# HG changeset patch
# User genouest
# Date 1646392510 0
# Node ID 896c5e0b51a6c9474a5cc386abcc5cc85c5029fe
"planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive commit 6419e960f00c0e1c3950bad500487d3681797b40"
diff -r 000000000000 -r 896c5e0b51a6 baric_archive.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/baric_archive.py Fri Mar 04 11:15:10 2022 +0000
@@ -0,0 +1,139 @@
+#!/usr/bin/env python
+# Retrieves data from external data source applications and stores in a dataset file.
+# Data source application parameters are temporarily stored in the dataset file.
+import os
+import socket
+import sys
+import urllib
+from json import dumps, loads
+from urllib.parse import urlparse
+from urllib.request import urlopen
+
+from galaxy.datatypes import sniff
+from galaxy.datatypes.registry import Registry
+from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE
+from galaxy.util import get_charset_from_http_headers
+
+GALAXY_PARAM_PREFIX = 'GALAXY'
+GALAXY_ROOT_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))
+GALAXY_DATATYPES_CONF_FILE = os.path.join(GALAXY_ROOT_DIR, 'datatypes_conf.xml')
+
+
+def stop_err(msg, json_file=None):
+ sys.stderr.write(msg)
+ # Need to write valid (but empty) json to avoid metadata collection failure
+ # leading to "unable to finish job" error with no logs
+ if json_file is not None:
+ json_file.write("%s\n" % dumps({}))
+ sys.exit(1)
+
+
+def load_input_parameters(filename, erase_file=True):
+ datasource_params = {}
+ try:
+ json_params = loads(open(filename, 'r').read())
+ datasource_params = json_params.get('param_dict')
+ except Exception:
+ json_params = None
+ for line in open(filename, 'r'):
+ try:
+ line = line.strip()
+ fields = line.split('\t')
+ datasource_params[fields[0]] = fields[1]
+ except Exception:
+ continue
+ if erase_file:
+ open(filename, 'w').close() # open file for writing, then close, removes params from file
+ return json_params, datasource_params
+
+
+def __main__():
+ filename = sys.argv[1]
+
+ user_email = sys.argv[2]
+ user_id = sys.argv[3]
+
+ try:
+ max_file_size = int(sys.argv[4])
+ except Exception:
+ max_file_size = 0
+
+ job_params, params = load_input_parameters(filename)
+ if job_params is None: # using an older tabular file
+ enhanced_handling = False
+ job_params = dict(param_dict=params)
+ job_params['output_data'] = [dict(out_data_name='output',
+ ext='auto',
+ file_name=filename,
+ extra_files_path=None)]
+ job_params['job_config'] = dict(GALAXY_ROOT_DIR=GALAXY_ROOT_DIR, GALAXY_DATATYPES_CONF_FILE=GALAXY_DATATYPES_CONF_FILE, TOOL_PROVIDED_JOB_METADATA_FILE=TOOL_PROVIDED_JOB_METADATA_FILE)
+ else:
+ enhanced_handling = True
+ json_file = open(job_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'w') # specially named file for output junk to pass onto set metadata
+
+ datatypes_registry = Registry()
+ datatypes_registry.load_datatypes(root_dir=job_params['job_config']['GALAXY_ROOT_DIR'], config=job_params['job_config']['GALAXY_DATATYPES_CONF_FILE'])
+
+ URL = params.get('URL', None) # using exactly URL indicates that only one dataset is being downloaded
+ export = params.get('export', None)
+ userkey = params.get('userkey', 'none')
+ URL_method = params.get('URL_method', None)
+
+ URL = URL + "&userkey=" + userkey + "&user_email=" + user_email + "&user_id=" + user_id
+
+ # The Python support for fetching resources from the web is layered. urllib uses the httplib
+ # library, which in turn uses the socket library. As of Python 2.3 you can specify how long
+ # a socket should wait for a response before timing out. By default the socket module has no
+ # timeout and can hang. Currently, the socket timeout is not exposed at the httplib or urllib2
+ # levels. However, you can set the default timeout ( in seconds ) globally for all sockets by
+ # doing the following.
+ socket.setdefaulttimeout(600)
+
+ for data_dict in job_params['output_data']:
+ cur_filename = data_dict.get('file_name', filename)
+ cur_URL = params.get('%s|%s|URL' % (GALAXY_PARAM_PREFIX, data_dict['out_data_name']), URL)
+ if not cur_URL or urlparse(cur_URL).scheme not in ('http', 'https', 'ftp'):
+ open(cur_filename, 'w').write("")
+ stop_err('The remote data source application has not sent back a URL parameter in the request.', json_file)
+
+ # The following calls to urlopen() will use the above default timeout
+ try:
+ if not URL_method or URL_method == 'get':
+ page = urlopen(cur_URL)
+ elif URL_method == 'post':
+ page = urlopen(cur_URL, urllib.parse.urlencode(params).encode("utf-8"))
+ except Exception as e:
+ stop_err('The remote data source application may be off line, please try again later. Error: %s' % str(e), json_file)
+ if max_file_size:
+ file_size = int(page.info().get('Content-Length', 0))
+ if file_size > max_file_size:
+ stop_err('The size of the data (%d bytes) you have requested exceeds the maximum allowed (%d bytes) on this server.' % (file_size, max_file_size), json_file)
+ # handle files available locally
+ if export:
+ try:
+ local_file = export + page.read()
+ os.remove(cur_filename)
+ os.symlink(local_file, cur_filename)
+ except Exception as e:
+ stop_err('Unable to symlink %s to %s:\n%s' % (local_file, cur_filename, e), json_file)
+ else:
+ try:
+ cur_filename = sniff.stream_to_open_named_file(page, os.open(cur_filename, os.O_WRONLY | os.O_CREAT), cur_filename, source_encoding=get_charset_from_http_headers(page.headers))
+ except Exception as e:
+ stop_err('Unable to fetch %s:\n%s' % (cur_URL, e), json_file)
+
+ # here import checks that upload tool performs
+ if enhanced_handling:
+ try:
+ ext = sniff.handle_uploaded_dataset_file(filename, datatypes_registry, ext=data_dict['ext'])
+ except Exception as e:
+ stop_err(str(e), json_file)
+ info = dict(type='dataset',
+ dataset_id=data_dict['dataset_id'],
+ ext=ext)
+
+ json_file.write("%s\n" % dumps(info))
+
+
+if __name__ == "__main__":
+ __main__()
diff -r 000000000000 -r 896c5e0b51a6 baric_archive_toulouse.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/baric_archive_toulouse.xml Fri Mar 04 11:15:10 2022 +0000
@@ -0,0 +1,7 @@
+
+
+
+ macros.xml
+
+
+
diff -r 000000000000 -r 896c5e0b51a6 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Mar 04 11:15:10 2022 +0000
@@ -0,0 +1,30 @@
+
+
+ 1.1.0
+
+
+ @SERVER@
+
+ python
+
+
+ operation_0224
+
+
+
+ Browse BARIC Archive (@SERVER@) $GALAXY_URL
+
+
+
+
+
+
+
+
+
+
+
+
+