Python get_base_json_dict 예제들

예제 #1

파일: meme_fimo_output_stats.py 프로젝트: gregvonkuster/cegr-galaxy

parser.add_argument('--input_xml', dest='input_xmls', action='append', nargs=5, help='Input XML datasets and attributes')
parser.add_argument('--output', dest='output', help='Output dataset')
parser.add_argument('--stats_tool_id', dest='stats_tool_id', help='The caller of this script')
parser.add_argument('--stderr', dest='stderr', help='Job stderr')
parser.add_argument('--tool_id', dest='tool_id', help='Tool that was executed to produce the input dataset')
parser.add_argument('--tool_parameters', dest='tool_parameters', help='Tool parameters that were set when producing the input dataset')
parser.add_argument('--workflow_step_id', dest='workflow_step_id', default=None, help='Workflow step id')
parser.add_argument('--user_email', dest='user_email', help='Current user email')
args = parser.parse_args()

payload = None
statistics = []
datasets = []
# Generate the statistics and datasets.
if args.input_gffs is None:
    payload = stats_util.get_base_json_dict(args.config_file, 'unknown', args.history_id, args.history_name, args.stats_tool_id, args.stderr, args.tool_id, args.tool_parameters, args.user_email, args.workflow_step_id)
else:
    for input in args.input_gffs:
        file_path, hid, input_id, input_datatype, dbkey = input
        if payload is None:
            # Initialize the payload.
            payload = stats_util.get_base_json_dict(args.config_file, dbkey, args.history_id, args.history_name, args.stats_tool_id, args.stderr, args.tool_id, args.tool_parameters, args.user_email, args.workflow_step_id)
        statistics.append({})
        datasets.append(stats_util.get_datasets(args.config_file, input_id, input_datatype))

input_xmls = args.input_xmls or []
for input in input_xmls:
    file_path, hid, input_id, input_datatype, dbkey = input
    statistics.append({})
    datasets.append(stats_util.get_datasets(args.config_file, input_id, input_datatype))

예제 #2

파일: cwpair2_output_stats.py 프로젝트: bongsoopark/cegr-galaxy

parser.add_argument('--input', dest='inputs', action='append', nargs=5, help='Input datasets and attributes')
parser.add_argument('--output', dest='output', help='Output dataset')
parser.add_argument('--stats_tool_id', dest='stats_tool_id', help='The caller of this script')
parser.add_argument('--stderr', dest='stderr', help='Job stderr')
parser.add_argument('--tool_id', dest='tool_id', help='Tool that was executed to produce the input dataset')
parser.add_argument('--tool_parameters', dest='tool_parameters', help='Tool parameters that were set when producing the input dataset')
parser.add_argument('--workflow_step_id', dest='workflow_step_id', default=None, help='Workflow step id')
parser.add_argument('--user_email', dest='user_email', help='Current user email')
args = parser.parse_args()

payload = None
statistics = []
datasets = []
# Generate the statistics and datasets.
if args.inputs is None:
    payload = stats_util.get_base_json_dict(args.config_file, 'unknown', args.history_id, args.history_name, args.stats_tool_id, args.stderr, args.tool_id, args.tool_parameters, args.user_email, args.workflow_step_id)
else:
    for input in args.inputs:
        file_path, hid, input_id, input_datatype, dbkey = input
        if payload is None:
            # Initialize the payload.
            payload = stats_util.get_base_json_dict(args.config_file, dbkey, args.history_id, args.history_name, args.stats_tool_id, args.stderr, args.tool_id, args.tool_parameters, args.user_email, args.workflow_step_id)
        statistics.append(stats_util.get_statistics(file_path, STATS))
        datasets.append(stats_util.get_datasets(args.config_file, input_id, input_datatype))
payload['statistics'] = statistics
payload['datasets'] = datasets
# Send the payload to PEGR.
pegr_url = stats_util.get_pegr_url(args.config_file)
response = stats_util.submit(args.config_file, payload)
# Make sure all is well.
stats_util.check_response(pegr_url, payload, response)

예제 #3

파일: mark_duplicates_bam_output_stats.py 프로젝트: bgruening/cegr-galaxy

#!/usr/bin/env python
import argparse
import json
import stats_util

stats_util.check_samtools()

parser = argparse.ArgumentParser()
parser.add_argument('--config_file', dest='config_file', help='stats_config.ini')
parser.add_argument('--input', dest='input', help='Input dataset')
parser.add_argument('--dbkey', dest='dbkey', help='Input dbkey')
parser.add_argument('--history_name', dest='history_name', help='History name')
parser.add_argument('--output', dest='output', help='Output dataset')
args = parser.parse_args()

payload = stats_util.get_base_json_dict(args.dbkey, args.history_name)
payload['dedupUniquelyMappedReads'] = stats_util.get_deduplicated_uniquely_mapped_reads(args.input)
payload['mappedReads'] = stats_util.get_mapped_reads(args.input)
payload['totalReads'] = stats_util.get_total_reads(args.input)
payload['uniquelyMappedReads'] = stats_util.get_uniquely_mapped_reads(args.input)
url = stats_util.get_url(args.config_file)

response = stats_util.submit(args.config_file, payload)

with open(args.output, 'w') as fh:
    fh.write("url:\n%s\n\n" % url)
    fh.write("payload:\n%s\n\n" % json.dumps(payload))
    fh.write("response:\n%s\n" % str(response))
    fh.close()