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fixed the issues with the last pull

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This commit is contained in:
Anastasia Tyryshkina
2018-06-04 11:53:14 -04:00
parent 11575132dc
commit aa062f8546
1 changed files with 40 additions and 29 deletions
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scripts/grt/export.py
+40 -29
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@@ -280,41 +280,52 @@ 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', 'name', 'param_name')) + '\n')
handle_datasets.write('\t'.join(('job_id', 'dataset_id', 'extension', 'file_size', 'param_name')) + '\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))
for job in sa_session.query(model.Job) \
.filter(model.Job.id > offset_start) \
.filter(model.Job.id <= min(end_job_id, offset_start + args.batch_size)) \
.all():
# If the tool is blacklisted, exclude everywhere
if job.tool_id in blacklisted_tools:
continue
# three queries: JobToInputDatasetAssociation, HistoryDatasetAssociation, Dataset
input_datasets=(job.input_datasets)
for input_dataset in input_datasets:
hda = input_dataset.dataset
dataset = hda.dataset
datasets=({'dataset_id': str(hda.dataset_id),
'extension': hda.extension,
'file_size': int(dataset.file_size),
'name': hda.name,
'param_name': input_dataset.name})
job_to_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()
handle_datasets.write(str(job.id))
handle_datasets.write('\t')
handle_datasets.write(datasets['dataset_id'])
handle_datasets.write('\t')
handle_datasets.write(datasets['extension'])
handle_datasets.write('\t')
handle_datasets.write(str(datasets['file_size']))
handle_datasets.write('\t')
handle_datasets.write(datasets['name'])
handle_datasets.write('\t')
handle_datasets.write(datasets['param_name'])
handle_datasets.write('\n')
# put all of the hda_ids into a list
hda_ids=[i[1] for i in job_to_hda_ids]
hdas=sa_session.query(model.HistoryDatasetAssociation.id, model.HistoryDatasetAssociation.dataset_id,
model.HistoryDatasetAssociation.extension) \
.filter(model.HistoryDatasetAssociation.id.in_(hda_ids)) \
.all()
# put all the dataset ids into a list
dataset_ids=[i[1] for i in hdas]
# get the sizes of the datasets
datasets=sa_session.query(model.Dataset.id, model.Dataset.total_size) \
.filter(model.HistoryDatasetAssociation.id.in_(dataset_ids)) \
.all()
# datasets to dictionay for easy search
hdas={i[0]:i[1:] for i in hdas}
datasets={i[0]:i[1:] for i in datasets}
for job in job_to_hda_ids:
hda_id=job[1]
dataset_id=hdas[hda_id][0]
handle_datasets.write(str(job[0]))
handle_datasets.write('\t')
handle_datasets.write(str(hda_id))
handle_datasets.write('\t')
handle_datasets.write(hdas[hda_id][1]) # not sure if this results in a query, but this was the only way I managed to retrive it.
handle_datasets.write('\t')
handle_datasets.write(str(datasets[dataset_id][0]))
handle_datasets.write('\t')
handle_datasets.write(job[2])
handle_datasets.write('\n')
handle_datasets.close()
annotate('export_datasets_end')