def create_project_report_on_gdocs(fc, qc, encoded_credentials, gdocs_folder):
"""Upload the sample read distribution for a project to google docs.
"""
success = True
# Create a client class which will make HTTP requests with Google Docs server.
client = g_spreadsheet.get_client(encoded_credentials)
doc_client = g_document.get_client(encoded_credentials)
# Get a reference to the parent folder
parent_folder = g_document.get_folder(doc_client, gdocs_folder)
if not parent_folder:
parent_folder = g_document.add_folder(doc_client, gdocs_folder)
log.info("Folder {!r} created".format(gdocs_folder))
parent_folder_title = _from_unicode(parent_folder.title.text)
# Loop over the projects
for project_name in fc.get_project_names():
# Get a flowcell object containing just the data for the project
project_fc = fc.prune_to_project(project_name)
ssheet_title = project_name + "_sequencing_results"
ssheet = g_spreadsheet.get_spreadsheet(client, ssheet_title)
if not ssheet:
ssheet = g_document.add_spreadsheet(doc_client, ssheet_title)
g_document.move_to_folder(doc_client, ssheet, parent_folder)
ssheet = g_spreadsheet.get_spreadsheet(client, ssheet_title)
log.info("Spreadsheet {!r} created in " \
"folder {!r}".format(_from_unicode(ssheet.title.text), \
parent_folder_title))
success &= bc_metrics._write_project_report_to_gdocs(
client, ssheet, project_fc)
success &= bc_metrics.write_project_report_summary_to_gdocs(
client, ssheet)
success &= qc_metrics.write_run_report_to_gdocs(project_fc, \
qc, \
ssheet_title, \
encoded_credentials)
log.info("Sequencing results report written to spreadsheet '%s'" \
% _from_unicode(ssheet.title.text))
return success
def create_project_report_on_gdocs(fc, qc, encoded_credentials, gdocs_folder):
"""Upload the sample read distribution for a project to google docs.
"""
success = True
# Create a client class which will make HTTP requests with Google Docs server.
client = g_spreadsheet.get_client(encoded_credentials)
doc_client = g_document.get_client(encoded_credentials)
# Get a reference to the parent folder
parent_folder = g_document.get_folder(doc_client, gdocs_folder)
if not parent_folder:
parent_folder = g_document.add_folder(doc_client, gdocs_folder)
log.info("Folder {!r} created".format(gdocs_folder))
parent_folder_title = _from_unicode(parent_folder.title.text)
# Loop over the projects
for project_name in fc.get_project_names():
# Get a flowcell object containing just the data for the project
project_fc = fc.prune_to_project(project_name)
ssheet_title = project_name + "_sequencing_results"
ssheet = g_spreadsheet.get_spreadsheet(client, ssheet_title)
if not ssheet:
ssheet = g_document.add_spreadsheet(doc_client, ssheet_title)
g_document.move_to_folder(doc_client, ssheet, parent_folder)
ssheet = g_spreadsheet.get_spreadsheet(client, ssheet_title)
log.info("Spreadsheet {!r} created in " \
"folder {!r}".format(_from_unicode(ssheet.title.text), \
parent_folder_title))
success &= bc_metrics._write_project_report_to_gdocs(client, ssheet, project_fc)
success &= bc_metrics.write_project_report_summary_to_gdocs(client, ssheet)
success &= qc_metrics.write_run_report_to_gdocs(project_fc, \
qc, \
ssheet_title, \
encoded_credentials)
log.info("Sequencing results report written to spreadsheet '%s'" \
% _from_unicode(ssheet.title.text))
return success
def write_project_report_to_gdocs(fc_date, fc_name, project_bc_metrics, encoded_credentials, gdocs_folder=""):
"""Upload the sample read distribution for a project to google docs"""
# Create a client class which will make HTTP requests with Google Docs server.
client = bcbio.google.spreadsheet.get_client(encoded_credentials)
doc_client = bcbio.google.document.get_client(encoded_credentials)
# Get a reference to the parent folder
parent_folder = bcbio.google.document.get_folder(doc_client, gdocs_folder)
# Group the barcode data by project
grouped = group_bc_stats(project_bc_metrics)
# Loop over the projects and write the project summary for each
for pdata in grouped:
project_name = pdata.get("project_name", "")
ssheet_title = project_name + "_sequencing_results"
ssheet = bcbio.google.spreadsheet.get_spreadsheet(client, ssheet_title)
if not ssheet:
bcbio.google.document.add_spreadsheet(doc_client, ssheet_title)
ssheet = bcbio.google.spreadsheet.get_spreadsheet(client, ssheet_title)
_write_project_report_to_gdocs(client, ssheet, fc_date, fc_name, pdata)
_write_project_report_summary_to_gdocs(client, ssheet)
# Just to make it look a bit nicer, remove the default 'Sheet1' worksheet
wsheet = bcbio.google.spreadsheet.get_worksheet(client, ssheet, "Sheet 1")
if wsheet:
client.DeleteWorksheet(wsheet)
folder_name = project_name
folder = bcbio.google.document.get_folder(doc_client, folder_name)
if not folder:
log.info("creating folder '%s'" % _from_unicode(folder_name))
folder = bcbio.google.document.add_folder(doc_client, folder_name, parent_folder)
ssheet = bcbio.google.document.move_to_folder(doc_client, ssheet, folder)
log.info(
"'%s' spreadsheet written to folder '%s'" % (_from_unicode(ssheet.title.text), _from_unicode(folder_name))
)
def _get_query(title, exact_match):
"""Get a query object for the supplied parameters"""
p = {}
if title:
# The urllib.quote method does not handle unicode, so encode the title in utf-8
p['title'] = _from_unicode(title)
if exact_match:
p['title-exact'] = 'true'
else:
p['title-exact'] = 'false'
return gdata.spreadsheet.service.DocumentQuery(params=p)
def _get_query(title, exact_match):
"""Get a query object for the supplied parameters"""
p = {}
if title:
# The urllib.quote method does not handle unicode, so encode the title in utf-8
p['title'] = _from_unicode(title)
if exact_match:
p['title-exact'] = 'true'
else:
p['title-exact'] = 'false'
return gdata.spreadsheet.service.DocumentQuery(params=p)
def get_barcode_id(self):
return _from_unicode(self.barcode_id)
def get_description(self):
return _from_unicode(self.description)
def get_project(self):
return _from_unicode(self.project)
def get_full_name(self):
return _from_unicode(self.full_name)
def get_name(self):
return _from_unicode(self.name)
def get_name(self):
return _from_unicode(self.name)
def get_project(self):
return _from_unicode(self.project)
def get_barcode_type(self):
return _from_unicode(self.barcode_type)
def get_barcode_type(self):
return _from_unicode(self.barcode_type)
def get_barcode_sequence(self):
return _from_unicode(self.barcode_sequence)
def get_barcode_full_name(self):
return _from_unicode(self.barcode_full_name)
def get_barcode_id(self):
return _from_unicode(self.barcode_id)
def get_description(self):
return _from_unicode(self.description)
def get_barcode_full_name(self):
return _from_unicode(self.barcode_full_name)
def get_barcode_sequence(self):
return _from_unicode(self.barcode_sequence)
def get_full_name(self):
return _from_unicode(self.full_name)
def get_analysis(self):
return _from_unicode(self.analysis)
def get_genome_build(self):
return _from_unicode(self.genome_build)
def get_analysis(self):
return _from_unicode(self.analysis)
def get_genome_build(self):
return _from_unicode(self.genome_build)