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 get_spreadsheet(ssheet_title, encoded_credentials):
"""Connect to Google docs and get a spreadsheet"""
# Convert the spreadsheet title to unicode
ssheet_title = _to_unicode(ssheet_title)
# Create a client class which will make HTTP requests with Google Docs server.
client = g_spreadsheet.get_client()
bcbio.google.connection.authenticate(client, encoded_credentials)
# Locate the spreadsheet
ssheet = g_spreadsheet.get_spreadsheet(client, ssheet_title)
# Check that we got a result back
if not ssheet:
logger2.warn("No document with specified title '%s' found in \
GoogleDocs repository" % ssheet_title)
return (None, None)
return (client, ssheet)
