self.make_app(argv = ['qc', 'update', '--sample_prj', projects[0], '--names', "{}".format(sample_map), '--debug', '--force'], extensions=['scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'])
self._run_app()
s1 = self.s_con.get_entry("1_120924_AC003CCCXX_TGACCA")
s2 = self.s_con.get_entry("2_120924_AC003CCCXX_ACAGTG")
self.assertEqual(s1["project_sample_name"], "P001_101_index3")
self.assertEqual(s2["project_sample_name"], "P001_102")
