opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Ensure correct encoding, no partial lines

Browse Source
This commit is contained in:
Helena Rasche
2019-09-26 12:12:22 +02:00
parent 8ac4dc65ab
commit f200835445
1 changed files with 30 additions and 31 deletions
Download Patch File Download Diff File Expand all files Collapse all files
scripts/grt/export.py
+30 -31
View File
@@ -21,6 +21,7 @@ import galaxy.config
from galaxy.objectstore import build_object_store_from_config
from galaxy.util import hash_util
from galaxy.util.script import app_properties_from_args, populate_config_args
from galaxy.util import unicodify
sample_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml.sample'))
default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml'))
@@ -155,16 +156,15 @@ def main(argv):
continue
try:
handle_job.write(str(job[0])) # id
handle_job.write('\t')
handle_job.write(job[2]) # tool_id
handle_job.write('\t')
handle_job.write(job[3]) # tool_version
handle_job.write('\t')
handle_job.write(job[4]) # state
handle_job.write('\t')
handle_job.write(str(job[5])) # create_time
handle_job.write('\n')
line = [
str(job[0]), # id
job[2], # tool_id
job[3], # tool_version
job[4], # state
str(job[5]) # create_time
]
cline = unicodify('\t'.join(line) + '\n')
handle_job.write(cline.encode('utf-8'))
except Exception:
logging.warning("Unable to write out a 'handle_job' row. Ignoring the row.", exc_info=True)
continue
@@ -241,18 +241,16 @@ def main(argv):
continue
try:
handle_datasets.write(str(job[0]))
handle_datasets.write('\t')
handle_datasets.write(str(hda_id))
handle_datasets.write('\t')
handle_datasets.write(str(hdas[hda_id][1]))
handle_datasets.write('\t')
handle_datasets.write(round_to_2sd(datasets[dataset_id][0]))
handle_datasets.write('\t')
handle_datasets.write(str(job[2]))
handle_datasets.write('\t')
handle_datasets.write(str(filetype))
handle_datasets.write('\n')
line = [
str(job[0]), # Job ID
str(hda_id), # HDA ID
str(hdas[hda_id][1]), # Extension
round_to_2sd(datasets[dataset_id][0]), # File size
job[2], # Parameter name
str(filetype) # input/output
]
cline = unicodify('\t'.join(line) + '\n')
handle_datasets.write(cline.encode('utf-8'))
except Exception:
logging.warning("Unable to write out a 'handle_datasets' row. Ignoring the row.", exc_info=True)
continue
@@ -276,14 +274,15 @@ def main(argv):
continue
try:
handle_metric_num.write(str(metric[0]))
handle_metric_num.write('\t')
handle_metric_num.write(metric[1])
handle_metric_num.write('\t')
handle_metric_num.write(metric[2])
handle_metric_num.write('\t')
handle_metric_num.write(str(metric[3]))
handle_metric_num.write('\n')
line = [
str(metric[0]),
metric[1],
metric[2],
str(metric[3])
]
cline = unicodify('\t'.join(line) + '\n')
handle_metric_num.write(cline.encode('utf-8'))
except Exception:
logging.warning("Unable to write out a 'handle_metric_num' row. Ignoring the row.", exc_info=True)
continue
@@ -303,7 +302,7 @@ def main(argv):
os.unlink(REPORT_BASE + '.' + name + '.tsv')
_times.append(('job_finish', time.time() - _start_time))
sha = hash_util.memory_bound_hexdigest(hash_util.sha256, REPORT_BASE + ".tar.gz")
sha = hash_util.memory_bound_hexdigest(hash_func=hash_util.sha256, path=REPORT_BASE + ".tar.gz")
_times.append(('hash_finish', time.time() - _start_time))
# Now serialize the individual report data.