def _write_to_worksheet(client, ssheet, wsheet_title, rows, header, append, keys=[]):
"""Generic method to write a set of rows to a worksheet on google docs.
"""
# Convert the worksheet title to unicode
wsheet_title = _to_unicode(wsheet_title)
# Add a new worksheet, possibly appending or replacing a pre-existing
# worksheet according to the append-flag.
wsheet = g_spreadsheet.add_worksheet(client, \
ssheet, \
wsheet_title, \
len(rows) + 1, \
len(header), \
append)
if wsheet is None:
logger2.error("ERROR: Could not add a worksheet {!r} to " \
"spreadsheet {!r}".format(wsheet_title, ssheet.title.text))
return False
# If keys are specified (will correspond to indexes in the header), delete pre-existing rows with matching keys
if append and len(keys) > 0:
wsheet_data = g_spreadsheet.get_cell_content(client, ssheet, wsheet, '2')
wsheet_header = g_spreadsheet.get_header(client, ssheet, wsheet)
try:
wsheet_indexes = [wsheet_header.index(key) for key in keys]
header_indexes = [header.index(key) for key in keys]
except ValueError:
logger2.warn("WARNING: Could not identify correct header for duplicate detection")
else:
for row in rows:
try:
key = "#".join([row[i] for i in header_indexes])
for i, wrow in enumerate(wsheet_data):
wkey = "#".join([wrow[j] for j in wsheet_indexes])
if wkey == key:
g_spreadsheet.delete_row(client, ssheet, wsheet, i+1)
wsheet_data.pop(i)
break
except:
logger2.warn("WARNING: Could not identify/replace duplicate rows")
# Write the data to the worksheet
success = g_spreadsheet.write_rows(client, ssheet, wsheet, header, rows)
if success:
logger2.info("Wrote data to the {!r}:{!r} " \
"worksheet".format(ssheet.title.text, wsheet_title))
else:
logger2.error("ERROR: Could not write data to the {!r}:{!r} " \
"worksheet".format(ssheet.title.text, wsheet_title))
return success
def write_project_report_summary_to_gdocs(client, ssheet):
"""Summarize the data from the worksheets and write them to a "Summary"
worksheet.
"""
# Summary data
flowcells = {}
samples = {}
# Get the list of worksheets in the spreadsheet
wsheet_feed = g_spreadsheet.get_worksheets_feed(client, ssheet)
# Loop over the worksheets and parse the data from the ones that contain
# flowcell data.
for wsheet in wsheet_feed.entry:
wsheet_title = wsheet.title.text
if wsheet_title.endswith("_QC"):
continue
# Use the bcbio.solexa.flowcell.get_flowcell_info method to determine if the wsheet title contains a valid flowcell id
try:
bcbio.solexa.flowcell.get_flowcell_info(wsheet_title)
except ValueError:
continue
# Get the worksheet header
wsheet_header = g_spreadsheet.get_header(client, ssheet, wsheet)
wsheet_data = g_spreadsheet.get_cell_content(client, ssheet, wsheet, '2')
delim = ';'
# Map the column names to the correct index using the header
sample_col, run_col, lane_col, count_col, bc_col = [_header_index(SEQUENCING_RESULT_HEADER,col_name,wsheet_header) for col_name in ('sample_name', 'run', 'lane', 'read_count', 'barcode_sequence')]
# Add the results from the worksheet to the summarized data.
for row in wsheet_data:
sample_name, run_name, lane_name, read_count, barcode_sequence = [row[col] if col >= 0 else None for col in (sample_col, run_col, lane_col, count_col, bc_col)]
data = {"name": sample_name,
"read_count": read_count,
"sequence": barcode_sequence}
lane = bcbio.pipeline.flowcell.Lane({"lane": lane_name})
sample = bcbio.pipeline.flowcell.BarcodedSample(data, lane)
if sample_name in samples:
samples[sample_name]["object"].add_sample(sample, delim)
samples[sample_name]["flowcells"] += "{}{}".format(delim, run_name)
if not samples[sample_name]["object"].barcode_sequence and barcode_sequence:
samples[sample_name]["object"].barcode_sequence = barcode_sequence
else:
samples[sample_name] = {"object": sample, "flowcells": run_name}
wsheet_title = "Summary"
# Try getting already existing 'comment' and 'pass' values.
name_data = {}
existing_summary_wsheet = g_spreadsheet.get_worksheet(client, ssheet, wsheet_title)
if existing_summary_wsheet:
summary_header = g_spreadsheet.get_header(client, ssheet, existing_summary_wsheet)
summary_data = g_spreadsheet.get_cell_content(client, ssheet, existing_summary_wsheet, '2')
sample_col, comment_col, pass_col = [_header_index(SEQUENCING_RESULT_HEADER,col_name,summary_header) for col_name in ('sample_name', 'comment', 'pass')]
for content in summary_data:
sample_name, comment, pass_field = [content[col] if col >= 0 else None for col in (sample_col, comment_col, pass_col)]
name_data[sample_name] = [comment, pass_field]
# Flatten the project_data structure into a list
rows = []
for sample_data in samples.values():
sample = sample_data["object"]
flowcells = sample_data["flowcells"]
sample_name = sample.get_name()
comment, pass_field = name_data.get(sample_name, ["", ""])
row = [sample_name, \
flowcells, \
sample.get_lane(), \
sample.get_read_count(), \
sample.get_rounded_read_count(), \
sample.barcode_sequence, \
comment, \
pass_field]
rows.append(row)
# Write the data to the worksheet
column_headers = [col_header[0] for col_header in SEQUENCING_RESULT_HEADER]
return _write_to_worksheet(client, \
ssheet, \
wsheet_title, \
rows, \
column_headers, \
False)
