def f2h_action(gfile_ids, f2h, galaxy_pass):
selected_files = GenericFile.objects.filter(pk__in=gfile_ids)
history_name = f2h.history_name
git = f2h.galaxyinstancetracking
user = f2h.added_by
filelist = files2paths(selected_files)
if not filelist:
print('filelist empty')
return []
gu = GalaxyUser.objects.get(internal_user=user, galaxyinstancetracking=git)
api_key = gu.api_key
galaxy_url = git.url
gi = GalaxyInstance(galaxy_url, key=api_key)
gi.verify = False
filelist = files2paths(selected_files)
print('ftp_host and port', git.ftp_host, git.ftp_port, gu.email,
galaxy_pass)
send_to_ftp(filelist,
host=git.ftp_host,
port=git.ftp_port,
user=gu.email,
password=galaxy_pass)
uploaded_files, hist = transfer_filelist_from_ftp(
gi, filelist, history_name=history_name)
link_files_in_galaxy(uploaded_files, selected_files, git, library=False)
def get_gi_gu(user, git):
gu = GalaxyUser.objects.get(internal_user=user, galaxyinstancetracking=git)
galaxy_url = git.url
gi = GalaxyInstance(galaxy_url, key=gu.api_key)
gi.verify = False
return gi, gu
def check_galaxy(api_key, galaxy_url):
gi = GalaxyInstance(galaxy_url, key=api_key)
gi.verify = False
wc = WorkflowClient(gi)
try:
wc.get_workflows()
except ConnectionError as e:
raise forms.ValidationError(
'Something is wrong with Galaxy connection, please check')
def run():
requests.packages.urllib3.disable_warnings(
requests.packages.urllib3.exceptions.InsecureRequestWarning)
logging.getLogger("requests").setLevel(logging.ERROR)
parser = argparse.ArgumentParser(description="Galaxy instance tool\
parsing, for integration in biotools/bioregistry")
parser.add_argument("--config_file",
help="config.ini file for regate or remag")
parser.add_argument("--templateconfig",
action='store_true',
help="generate a config_file template")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
if not args.templateconfig:
if not os.path.exists(args.config_file):
raise IOError("{0} doesn't exist".format(args.config_file))
config = Config(args.config_file, "regate")
if not config.onlypush:
gi = GalaxyInstance(config.galaxy_url_api, key=config.api_key)
gi.verify = False
try:
TOOLS = gi.tools.get_tools()
except ConnectionError, e:
raise ConnectionError(
"Connection with the Galaxy server {0} failed, {1}".format(
config.galaxy_url_api, e))
tools_meta_data = []
if config.yaml_file:
edam_dict = build_edam_dict(config.yaml_file)
else:
edam_dict = build_edam_dict(get_data_path('yaml_mapping.yaml'))
tools_list = config.tools_default.split(',')
detect_toolid_duplicate(TOOLS)
for tool in TOOLS:
if not tool['id'] in tools_list:
try:
tool_metadata = gi.tools.show_tool(tool_id=tool['id'],
io_details=True,
link_details=True)
tools_meta_data.append(tool_metadata)
except ConnectionError, e:
logger.error(
"Error during connection with exposed API method for tool {0}"
.format(str(tool['id'])),
exc_info=True)
build_biotools_files(tools_meta_data, config, edam_dict)
def set_section_id(ts, repos, url_galaxy_ref):
gi = GalaxyInstance(url_galaxy_ref)
gi.verify = False
tools = gi.tools.get_tools()
clean_repos = []
for repo in repos:
for revision in repo['revisions']:
if not repo['tool_panel_section_id']:
revision_info = ts.repositories.get_repository_revision_install_info(repo['name'], repo['owner'], revision)
if 'valid_tools' in revision_info[1]:
for tool in revision_info[1]['valid_tools']:
panel_info = return_panel(tool['guid'], tools)
if panel_info:
repo['tool_panel_section_id'] = panel_info[0]
repo['tool_panel_section_label'] = panel_info[1]
clean_repos.append(repo)
break
return clean_repos
def run():
requests.packages.urllib3.disable_warnings(requests.packages.urllib3.exceptions.InsecureRequestWarning)
logging.getLogger("requests").setLevel(logging.ERROR)
parser = argparse.ArgumentParser(description="Galaxy instance tool\
parsing, for integration in biotools/bioregistry")
parser.add_argument("--config_file", help="config.ini file for regate or remag")
parser.add_argument("--templateconfig", action='store_true', help="generate a config_file template")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
if not args.templateconfig:
if not os.path.exists(args.config_file):
raise IOError("{0} doesn't exist".format(args.config_file))
config = Config(args.config_file, "regate")
if not config.onlypush:
gi = GalaxyInstance(config.galaxy_url_api, key=config.api_key)
gi.verify = False
try:
TOOLS = gi.tools.get_tools()
except ConnectionError, e:
raise ConnectionError("Connection with the Galaxy server {0} failed, {1}".format(config.galaxy_url_api,
e))
tools_meta_data = []
if config.yaml_file:
edam_dict = build_edam_dict(config.yaml_file)
else:
edam_dict = build_edam_dict(get_data_path('yaml_mapping.yaml'))
tools_list = config.tools_default.split(',')
detect_toolid_duplicate(TOOLS)
for tool in TOOLS:
if not tool['id'] in tools_list:
try:
tool_metadata = gi.tools.show_tool(tool_id=tool['id'], io_details=True, link_details=True)
tools_meta_data.append(tool_metadata)
except ConnectionError, e:
logger.error(
"Error during connection with exposed API method for tool {0}".format(str(tool['id'])),
exc_info=True)
build_biotools_files(tools_meta_data, config, edam_dict)
def get_galaxy_workflow_inputs(w, user):
wf = w.workflowfile
git = w.galaxyinstancetracking
wf_name = w.name
api_key = GalaxyUser.objects.get(internal_user=user,
galaxyinstancetracking=git).api_key
galaxy_url = git.url
gi = GalaxyInstance(galaxy_url, key=api_key)
gi.verify = False
wc = WorkflowClient(gi)
wfd = wf.read()
jsonload = json.loads(wfd)
now = datetime.datetime.now()
jsonload['name'] = '{} dj-upload[{} {}]'.format(jsonload['name'], wf_name,
now.strftime("%Y-%m-%d"))
wfimp = wc.import_workflow_json(jsonload)
return check_workflow_data_inputs(wfimp['id'], wc), wfimp['id']
conf = yaml.load(fernet.decrypt(enc_conf).decode())
server = conf['server']
rest_protocol = conf['rest_protocol']
rest_port = conf['rest_port']
user = conf['user']
password = conf['password']
ftp_port = int(conf['ftp_port'])
api_key = conf['api_key']
rest_url = '%s://%s:%d' % (rest_protocol, server, rest_port)
history_name = 'bioinf_example'
gi = GalaxyInstance(url=rest_url, key=api_key)
gi.verify = False
histories = gi.histories
print('Existing histories:')
for history in histories.get_histories():
if history['name'] == history_name:
histories.delete_history(history['id'])
print(' - ' + history['name'])
print()
ds_history = histories.create_history(history_name)
print('Uploading file')
ftp = ftplib.FTP()
ftp.connect(host=server, port=ftp_port)
ftp.login(user=user, passwd=password)
parsing, for integration in biotools/bioregistry")
parser.add_argument("--config_file", help="config.ini file for regate or remag")
parser.add_argument("--templateconfig", action='store_true', help="generate a config_file template")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
if not args.templateconfig:
if not os.path.exists(args.config_file):
raise IOError("{0} doesn't exist".format(args.config_file))
config = Config(args.config_file, "regate")
if not config.onlypush:
gi = GalaxyInstance(config.galaxy_url_api, key=config.api_key)
gi.verify = False
try:
TOOLS = gi.tools.get_tools()
except ConnectionError, e:
raise ConnectionError("Connection with the Galaxy server {0} failed, {1}".format(config.galaxy_url_api,
e))
tools_meta_data = []
if config.yaml_file:
edam_dict = build_edam_dict(config.yaml_file)
else:
edam_dict = build_edam_dict(os.path.join('$PREFIXDATA', 'yaml_mapping.yaml'))
tools_list = config.tools_default.split(',')
for tool in TOOLS:
if not tool['id'] in tools_list: