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get output datasets as well

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Anastasia Tyryshkina
2018-06-04 13:33:59 -04:00
parent 5b7055fc6f
commit 4630994fd0
1 changed files with 20 additions and 5 deletions
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scripts/grt/export.py
+20 -5
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@@ -280,20 +280,30 @@ def main(argv):
annotate('export_datasets_start', 'Exporting Datasets')
handle_datasets = open(REPORT_BASE + '.datasets.tsv', 'w')
handle_datasets.write('\t'.join(('job_id', 'dataset_id', 'extension', 'file_size', 'param_name')) + '\n')
handle_datasets.write('\t'.join(('job_id', 'dataset_id', 'extension', 'file_size', 'param_name', 'type')) + '\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
# three queries: JobToInputDatasetAssociation, HistoryDatasetAssociation, Dataset
# four queries: JobToInputDatasetAssociation, JobToOutputDatasetAssociation, HistoryDatasetAssociation, Dataset
job_to_hda_ids=sa_session.query(model.JobToInputDatasetAssociation.job_id, model.JobToInputDatasetAssociation.dataset_id,
job_to_input_hda_ids=sa_session.query(model.JobToInputDatasetAssociation.job_id, model.JobToInputDatasetAssociation.dataset_id,
model.JobToInputDatasetAssociation.name) \
.filter(model.JobToInputDatasetAssociation.job_id > offset_start) \
.filter(model.JobToInputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all()
job_to_output_hda_ids=sa_session.query(model.JobToOutputDatasetAssociation.job_id, model.JobToOutputDatasetAssociation.dataset_id,
model.JobToOutputDatasetAssociation.name) \
.filter(model.JobToOutputDatasetAssociation.job_id > offset_start) \
.filter(model.JobToOutputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all()
# add type and concat
job_to_hda_ids=[[list(i),"input"] for i in job_to_input_hda_ids]+[[list(i),"output"] for i in job_to_output_hda_ids]
# put all of the hda_ids into a list
hda_ids=[i[1] for i in job_to_hda_ids]
hda_ids=[i[0][1] for i in job_to_hda_ids]
hdas=sa_session.query(model.HistoryDatasetAssociation.id, model.HistoryDatasetAssociation.dataset_id,
model.HistoryDatasetAssociation.extension) \
@@ -305,7 +315,7 @@ def main(argv):
# get the sizes of the datasets
datasets=sa_session.query(model.Dataset.id, model.Dataset.total_size) \
.filter(model.HistoryDatasetAssociation.id.in_(dataset_ids)) \
.filter(model.Dataset.id.in_(dataset_ids)) \
.all()
# datasets to dictionay for easy search
@@ -314,6 +324,9 @@ def main(argv):
for job in job_to_hda_ids:
filetype=job[1]
job=job[0]
# No associated job
if job[0] not in job_tool_map:
continue
@@ -333,6 +346,8 @@ def main(argv):
handle_datasets.write(str(datasets[dataset_id][0]))
handle_datasets.write('\t')
handle_datasets.write(job[2])
handle_datasets.write('\t')
handle_datasets.write(filetype)
handle_datasets.write('\n')
handle_datasets.close()