class MultiQC_clarity_metadata(BaseMultiqcModule):
def __init__(self):
self.log = logging.getLogger('multiqc')
# Check that this plugin hasn't been disabled
if config.kwargs.get('disable_clarity', False) is True:
self.log.info(
"Skipping MultiQC_Clarity as disabled on command line")
return None
if getattr(config, 'disable_clarity', False) is True:
self.log.debug(
"Skipping MultiQC_Clarity as specified in config file")
return None
super(MultiQC_clarity_metadata, self).__init__(name='Clarity LIMS',
anchor='clarity')
self.intro = '''<p>The <a href="https://github.com/MultiQC/MultiQC_Clarity" target="_blank">MultiQC_Clarity</a>
plugin fetches data from a specified
<a href="https://www.genologics.com/clarity-lims/" target="_blank">Basespace Clarity LIMS</a> instance.</p>'''
self.lims = Lims(BASEURI, USERNAME, PASSWORD)
self.metadata = {}
self.header_metadata = {}
self.general_metadata = {}
self.tab_metadata = {}
self.samples = []
self.schema = getattr(config, 'clarity', None)
if self.schema is None:
self.log.debug("No config found for MultiQC_Clarity")
return None
self.get_samples()
self.get_metadata('report_header_info')
self.get_metadata('general_stats')
self.get_metadata('clarity_module')
self.update_multiqc_report()
self.make_sections()
report.modules_output.append(self)
def get_samples(self):
if config.kwargs.get('clarity_project_name'):
pj = self.lims.get_projects(
name=config.kwargs['clarity_project_name'])
self.samples = pj.samples
else:
names = set()
for x in report.general_stats_data:
names.update(x.keys())
for d in report.saved_raw_data.values():
try:
self.names.update(d.keys())
except AttributeError:
pass
if not config.kwargs.get('clarity_skip_edit_names'):
names = self.edit_names(names)
self.log.debug("Looking into Clarity for samples {}".format(
", ".join(names)))
found = 0
try:
for name in names:
matching_samples = self.lims.get_samples(name=name)
if not matching_samples:
self.log.error(
"Could not find a sample matching {0}, skipping.".
format(name))
continue
if len(matching_samples) > 1:
self.log.error(
"Found multiple samples matching {0}, skipping".
format(name))
continue
found += 1
self.samples.append(matching_samples[0])
except Exception as e:
self.log.warn(
"Could not connect to Clarity LIMS: {}".format(e))
return None
self.log.info("Found {} out of {} samples in LIMS.".format(
found, len(names)))
def edit_names(self, names):
edited = []
for name in names:
if name.endswith("_1") or name.endswith("_2"):
edited.append(name[:-2])
elif name.endswith("_R1") or name.endswith("_R2"):
edited.append(name[:-3])
else:
edited.append(name)
return edited
def flatten_metadata(self, metadata):
for first_level in metadata:
for second_level in metadata[first_level]:
if isinstance(metadata[first_level][second_level],
set) or isinstance(
metadata[first_level][second_level], list):
metadata[first_level][second_level] = ", ".join(
metadata[first_level][second_level])
return metadata
def get_project_metadata(self, udfs):
project_metadata = {}
for sample in self.samples:
project_metadata[sample.project.name] = {}
for udf in udfs:
if udf in sample.project.udf:
try:
project_metadata[sample.project.name][udf].add(
str(sample.project.udf[udf]))
except:
project_metadata[sample.project.name][udf] = set()
project_metadata[sample.project.name][udf].add(
str(sample.project.udf[udf]))
return self.flatten_metadata(project_metadata)
def get_sample_metadata(self, udfs):
sample_metadata = {}
for sample in self.samples:
sample_metadata[sample.name] = {}
for udf in udfs:
if udf in sample.udf:
try:
sample_metadata[sample.name][udf].add(
str(sample.udf[udf]))
except:
sample_metadata[sample.name][udf] = set()
sample_metadata[sample.name][udf].add(
str(sample.udf[udf]))
return self.flatten_metadata(sample_metadata)
def get_metadata(self, part):
for key in self.schema[part]:
if key == 'Project':
metadata = self.get_project_metadata(
self.schema[part]['Project'])
elif key == 'Sample':
metadata = self.get_sample_metadata(
self.schema[part]['Sample'])
else:
metadata = self.get_artifact_metadata(self.schema[part])
if part == "report_header_info":
self.header_metadata.update(metadata)
elif part == "general_stats":
self.general_metadata.update(metadata)
else:
self.tab_metadata.update(metadata)
def get_artifact_metadata(self, pt_to_udfs):
artifact_metadata = {}
for sample in self.samples:
artifact_metadata[sample.name] = {}
for process_type in pt_to_udfs:
if process_type == 'Sample':
continue
if process_type == 'Project':
continue
artifacts = self.lims.get_artifacts(sample_name=sample.name,
process_type=process_type)
for udf_name in pt_to_udfs[process_type].get("outputs", []):
values = []
for artifact in artifacts:
if udf_name in artifact.udf:
values.append(str(artifact.udf[udf_name]))
artifact_metadata[sample.name][udf_name] = values
processes = set([art.parent_process for art in artifacts])
inputs = []
for p in processes:
inputs.extend([
art for art in p.all_inputs()
if sample.name in [s.name for s in art.samples]
])
for udf_name in pt_to_udfs[process_type].get("inputs", []):
values = []
for artifact in inputs:
if udf_name in artifact.udf:
values.append(str(artifact.udf[udf_name]))
artifact_metadata[sample.name][udf_name] = values
return self.flatten_metadata(artifact_metadata)
def update_multiqc_report(self):
if config.report_header_info is None:
config.report_header_info = []
for first_level in self.header_metadata:
d = {}
for key in self.header_metadata[first_level]:
d[key] = self.header_metadata[first_level][key]
config.report_header_info.append(d)
headers = {}
for first_level in self.schema["general_stats"]:
for header in self.schema["general_stats"][first_level]:
headers[header] = {}
if isinstance(
self.schema["general_stats"][first_level][header],
dict):
for subsubkey, cfg in self.schema["general_stats"][
first_level][header].items():
if subsubkey == 'multiply_by':
mby = str(cfg)[:]
headers[header]['modify'] = lambda x: float(
x) * float(mby)
else:
headers[header][subsubkey] = cfg
headers[header]['description'] = headers[header].get(
'description', '{} - {}'.format(first_level, header))
headers[header]['namespace'] = headers[header].get(
'namespace', 'Clarity LIMS')
headers[header]['scale'] = headers[header].get('scale', 'YlGn')
report.general_stats_headers.append(headers)
report.general_stats_data.append(self.general_metadata)
def make_sections(self):
headers = OrderedDict()
for first_level in self.tab_metadata:
for header in self.tab_metadata[first_level]:
desc = header
if header not in headers:
headers[header] = {}
for key in self.schema['clarity_module']:
if header in self.schema['clarity_module'][key]:
desc = key
elif isinstance(self.schema['clarity_module'][key],
dict):
for subkey, val in self.schema['clarity_module'][
key].items():
# print(val)
if val is None:
break
elif header in val:
desc = key
if isinstance(val[header], dict):
for subsubkey, cfg in val[
header].items():
if subsubkey == 'multiply_by':
mby = str(cfg)[:]
headers[header][
'modify'] = lambda x: float(
x) * float(mby)
else:
headers[header][
subsubkey] = cfg
headers[header]['namespace'] = headers[header].get(
'namespace', desc)
headers[header]['title'] = headers[header].get(
'title', header)
headers[header]['description'] = headers[header].get(
'description', header)
self.intro += table.plot(self.tab_metadata, headers)
lims.check_version()
# Get the list of all artifacts.
## artifacts = lims.get_artifacts()
## print len(artifacts), 'total artifacts'
## artifacts = lims.get_artifacts(qc_flag='UNKNOWN')
## print len(artifacts), 'QC UNKNOWN artifacts'
## artifacts = lims.get_artifacts(qc_flag='PASSED')
## print len(artifacts), 'QC PASSED artifacts'
## artifacts = lims.get_artifacts(qc_flag='FAILED')
## print len(artifacts), 'QC FAILED artifacts'
## artifacts = lims.get_artifacts(working_flag=True)
## print len(artifacts), 'Working-flag True artifacts'
name = 'GRU54A236'
name = 'jgr33'
artifacts = lims.get_artifacts(sample_name=name)
print len(artifacts), 'Sample name', name, 'artifacts'
artifacts = lims.get_batch(artifacts)
for artifact in artifacts:
print artifact, artifact.name, artifact.state, artifact.working_flag, artifact.samples
artifacts = lims.get_artifacts(qc_flag='PASSED')
print len(artifacts), 'QC PASSED artifacts'
artifacts = lims.get_batch(artifacts)
for artifact in artifacts:
print artifact, artifact.name, artifact.state, artifact.working_flag, artifact.samples
class MultiQC_clarity_metadata(BaseMultiqcModule):
def __init__(self):
self.log = logging.getLogger('multiqc')
# Check that this plugin hasn't been disabled
if config.kwargs.get('disable_clarity', False) is True:
self.log.info(
"Skipping MultiQC_Clarity as disabled on command line")
return None
if getattr(config, 'disable_clarity', False) is True:
self.log.debug(
"Skipping MultiQC_Clarity as specified in config file")
return None
super(MultiQC_clarity_metadata, self).__init__(
name='Clarity',
anchor='clarity',
href='https://github.com/Galithil/MultiQC_Clarity',
info="fetches data from your Basespace Clarity LIMS instance.")
self.lims = Lims(BASEURI, USERNAME, PASSWORD)
self.metadata = {}
self.header_metadata = {}
self.general_metadata = {}
self.tab_metadata = {}
self.samples = []
self.sections = []
self.schema = getattr(config, 'clarity', None)
if self.schema is None:
self.log.warn("No config found for MultiQC_Clarity")
return None
self.get_samples()
self.get_metadata('Header')
self.get_metadata('General Statistics')
self.get_metadata('Clarity Tab')
self.update_multiqc_report()
self.make_sections()
report.modules_output.append(self)
def get_samples(self):
if config.kwargs.get('clarity_project_name'):
pj = self.lims.get_projects(
name=config.kwargs['clarity_project_name'])
self.samples = pj.samples
else:
names = set()
for x in report.general_stats_data:
names.update(x.keys())
for d in report.saved_raw_data.values():
try:
self.names.update(d.keys())
except AttributeError:
pass
if not config.kwargs.get('clarity_skip_edit_names'):
names = self.edit_names(names)
self.log.debug("Looking into Clarity for samples {}".format(
", ".join(names)))
found = 0
try:
for name in names:
matching_samples = self.lims.get_samples(name=name)
if not matching_samples:
self.log.error(
"Could not find a sample matching {0}, skipping.".
format(name))
continue
if len(matching_samples) > 1:
self.log.error(
"Found multiple samples matching {0}, skipping".
format(name))
continue
found += 1
self.samples.append(matching_samples[0])
except Exception as e:
self.log.warn(
"Could not connect to Clarity LIMS: {}".format(e))
return None
self.log.info("Found {} out of {} samples in LIMS.".format(
found, len(names)))
def edit_names(self, names):
edited = []
for name in names:
if name.endswith("_1") or name.endswith("_2"):
edited.append(name[:-2])
elif name.endswith("_R1") or name.endswith("_R2"):
edited.append(name[:-3])
else:
edited.append(name)
return edited
def flatten_metadata(self, metadata):
for first_level in metadata:
for second_level in metadata[first_level]:
if isinstance(metadata[first_level][second_level],
set) or isinstance(
metadata[first_level][second_level], list):
metadata[first_level][second_level] = ", ".join(
metadata[first_level][second_level])
return metadata
def get_project_metadata(self, udfs):
project_metadata = {}
for sample in self.samples:
project_metadata[sample.project.name] = {}
for udf in udfs:
if udf in sample.project.udf:
try:
project_metadata[sample.project.name][udf].add(
str(sample.project.udf[udf]))
except:
project_metadata[sample.project.name][udf] = set()
project_metadata[sample.project.name][udf].add(
str(sample.project.udf[udf]))
return self.flatten_metadata(project_metadata)
def get_sample_metadata(self, udfs):
sample_metadata = {}
for sample in self.samples:
sample_metadata[sample.name] = {}
for udf in udfs:
if udf in sample.udf:
try:
sample_metadata[sample.name][udf].add(
str(sample.udf[udf]))
except:
sample_metadata[sample.name][udf] = set()
sample_metadata[sample.name][udf].add(
str(sample.udf[udf]))
return self.flatten_metadata(sample_metadata)
def get_metadata(self, part):
for key in self.schema[part]:
if key == 'Project':
metadata = self.get_project_metadata(
self.schema[part]['Project'])
elif key == 'Sample':
metadata = self.get_sample_metadata(
self.schema[part]['Sample'])
else:
metadata = self.get_artifact_metadata(self.schema[part])
if part == "Header":
self.header_metadata.update(metadata)
elif part == "General Statistics":
self.general_metadata.update(metadata)
else:
self.tab_metadata.update(metadata)
def get_artifact_metadata(self, pt_to_udfs):
artifact_metadata = {}
for sample in self.samples:
artifact_metadata[sample.name] = {}
for process_type in pt_to_udfs:
if process_type == 'Sample':
continue
if process_type == 'Project':
continue
artifacts = self.lims.get_artifacts(sample_name=sample.name,
process_type=process_type)
for udf_name in pt_to_udfs[process_type].get("outputs", []):
values = []
for artifact in artifacts:
if udf_name in artifact.udf:
values.append(str(artifact.udf[udf_name]))
artifact_metadata[sample.name][udf_name] = values
processes = set([art.parent_process for art in artifacts])
inputs = []
for p in processes:
inputs.extend([
art for art in p.all_inputs()
if sample.name in [s.name for s in art.samples]
])
for udf_name in pt_to_udfs[process_type].get("inputs", []):
values = []
for artifact in inputs:
if udf_name in artifact.udf:
values.append(str(artifact.udf[udf_name]))
artifact_metadata[sample.name][udf_name] = values
return self.flatten_metadata(artifact_metadata)
def update_multiqc_report(self):
if config.report_header_info is None:
config.report_header_info = []
for first_level in self.header_metadata:
d = {}
for key in self.header_metadata[first_level]:
d[key] = self.header_metadata[first_level][key]
config.report_header_info.append(d)
headers = {}
for first_level in self.schema["General Statistics"]:
for header in self.schema["General Statistics"][first_level]:
headers[header] = {
'description': first_level,
'namespace': 'Clarity',
'scale': 'YlGn'
}
report.general_stats_headers.append(headers)
report.general_stats_data.append(self.general_metadata)
def make_sections(self):
headers = OrderedDict()
for first_level in self.tab_metadata:
for header in self.tab_metadata[first_level]:
desc = header
if header not in headers:
for key in self.schema['Clarity Tab']:
if header in self.schema['Clarity Tab'][key]:
desc = key
elif isinstance(self.schema['Clarity Tab'][key], dict):
for subkey in self.schema['Clarity Tab'][key]:
if header in self.schema['Clarity Tab'][key][
subkey]:
desc = key
headers[header] = {
'namespace': desc,
'title': header,
'description': header
}
self.sections.append({
'name':
'Clarity Data',
'anchor':
'clarity_data',
'content':
'<p> Data obtained from Illumina Basespace Clarity LIMS.</p>' +
table.plot(self.tab_metadata, headers)
})
# Get the list of all artifacts.
## artifacts = lims.get_artifacts()
## print len(artifacts), 'total artifacts'
# Get lists of artifacts with different QC flags
## artifacts = lims.get_artifacts(qc_flag='UNKNOWN')
## print len(artifacts), 'QC UNKNOWN artifacts'
## artifacts = lims.get_artifacts(qc_flag='PASSED')
## print len(artifacts), 'QC PASSED artifacts'
## artifacts = lims.get_artifacts(qc_flag='FAILED')
## print len(artifacts), 'QC FAILED artifacts'
## artifacts = lims.get_artifacts(working_flag=True)
## print len(artifacts), 'Working-flag True artifacts'
name = 'jgr33'
artifacts = lims.get_artifacts(sample_name=name)
print len(artifacts), 'artifacts for sample name', name
artifacts = lims.get_batch(artifacts)
for artifact in artifacts:
print artifact, artifact.name, artifact.state
print
artifacts = lims.get_artifacts(qc_flag='PASSED')
print len(artifacts), 'QC PASSED artifacts'
artifacts = lims.get_batch(artifacts)
for artifact in artifacts:
print artifact, artifact.name, artifact.state
class MultiQC_clarity_metadata(BaseMultiqcModule):
def __init__(self):
self.log = logging.getLogger('multiqc')
# Check that this plugin hasn't been disabled
if config.kwargs.get('disable_clarity', False) is True:
self.log.info(
"Skipping MultiQC_Clarity as disabled on command line")
return
if getattr(config, 'disable_clarity', False) is True:
self.log.debug(
"Skipping MultiQC_Clarity as specified in config file")
return
super(MultiQC_clarity_metadata, self).__init__(name='Clarity LIMS',
anchor='clarity')
self.intro = '''<p>The <a href="https://github.com/MultiQC/MultiQC_Clarity" target="_blank">MultiQC_Clarity</a>
plugin fetches data from a specified
<a href="https://www.genologics.com/clarity-lims/" target="_blank">Basespace Clarity LIMS</a> instance.</p>'''
try:
from genologics.lims import Lims
from genologics import config as genologics_config
except:
self.log.warning("Importing genologics failed: " +
traceback.format_exc())
return
try:
BASEURI, USERNAME, PASSWORD, VERSION, MAIN_LOG = genologics_config.load_config(
specified_config=config.kwargs.get('clarity_config'))
except SystemExit:
self.log.warning(
"Genologics config file is not specified as --clarity_config or in ~/.genologicsrc. "
"Skip running Clarity module")
return
self.lims = Lims(BASEURI, USERNAME, PASSWORD)
self.metadata = {}
self.header_metadata = {}
self.general_metadata = {}
self.tab_metadata = {}
self.samples = []
self.schema = getattr(config, 'clarity', None)
if self.schema is None:
self.log.debug("No config found for MultiQC_Clarity")
return
try:
self.get_samples()
if 'report_header_info' in self.schema:
self.get_metadata('report_header_info')
if 'general_stats' in self.schema:
self.get_metadata('general_stats')
if 'clarity_module' in self.schema:
self.get_metadata('clarity_module')
self.update_multiqc_report()
self.make_sections()
report.modules_output.append(self)
except:
self.log.error("MultiQC_Clarity failed: " + traceback.format_exc())
return
def csv_file_from_samplesheet(self, sample_sheet):
csv_lines = []
with open(sample_sheet) as f:
found_data = False
for line in f:
if found_data:
csv_lines.append(line.strip())
else:
if line.strip().startswith('[Data]'):
found_data = True
return csv_lines
def get_raw_sample_names(self, csv_fpath, names):
raw_sample_names = dict()
with open(csv_fpath) as f:
csv_reader = csv.DictReader(f)
name_col = csv_reader.fieldnames[0]
for r in csv_reader:
correct_name = r['description'] if 'description' in r else r[
name_col]
if correct_name not in names:
continue
raw_sample_names[correct_name] = r[name_col]
return raw_sample_names
def correct_sample_name(self, name):
import re
name = re.sub(r'_S\d+$', '', name)
return name.replace('.', '_')
def search_by_samplesheet(self, names):
sample_sheet_fpath = config.kwargs['samplesheet']
samples_by_container = defaultdict(dict)
raw_names = dict((name, name) for name in names)
if config.kwargs.get('bcbio_csv') and isfile(
config.kwargs.get('bcbio_csv')):
raw_names = self.get_raw_sample_names(config.kwargs['bcbio_csv'],
names)
correct_sample_names = dict(
(self.correct_sample_name(raw_names[name]), name)
for name in names)
for row in csv.DictReader(
self.csv_file_from_samplesheet(sample_sheet_fpath),
delimiter=','):
sample_name = row['SampleName'] if 'SampleName' in row else (
row['Sample_Name']
if 'Sample_Name' in row else row['SampleRef'])
sample_id = row['SampleID'] if 'SampleID' in row else row[
'Sample_ID']
sample_artifacts = self.lims.get_artifacts(samplelimsid=sample_id)
if sample_artifacts:
sample = sample_artifacts[0].samples[0]
sample.name = correct_sample_names[sample_name]
self.samples.append(sample)
elif sample_name and sample_name in correct_sample_names.keys():
try:
container, sample_well = row['SamplePlate'], row[
'SampleWell'].replace('_', ':')
samples_by_container[container][sample_well] = sample_name
except:
pass
for container_id, samples in samples_by_container.items():
artifacts = self.lims.get_artifacts(containerlimsid=container_id)
if not artifacts:
continue
placements = artifacts[0].container.get_placements()
for well, sample_name in samples.items():
sample = placements[well].samples[0]
sample.name = correct_sample_names[sample_name]
self.samples.append(sample)
def get_samples(self):
if config.kwargs.get('clarity_project_name'):
pj = self.lims.get_projects(
name=config.kwargs['clarity_project_name'])
self.samples = pj.samples
self.log.info("Found {} in LIMS.".format(
config.kwargs['clarity_project_name']))
else:
names = set()
for x in report.general_stats_data:
names.update(x.keys())
for d in report.saved_raw_data.values():
try:
self.names.update(d.keys())
except AttributeError:
pass
# if not config.kwargs.get('clarity_skip_edit_names'):
# names = self.edit_names(names)
self.log.debug("Looking into Clarity for samples {}".format(
", ".join(names)))
if config.kwargs.get('samplesheet'):
self.search_by_samplesheet(names)
if not self.samples:
try:
for name in names:
matching_samples = self.lims.get_samples(name=name)
if not matching_samples:
self.log.error(
"Could not find a sample matching {0}, skipping."
.format(name))
continue
if len(matching_samples) > 1:
self.log.error(
"Found multiple samples matching {0}, skipping"
.format(name))
continue
self.samples.append(matching_samples[0])
except Exception as e:
self.log.warn(
"Could not connect to Clarity LIMS: {}".format(e))
return None
self.log.info("Found {} out of {} samples in LIMS.".format(
len(self.samples), len(names)))
def edit_names(self, names):
edited = []
for name in names:
if name.endswith("_1") or name.endswith("_2"):
edited.append(name[:-2])
elif name.endswith("_R1") or name.endswith("_R2"):
edited.append(name[:-3])
else:
edited.append(name)
return edited
def flatten_metadata(self, metadata):
for first_level in metadata:
for second_level in metadata[first_level]:
if isinstance(metadata[first_level][second_level],
set) or isinstance(
metadata[first_level][second_level], list):
metadata[first_level][second_level] = ", ".join(
metadata[first_level][second_level])
return metadata
def get_project_metadata(self, udfs):
project_metadata = {}
for sample in self.samples:
project_metadata[sample.project.name] = {}
for udf in udfs:
if udf in sample.project.udf:
try:
project_metadata[sample.project.name][udf].add(
str(sample.project.udf[udf]))
except:
project_metadata[sample.project.name][udf] = set()
project_metadata[sample.project.name][udf].add(
str(sample.project.udf[udf]))
return self.flatten_metadata(project_metadata)
def get_sample_metadata(self, udfs):
sample_metadata = {}
report.lims_col = 'sample type'
for sample in self.samples:
sample_metadata[sample.name] = dict()
for udf in udfs:
if udf in sample.udf:
try:
sample_metadata[sample.name][udf].add(
str(sample.udf[udf]))
except:
sample_metadata[sample.name][udf] = set()
sample_metadata[sample.name][udf].add(
str(sample.udf[udf]))
sample_type = None
if 'Sample Tissue' in sample_metadata[sample.name]:
sample_type = sample_metadata[sample.name].pop('Sample Tissue')
elif 'Sample Type' in sample_metadata[sample.name]:
sample_type = sample_metadata[sample.name].pop('Sample Type')
sample_link = join(self.lims.baseuri, 'clarity',
'search?scope=Sample&query=' + sample.id)
if sample_type:
sample_metadata[sample.name][
'Sample Type'] = '<a href="' + sample_link + '" target="_blank">' + sample_type.pop(
) + '</a>'
report.lims_added = True
elif 'Sample Conc.' in sample_metadata[sample.name]:
sample_metadata[sample.name]['Sample Conc.'] = '<a href="' + sample_link + '" target="_blank">' + \
sample_metadata[sample.name]['Sample Conc.'].pop() + '</a>'
report.lims_added = True
if not any([
'Sample Type' in sample_metadata[sample.name]
for sample in self.samples
]):
report.lims_col = 'sample conc'
elif not all([
'Sample Type' in sample_metadata[sample.name]
for sample in self.samples
]):
report.lims_col = 'sample type or sample conc'
return self.flatten_metadata(sample_metadata)
def get_metadata(self, part):
for key in self.schema[part]:
if key == 'Project':
metadata = self.get_project_metadata(
self.schema[part]['Project'])
elif key == 'Sample':
metadata = self.get_sample_metadata(
self.schema[part]['Sample'])
else:
metadata = self.get_artifact_metadata(self.schema[part])
if part == "report_header_info":
self.header_metadata.update(metadata)
elif part == "general_stats":
self.general_metadata.update(metadata)
else:
self.tab_metadata.update(metadata)
def get_artifact_metadata(self, pt_to_udfs):
artifact_metadata = {}
for sample in self.samples:
artifact_metadata[sample.name] = {}
for process_type in pt_to_udfs:
if process_type == 'Sample':
continue
if process_type == 'Project':
continue
artifacts = self.lims.get_artifacts(sample_name=sample.name,
process_type=process_type)
for udf_name in pt_to_udfs[process_type].get("outputs", []):
values = []
for artifact in artifacts:
if udf_name in artifact.udf:
values.append(str(artifact.udf[udf_name]))
artifact_metadata[sample.name][udf_name] = values
processes = set([art.parent_process for art in artifacts])
inputs = []
for p in processes:
inputs.extend([
art for art in p.all_inputs()
if sample.name in [s.name for s in art.samples]
])
for udf_name in pt_to_udfs[process_type].get("inputs", []):
values = []
for artifact in inputs:
if udf_name in artifact.udf:
values.append(str(artifact.udf[udf_name]))
artifact_metadata[sample.name][udf_name] = values
return self.flatten_metadata(artifact_metadata)
def update_multiqc_report(self):
if config.report_header_info is None:
config.report_header_info = []
for first_level in self.header_metadata:
d = {}
for key in self.header_metadata[first_level]:
d[key] = self.header_metadata[first_level][key]
config.report_header_info.append(d)
headers = {}
for first_level in self.schema["general_stats"]:
for header in self.schema["general_stats"][first_level]:
headers[header] = {}
if isinstance(
self.schema["general_stats"][first_level][header],
dict):
for subsubkey, cfg in self.schema["general_stats"][
first_level][header].items():
if subsubkey == 'multiply_by':
mby = str(cfg)[:]
headers[header]['modify'] = lambda x: float(
x) * float(mby)
else:
headers[header][subsubkey] = cfg
headers[header]['description'] = headers[header].get(
'description', '{} - {}'.format(first_level, header))
headers[header]['namespace'] = headers[header].get(
'namespace', 'Clarity LIMS')
headers[header]['scale'] = headers[header].get('scale', 'YlGn')
report.general_stats_headers.append(headers)
report.general_stats_data.append(self.general_metadata)
def make_sections(self):
headers = OrderedDict()
for first_level in self.tab_metadata:
for header in self.tab_metadata[first_level]:
desc = header
if header not in headers:
headers[header] = {}
for key in self.schema['clarity_module']:
if header in self.schema['clarity_module'][key]:
desc = key
elif isinstance(self.schema['clarity_module'][key],
dict):
for subkey, val in self.schema['clarity_module'][
key].items():
# print(val)
if val is None:
break
elif header in val:
desc = key
if isinstance(val[header], dict):
for subsubkey, cfg in val[
header].items():
if subsubkey == 'multiply_by':
mby = str(cfg)[:]
headers[header][
'modify'] = lambda x: float(
x) * float(mby)
else:
headers[header][
subsubkey] = cfg
headers[header]['namespace'] = headers[header].get(
'namespace', desc)
headers[header]['title'] = headers[header].get(
'title', header)
headers[header]['description'] = headers[header].get(
'description', header)
self.intro += table.plot(self.tab_metadata, headers)