def load(species, chipseq, paired, project_name, rerun_number, pi, investigator, tumor_type, pipeline, revision_number, project_dir, conn, log_file):
stats = list()
if species.lower() in ['human','hg18','hg19','hybrid','b37','grch37','xenograft']:
stats = load_exome_stats.human_stats.values()
if chipseq:
stats = load_exome_stats.human_chipseq_stats.values()
elif species.lower() in ['mouse','mm9','mm10']:
stats = load_exome_stats.mouse_stats.values()
if chipseq:
stats = load_exome_stats.mouse_chipseq_stats.values()
else:
log_helper.report_error_and_exit(log_file, "species is not recognized: '%s'" % (species))
## If paired add the one PE dependent stat
if paired:
stats.extend(load_exome_stats.paired_end_stats.values())
validate_files(project_name, project_dir, stats, log_file)
# now load data
log_file.write("LOG: Loading title file\n")
load_exome_samples.load(project_name, rerun_number, pi, investigator, 'unknown', pipeline, revision_number, get_title_file(project_name, project_dir), conn, log_file)
for stat in stats:
file_name = get_stat_file(project_name, project_dir, stat)
log_file.write("LOG: Loading stat '%s' from '%s'\n" % (stat.name, file_name))
load_exome_stats.load(species, chipseq, paired, stat.name, project_name, pi, investigator, rerun_number, revision_number, file_name, conn, log_file)
def load(species, assay, chipseq, paired, project_name, rerun_number, pi, investigator, tumor_type, pipeline, revision_number, project_dir, conn, log_file):
stats = list()
if species.lower() in ['human','hg18','hg19','hybrid','b37','grch37','xenograft']:
stats = load_exome_stats.human_stats.values()
if chipseq:
stats = load_exome_stats.human_chipseq_stats.values()
if 'wgs' in assay.lower():
stats = load_exome_stats.human_wgs_stats.values()
elif species.lower() in ['mouse','mm9','mm10']:
stats = load_exome_stats.mouse_stats.values()
if chipseq:
stats = load_exome_stats.mouse_chipseq_stats.values()
else:
log_helper.report_error_and_exit(log_file, "species is not recognized: '%s'" % (species))
## If paired add the one PE dependent stat
if paired:
stats.extend(load_exome_stats.paired_end_stats.values())
validate_files(project_name, project_dir, stats, log_file)
# now load data
log_file.write("LOG: Loading title file\n")
load_exome_samples.load(project_name, rerun_number, pi, investigator, 'unknown', pipeline, revision_number, get_title_file(project_name, project_dir), conn, log_file)
for stat in stats:
file_name = get_stat_file(project_name, project_dir, stat)
log_file.write("LOG: Loading stat '%s' from '%s'\n" % (stat.name, file_name))
load_exome_stats.load(species, assay, chipseq, paired, stat.name, project_name, pi, investigator, rerun_number, revision_number, file_name, conn, log_file)
def validate_files(project_name, project_dir, stats, log_file):
if not os.path.exists(project_dir):
log_helper.report_error_and_exit(
log_file, "Project directory '%s' does not exist" % (project_dir))
title_file = get_title_file(project_name, project_dir)
if not os.path.exists(title_file):
log_helper.report_error_and_exit(
log_file, "Sample title file '%s' does not exist" % (title_file))
for stat in stats:
file = get_stat_file(project_name, project_dir, stat)
if not file: # get_stat_file checks that it exists
log_helper.report_error_and_exit(
log_file, "%s '%s[%s]' does not exist" %
(stat.name,
os.path.join(project_dir, "metrics/Proj_" + project_name),
"|".join(stat.file_suffixes)))
## check for MarkDuplicates, CutAdapt file separately - TEMPORARILY
## TO DO: add these to load_stats.stats once database is updated
if not os.path.exists(
os.path.join(
project_dir,
"results/metrics/Proj_%s_markDuplicatesMetrics.txt" %
(project_name))):
if not os.path.exists(
os.path.join(
project_dir, "metrics/Proj_%s_markDuplicatesMetrics.txt" %
(project_name))):
log_helper.report_error_and_exit(
log_file, "%s '%s[%s]' does not exist" %
(MarkDuplicates,
os.path.join(project_dir, "metrics/Proj_" + project_name),
"_markDuplicatesMetrics.txt"))
if not os.path.exists(
os.path.join(
project_dir, "results/metrics/Proj_%s_CutAdaptStats.txt" %
(project_name))):
if not os.path.exists(
os.path.join(
project_dir, "metrics/Proj_%s_CutAdaptStats.txt" %
(project_name))):
log_helper.report_error_and_exit(
log_file, "%s '%s[%s]' does not exist" %
(CutAdaptStats,
os.path.join(project_dir, "metrics/Proj_" + project_name),
"_CutAdaptStats.txt"))
def validate_files(project_name, project_dir, stats, log_file):
if not os.path.exists(project_dir):
log_helper.report_error_and_exit(log_file, "Project directory '%s' does not exist" % (project_dir))
title_file = get_title_file(project_name, project_dir)
if not os.path.exists(title_file):
log_helper.report_error_and_exit(log_file, "Sample title file '%s' does not exist" % (title_file))
for stat in stats:
file = get_stat_file(project_name, project_dir, stat)
if not file: # get_stat_file checks that it exists
log_helper.report_error_and_exit(log_file, "%s '%s[%s]' does not exist" % (stat.name, os.path.join(project_dir, "metrics/Proj_" + project_name), "|".join(stat.file_suffixes)))
## check for MarkDuplicates, CutAdapt file separately - TEMPORARILY
## TO DO: add these to load_stats.stats once database is updated
if not os.path.exists(os.path.join(project_dir, "results/metrics/Proj_%s_markDuplicatesMetrics.txt" %(project_name))):
if not os.path.exists(os.path.join(project_dir, "metrics/Proj_%s_markDuplicatesMetrics.txt" %(project_name))):
log_helper.report_error_and_exit(log_file, "%s '%s[%s]' does not exist" %(MarkDuplicates, os.path.join(project_dir, "metrics/Proj_" + project_name), "_markDuplicatesMetrics.txt"))
if not os.path.exists(os.path.join(project_dir, "results/metrics/Proj_%s_CutAdaptStats.txt" %(project_name))):
if not os.path.exists(os.path.join(project_dir, "metrics/Proj_%s_CutAdaptStats.txt" %(project_name))):
log_helper.report_error_and_exit(log_file, "%s '%s[%s]' does not exist" %(CutAdaptStats, os.path.join(project_dir, "metrics/Proj_" + project_name), "_CutAdaptStats.txt"))
def validate_files(project_name, project_dir, stats, log_file):
if not os.path.exists(project_dir):
log_helper.report_error_and_exit(log_file, "Project directory '%s' does not exist" % (project_dir))
title_file = get_title_file(project_name, project_dir)
if not os.path.exists(title_file):
log_helper.report_error_and_exit(log_file, "Sample title file '%s' does not exist" % (title_file))
for stat in stats:
file = get_stat_file(project_name, project_dir, stat)
if not file: # get_stat_file checks that it exists
log_helper.report_error_and_exit(log_file, "%s '%s[%s]' does not exist" % (stat.name, os.path.join(project_dir, "metrics/Proj_" + project_name), "|".join(stat.file_suffixes)))
paired = False
stat_type, request_file, revision_number, in_file_name = args
if not os.path.exists(request_file):
print "ERROR: Can't find request file %s" %request_file
sys.exit(-1)
project_id, rerun_number, pi, investigator, species, tumor_type, pipeline = parse_request(request_file)
if not project_id or not rerun_number or not pi or not investigator:
print "ERROR: Required info missing from request file"
sys.exit(-1)
conn = None
with open(log_file_name, "w") as log_file:
try:
conn = mysql.connector.connect(**db_config.params)
in_file_name = os.path.abspath(in_file_name)
load(species, chipseq, paired, stat_type, project_id, pi, investigator, rerun_number, revision_number, in_file_name, conn, log_file)
conn.commit()
conn.close()
except Exception as e:
if conn:
conn.close()
#raise
log_helper.report_error_and_exit(log_file, str(e))
paired = False
stat_type, request_file, revision_number, in_file_name = args
if not os.path.exists(request_file):
print "ERROR: Can't find request file %s" %request_file
sys.exit(-1)
project_id, rerun_number, pi, investigator, species, tumor_type, pipeline = parse_request(request_file)
if not project_id or not rerun_number or not pi or not investigator:
print "ERROR: Required info missing from request file"
sys.exit(-1)
conn = None
with open(log_file_name, "w") as log_file:
try:
conn = mysql.connector.connect(**db_config.params)
in_file_name = os.path.abspath(in_file_name)
load(species, chipseq, paired, stat_type, project_id, pi, investigator, rerun_number, revision_number, in_file_name, conn, log_file)
conn.commit()
conn.close()
except Exception as e:
if conn:
conn.close()
#raise
log_helper.report_error_and_exit(log_file, str(e))
