def __init__(self, url, key):
GalaxyInstance.__init__(self, url, key)
self.galaxy_input_path = ''
self.library_name = '' #library to store data folder
self.MGS_folder = '' #name folder to store library of MetaGenSense in galaxy
self.roles = ''
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 __init__(self, url, key):
GalaxyInstance.__init__(self, url, key)
self.galaxy_input_path = ''
self.library_name = '' #library to store data folder
self.MGS_folder = '' #name folder to store library of MetaGenSense in galaxy
self.roles = ''
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 __init__(self, url, user):
u = urlsplit(url)
if u.scheme != 'http' and u.scheme != 'https':
raise ValueError("Invalid name node address")
self.url = urlunparse((u.scheme, u.netloc, '', '', '', ''))
self.localdir = ""
self.prefix = 'GalaxyFS'
self.lddaprefix = 'Libraries'
self.hdaprefix = 'Histories'
self.client = GalaxyInstance(self.url, user)
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 read_galaxy_history(self):
"""
Read Galaxy's current history and inherit all the tags from a parent
to a child history item
"""
# connect to running Galaxy's instance
g_instance = GalaxyInstance(self.galaxy_url, self.galaxy_api_key,
self.history_id)
history = g_instance.histories
job = g_instance.jobs
# if the history id is not supplied, then update tags for the most recently used history
if self.history_id is None:
update_history = history.get_most_recently_used_history()
else:
try:
update_history = history.show_history(self.history_id)
except Exception as exception:
print("Some problem occurred with history: %s" %
self.history_id)
print(exception)
return
update_history_id = update_history["id"]
print("History name: %s" % update_history["name"])
print("History id: %s" % update_history_id)
self.find_dataset_parents_update_tags(history, job, update_history_id)
def update_file(finfo, sample_info, config):
"""Update file in Galaxy data libraries.
"""
if GalaxyInstance is None:
raise ImportError("Could not import bioblend.galaxy")
if "dir" not in config:
raise ValueError("Galaxy upload requires `dir` parameter in config specifying the "
"shared filesystem path to move files to.")
folder_name = "%s_%s" % (config["fc_date"], config["fc_name"])
storage_dir = utils.safe_makedir(os.path.join(config["dir"], folder_name))
if finfo.get("type") == "directory":
storage_file = None
if finfo.get("ext") == "qc":
pdf_file = qcsummary.prep_pdf(finfo["path"], config)
if pdf_file:
finfo["path"] = pdf_file
finfo["type"] = "pdf"
storage_file = filesystem.copy_finfo(finfo, storage_dir, pass_uptodate=True)
else:
storage_file = filesystem.copy_finfo(finfo, storage_dir, pass_uptodate=True)
if "galaxy_url" in config and "galaxy_api_key" in config:
galaxy_url = config["galaxy_url"]
if not galaxy_url.endswith("/"):
galaxy_url += "/"
gi = GalaxyInstance(galaxy_url, config["galaxy_api_key"])
else:
raise ValueError("Galaxy upload requires `galaxy_url` and `galaxy_api_key` in config")
if storage_file and sample_info and not finfo.get("index", False):
_to_datalibrary_safe(storage_file, gi, folder_name, sample_info, config)
def _runworkflow(hid, dsid):
'''
http://61.50.134.132/runworkflow/?key=3c0ce871b56dbe1dd6b745144fd323bf&wid=c6ef01d8a6d43836
Use [email protected]'s api-key "3c0ce871b56dbe1dd6b745144fd323bf"
'''
# wid = c6ef01d8a6d43836
# ldda = d368c393b367e434
# hda = 3608c6e62163f50a
wname = wnameList[start_stage]
try:
gi = GalaxyInstance(settings.GALAXY_URL, key=apikey)
workflows = gi.workflows.get_workflows(name=wname)
wid = workflows[0]['id']
wf = gi.workflows.show_workflow(wid)
#result = json.dumps(wf, cls=DjangoJSONEncoder)
#return HttpResponse(result)
datamap = {}
for step_id in wf['inputs']:
datamap[step_id] = {'src': 'hda', 'id': dsid}
res = gi.workflows.run_workflow(wid, datamap, history_id=hid)
print res
except:
print 'error when _runworkflow'
return 0
def get_galaxy_instance(galaxy_url=None, galaxy_api_key=None):
"""
Private utility function to instantiate and configure a :class:`bioblend.GalaxyInstance`
:type galaxy_url: str
:param galaxy_url: the URL of the Galaxy server
:type galaxy_api_key: str
:param galaxy_api_key: a registered Galaxy API KEY
:rtype: :class:`bioblend.GalaxyInstance`
:return: a new :class:`bioblend.GalaxyInstance` instance
"""
# configure `galaxy_url`
if galaxy_url is None:
if ENV_KEY_GALAXY_URL not in _os.environ:
raise RuntimeError(
"Galaxy URL not defined! Use --server or the environment variable {} "
"or specify it in the test configuration".format(
ENV_KEY_GALAXY_URL))
else:
galaxy_url = _os.environ[ENV_KEY_GALAXY_URL]
# configure `galaxy_api_key`
if galaxy_api_key is None:
if ENV_KEY_GALAXY_API_KEY not in _os.environ:
raise RuntimeError(
"Galaxy API key not defined! Use --api-key or the environment variable {} "
"or specify it in the test configuration".format(
ENV_KEY_GALAXY_API_KEY))
else:
galaxy_api_key = _os.environ[ENV_KEY_GALAXY_API_KEY]
# initialize the galaxy instance
return GalaxyInstance(galaxy_url, galaxy_api_key)
def __main__():
parser = argparse.ArgumentParser(description = 'Import workflows from a local directory')
parser.add_argument('-p', '--port', help = 'port number from your docker container that you map to your host machine. The default is 80', default = '80')
parser.add_argument('-k', '--key', help = 'user API key')
args = parser.parse_args()
# port and api key
port = args.port
api_key = args.key
# galaxy client instance
galaxy_home = environ['GALAXY_HOME']
galaxy_client = GalaxyInstance(url = "http://127.0.0.1:" + port, key = api_key)
if galaxy_client:
# workflow client instance
workflow_client = WorkflowClient(galaxy_client)
my_workflows_dir = environ['GALAXY_HOME'] + '/my_workflows'
workflow_files = []
for f in listdir(my_workflows_dir):
if isfile(join(my_workflows_dir, f)):
f_path = join(my_workflows_dir, f)
workflow_client.import_workflow_from_local_path(f_path)
print('Imported workflow: ' + f)
def run(self):
try:
self.load() # Load from config
self.gi = GalaxyInstance(self.IP, key=self.API_KEY)
if not self.manual and self.reference is None:
# No reference and it isn't using files in upload folder
self.t.time_print(
"No reference file specified with -r, please input one or use the --manual"
" flag to use a reference file that you put in the upload folder."
)
exit(1)
if self.noextract and not self.manual:
self.t.time_print(
"[Warning] Using manual flag since noextract was specified without manual."
)
self.manual = True
return self.main() # Return the path to the results zip
except:
import traceback
# Print error to file
self.t.time_print("[Error Dump]\n" + traceback.format_exc())
raise
def main():
parser = argparse.ArgumentParser(
description=
'Writes True to stdout if a tool/owner combination does not exist on a Galaxy instance'
)
parser.add_argument('-g', '--galaxy_url', help='Galaxy server URL')
parser.add_argument('-a', '--api_key', help='API key for galaxy server')
parser.add_argument('-n', '--name', help='Tool name')
parser.add_argument('-o', '--owner', help='Tool owner')
args = parser.parse_args()
galaxy_url = args.galaxy_url
api_key = args.api_key
name = args.name
owner = args.owner
gal = GalaxyInstance(galaxy_url, api_key)
cli = ToolShedClient(gal)
u_repos = cli.get_repositories()
tools_with_name_and_owner = [
t for t in u_repos if t['name'] == name and t['owner'] == owner
and t['status'] == 'Installed'
]
if not tools_with_name_and_owner:
sys.stdout.write(
'True'
) # we did not find the name/owner combination so we say that the tool is new
else:
sys.stdout.write('False')
def test_missing_scheme_real_url(self):
galaxy_url = os.environ['BIOBLEND_GALAXY_URL']
# Strip the scheme from galaxy_url
scheme_sep = '://'
if scheme_sep in galaxy_url:
galaxy_url = galaxy_url.partition(scheme_sep)[2]
GalaxyInstance(url=galaxy_url)
def _galaxy_library_upload(finfo, sample_info, config):
"""Upload results to galaxy library.
"""
folder_name = "%s_%s" % (config["fc_date"], config["fc_name"])
storage_dir = utils.safe_makedir(os.path.join(config["dir"], folder_name))
if finfo.get("type") == "directory":
storage_file = None
if finfo.get("ext") == "qc":
pdf_file = qcsummary.prep_pdf(finfo["path"], config)
if pdf_file:
finfo["path"] = pdf_file
finfo["type"] = "pdf"
storage_file = filesystem.copy_finfo(finfo,
storage_dir,
pass_uptodate=True)
else:
storage_file = filesystem.copy_finfo(finfo,
storage_dir,
pass_uptodate=True)
if "galaxy_url" in config and "galaxy_api_key" in config:
galaxy_url = config["galaxy_url"]
if not galaxy_url.endswith("/"):
galaxy_url += "/"
gi = GalaxyInstance(galaxy_url, config["galaxy_api_key"])
else:
raise ValueError(
"Galaxy upload requires `galaxy_url` and `galaxy_api_key` in config"
)
if storage_file and sample_info and not finfo.get(
"index", False) and not finfo.get("plus", False):
_to_datalibrary_safe(storage_file, gi, folder_name, sample_info,
config)
def add_instance(cls, url):
instance = Instance.query.filter_by(url=url).first()
if instance is None:
instance = Instance(url=url)
db.session.add(instance)
try:
galaxy_instance = GalaxyInstance(url=url)
instance_config = galaxy_instance.config.get_config()
instance.update_date = datetime.now()
instance.allow_user_creation = instance_config[
'allow_user_creation']
instance.brand = instance_config['brand']
instance.enable_quotas = 'enable_quotas' in instance_config and instance_config[
'enable_quotas']
instance.require_login = '******' in instance_config and instance_config[
'require_login']
instance.terms_url = instance_config['terms_url']
instance.version = instance_config['version_major']
url_data = urlparse(url)
try:
instance_location = requests.get('http://ip-api.com/json/%s' %
url_data.netloc)
except requests.exceptions.ConnectionError, requests.exceptions.ReadTimeout:
print "Unable to get location data for %s" % url_data.netloc
else:
def runworkflow(req):
'''
http://61.50.134.132/runworkflow/?key=3c0ce871b56dbe1dd6b745144fd323bf&wid=c6ef01d8a6d43836
Use [email protected]'s api-key "3c0ce871b56dbe1dd6b745144fd323bf"
'''
# wid = c6ef01d8a6d43836
# ldda = d368c393b367e434
# hda = 3608c6e62163f50a
wname = req.POST['wid']
apikey = '3c0ce871b56dbe1dd6b745144fd323bf' #req.POST['key']
try:
gi = GalaxyInstance(settings.GALAXY_URL, key=apikey)
workflows = gi.workflows.get_workflows(name=wname)
wid = workflows[0]['id']
wf = gi.workflows.show_workflow(wid)
result = json.dumps(wf, cls=DjangoJSONEncoder)
return HttpResponse(result)
datamap = {}
for step_id in wf['inputs']:
datamap[step_id] = {'src': 'ld', 'id': 'd368c393b367e434'}
res = gi.workflows.run_workflow(wid,
datamap,
history_name='New output history')
result = json.dumps(res, cls=DjangoJSONEncoder)
return HttpResponse(result)
except:
return HttpResponse([])
def connectgalaxy(apikey, galaxyurl):
"""
@param apikey:
@param galaxyurl:
returns an object galaxyinstance
"""
return GalaxyInstance(url=galaxyurl, key=apikey)
def start_container(**kwargs):
"""Starts a docker container with the galaxy image. Returns a named tuple with the url, a GalaxyInstance object,
the container attributes, and the container itself."""
# We start a container from the galaxy image. We detach it. Port 80 is exposed to the host at a random port.
# The random port is because we need mac compatibility. On GNU/linux a better option would be not to expose it
# and use the internal ip address instead.
# But alas, the trappings of a proprietary BSD kernel compel us to do ugly workarounds.
container = client.containers.run(GALAXY_IMAGE,
detach=True,
ports={'80/tcp': None},
**kwargs)
container_id = container.attrs.get('Id')
print(container_id)
# This seems weird as we also can just get container.attrs but for some reason
# the network settings are not loaded in container.attrs. With the get request
# these attributes are loaded
container_attributes = client.containers.get(container_id).attrs
# Venturing into deep nested dictionaries.
exposed_port = container_attributes.get('NetworkSettings').get(
'Ports').get('80/tcp')[0].get('HostPort')
container_url = "http://localhost:{0}".format(exposed_port)
galaxy_wait(
container_url, timeout=60
) # We are only going to wait 60 seconds. These are tests, and we are impatient!
yield GalaxyContainer(url=container_url,
container=container,
attributes=container_attributes,
gi=GalaxyInstance(container_url, key="admin"))
container.remove(force=True)
def main():
galaxyInstance = GalaxyInstance(url=GALAXY_URL, key=API_KEY)
toolClient = ToolClient(galaxyInstance)
histories = HistoryClient(galaxyInstance)
workflowsClient = WorkflowClient(galaxyInstance)
libraryClient = LibraryClient(galaxyInstance)
brassica_library = libraryClient.get_libraries(
name=' Evolutionary Systems Biology')
files = libraryClient.show_library(brassica_library[0]['id'],
contents=True)
#print(files)
itemp = 0
for f in files:
if f['type'] == 'folder':
continue # do nothing, try next
#initial set
#if itemp == 31:
# break
#print ("Name " + f['name'])
replicate = f['name'].split('_')[-1].split('.')[0]
#print replicate
if replicate == '1':
itemp = itemp + 1
if not (itemp >= 71 and itemp <= 92):
continue
base = f['name'].split('_')[:-1]
#print base
forward_name = f['name']
reverse_name = '_'.join(base) + '_2.fastq.bz2'
forward_id = f['id']
files2 = libraryClient.show_library(brassica_library[0]['id'],
contents=True)
for f2 in files2:
if f2['name'] == reverse_name:
reverse_id = f2['id']
print forward_name
print reverse_name
new_history_name = f['name'].split('_')[7] + "_" + f['name'].split(
'_')[-3] + "_" + f['name'].split('_')[-2]
print new_history_name
hist = histories.create_history(name=new_history_name)
dataset_F = histories.upload_dataset_from_library(
hist['id'], forward_id)
dataset_R = histories.upload_dataset_from_library(
hist['id'], reverse_id)
datamap = {}
datamap['0'] = {'src': 'hda', 'id': dataset_F['id']}
datamap['1'] = {'src': 'hda', 'id': dataset_R['id']}
workflows = workflowsClient.get_workflows(name="Maize HISAT 2.1")
workflow = workflows[0]
try:
w = workflowsClient.run_workflow(workflow['id'],
datamap,
history_id=hist['id'])
except:
print('Next')
def implementation(logger, args):
list_of_files = {}
if path_exists(args.sg_local_path, logger=logger, force=True):
for (dirpath, dirnames, filenames) in os.walk(args.sg_local_path):
for filename in filenames:
list_of_files[filename] = os.sep.join([dirpath, filename])
logger.debug(list_of_files)
gi = GalaxyInstance(args.url, key=args.key)
tools = gi.tools.get_tools()
counter_singularity = 0
counter_docker = 0
match = {}
unmatch = []
for t in tools:
t_id = t['id']
t_xml_file = gi.tools.show_tool(t['id'])['config_file']
container_name = None
try:
tool_xml = load(t_xml_file)
requirements, containers = parse_requirements_from_xml(tool_xml)
conda_targets = requirements_to_conda_targets(requirements)
mulled_targets = [
build_target(c.package, c.version) for c in conda_targets
]
container_name = mulled_container_name("biocontainers",
mulled_targets)
except Exception as ex:
logger.exception('Caught an error at {} with tid: {}'.format(
args.url, t_id))
pass
singularity = 'not_found'
if container_name:
container_name = container_name.lower()
counter_docker += 1
if os.path.basename(container_name) in list_of_files:
singularity = os.path.join(args.sg_local_path,
os.path.basename(container_name))
counter_singularity += 1
match[t_id] = {
'docker': "docker://{}".format(container_name),
'singularity': singularity
}
unmatch.append(t_id)
print(t_id, container_name, singularity)
dump(match, "{}_{}".format(args.url.split('/')[2], args.matched))
dump(unmatch, "{}_{}".format(args.url.split('/')[2], args.notmatched))
print("number of tools {}".format(len(tools)))
print("number of docker images matched {}".format(counter_docker))
print("number of singularity images in CVMFS {}".format(
len(list_of_files)))
print(
"number of singularity images matched {}".format(counter_singularity))
def get_gi(api_key, galaxy_url='http://192.168.2.218'):
# api_key = get_galaxy_api_key(email)
if api_key is not None:
# 192.168.2.218 is ctbgx.sanbi.ac.za
gi = GalaxyInstance(url=galaxy_url, key=api_key)
else:
gi = None
return gi
def api_gal_instance(url, key, verify_cert=True):
## catch_warnings is not thread-safe
with warnings.catch_warnings():
if not verify_cert:
import urllib3
warnings.filterwarnings(
"ignore", category=urllib3.exceptions.InsecureRequestWarning)
return GalaxyInstance(url=url, key=key, verify=verify_cert)
def main():
log.basicConfig(stream=sys.stdout,
level=log.INFO,
format='%(asctime)s - %(message)s')
short_options = "hg:a:l:d:m:"
long_options = [
"help", "galaxy=", "api_key=", "library_name=", "description=",
"manifest="
]
# The following assumes all but the first option lisetd in long_options is requried
required_options = RequiredOptions(
[o.rstrip('=') for o in long_options[1:]])
try:
arguments, values = getopt.getopt(sys.argv[1:], short_options,
long_options)
except getopt.error as err:
log.error("Error parsing arguments: %s" % err)
sys.exit(2)
for current_argument, current_value in arguments:
if current_argument in ("-g", "--galaxy"):
galaxy = current_value
required_options.resolve('galaxy')
elif current_argument in ("-a", "--api_key"):
api_key = current_value
required_options.resolve('api_key')
elif current_argument in ("-l", "--library_name"):
lib_name = current_value
required_options.resolve('library_name')
elif current_argument in ("-d", "--library_description"):
lib_description = current_value
required_options.resolve('description')
elif current_argument in ("-m", "--manifest"):
data_manifest = current_value
required_options.resolve('manifest')
elif current_argument in ("-h", "--help"):
print_help()
sys.exit(0)
# Verify that all of the required options have been specified
if not required_options.optionsResolved():
print("Required option(s) missing: " +
', '.join(required_options.required_options))
print_help()
sys.exit(1)
if is_url(data_manifest):
r = requests.get(data_manifest)
data_manifest = 'dm.yaml'
with open(data_manifest, 'wb') as f:
f.write(r.content)
with open(data_manifest) as f:
data_manifest = yaml.safe_load(f)
gi = GalaxyInstance(galaxy, api_key)
lib_name = lib_name
lib_description = lib_description
lib = create_library(gi, lib_name, lib_description)
upload_data(gi, lib, data_manifest)
def uninstall_tools(galaxy_server, api_key, names, force):
galaxy_instance = GalaxyInstance(url=galaxy_server, key=api_key)
toolshed_client = ToolShedClient(galaxy_instance)
temp_tool_list_file = 'tmp/installed_tool_list.yml'
# TODO: Switch to using bioblend to obtain this list
# ephemeris uses bioblend but without using ephemeris we cut out the need to for a temp file
os.system('get-tool-list -g %s -a %s -o %s --get_all_tools' %
(galaxy_server, api_key, temp_tool_list_file))
tools_to_uninstall = []
with open(temp_tool_list_file) as tool_file:
installed_tools = yaml.safe_load(tool_file.read())['tools']
if not installed_tools:
raise Exception('No tools to uninstall')
os.system('rm %s' % temp_tool_list_file)
for name in names:
revision = None
if '@' in name:
(name, revision) = name.split('@')
matching_tools = [
t for t in installed_tools if t['name'] == name and (
not revision or revision in t['revisions'])
]
if len(matching_tools) == 0:
id_string = 'name %s revision %s' % (
name, revision) if revision else 'name %s' % name
sys.stderr.write('*** Warning: No tool with %s\n' % id_string)
elif len(matching_tools) > 1 and not force:
sys.stderr.write(
'*** Warning: More than one toolshed tool found for %s. ' %
name +
'Not uninstalling any of these tools. Run script with --force (-f) flag to uninstall anyway\n'
)
else: # Either there is only one matching tool for the name and revision, or there are many and force=True
for tool in matching_tools:
tool_copy = tool.copy()
if revision:
tool_copy['revisions'] = [revision]
tools_to_uninstall.append(tool_copy)
for tool in tools_to_uninstall:
try:
name = tool['name']
owner = tool['owner']
tool_shed_url = tool['tool_shed_url']
revision = tool['revisions'][0]
sys.stderr.write('Uninstalling %s at revision %s\n' %
(name, revision))
return_value = toolshed_client.uninstall_repository_revision(
name=name,
owner=owner,
changeset_revision=revision,
tool_shed_url=tool_shed_url)
sys.stderr.write(str(return_value) + '\n')
except KeyError as e:
sys.stderr.write(e)
def check_histories(run, api_key, host, logger):
galaxy_instance = GalaxyInstance(host, key=api_key)
history_client = HistoryClient(galaxy_instance)
history_json_d = run + '/output'
histories = read_all_histories(history_json_d, logger)
(all_successful, all_running, all_failed, all_except, all_waiting,
upload_history) = get_history_status(histories, history_client, logger)
return (all_successful, all_running, all_failed, all_except, all_waiting,
upload_history)
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 upload_query_into_galaxy(self):
"""Upload a json query into galaxy"""
if not self.galaxy_history:
self.init_galaxy()
file_path = "tests/data/graphState_simple_query.json"
filename = "graphstate.json"
galaxy = GalaxyInstance(self.gurl, self.gkey)
return galaxy.tools.upload_file(file_path, self.galaxy_history['id'], file_name=filename, file_type='json')
def impersonate(self, user=None, user_key=None) -> GalaxyInstance:
"""
Returns a GalaxyInstance for the given user_key. If user is provided,
user_key is fetched from Galaxy.
"""
if user is not None:
user_id = self.instance.users.get_users(f_name=user)[0]["id"]
user_key = self.instance.users.get_user_apikey(user_id)
return GalaxyInstance(self.url, key=user_key)
def set_user_api(self):
"""
Note: error message tacked on to self.data_stores for display back to user.
"""
self.user_api = GalaxyInstance(url=self.api_url, key=self.user_api_key)
if not self.user_api:
self.data_stores.append({'name':'Error: user Galaxy API connection was not set up correctly. Try getting another user API key.', 'id':'none'})
return
def upload_dataset_into_galaxy(self):
"""Upload a dataset into galaxy"""
if not self.galaxy_history:
self.init_galaxy()
file_path = "test-data/transcripts.tsv"
filename = "transcripts.tsv"
galaxy = GalaxyInstance(self.gurl, self.gkey)
return galaxy.tools.upload_file(file_path, self.galaxy_history['id'], file_name=filename, file_type='tabular')
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 main( options ):
# read from config
config = ConfigParser.ConfigParser()
config.read(options.config)
fetch_tool = config.get('main', 'genome_fetch_tool')
url = "http://localhost"
sleep_time = float(config.get('main', 'sleep_time'))
# The environment variables are set by the parent container
admin_email = os.environ.get('GALAXY_DEFAULT_ADMIN_USER', '*****@*****.**')
admin_pass = os.environ.get('GALAXY_DEFAULT_ADMIN_PASSWORD', 'admin')
genomes = config.get('genomes', 'ids').strip().split('\n')
index_tools = config.get('build_indexers', 'ids').strip().split('\n')
# should test for valid config options
# establish connection to galaxy instance
gi = GalaxyInstance(url=url, email=admin_email, password=admin_pass)
# should test valid connection
log.info("List of valid histories: %s" % gi.histories.get_histories())
# fetch genomes
dbkeys = dict()
for dbkey in genomes:
if dbkey not in dbkeys:
tool_inputs={'dbkey':dbkey, 'reference_source|reference_source_selector': 'ucsc', 'reference_source|requested_dbkey': dbkey }
log.info("Fetching dbkey: %s" % dbkey)
try:
dbkeys[ dbkey ] = gi.tools.run_tool(history_id=None, tool_id=fetch_tool, tool_inputs=tool_inputs)
except ConnectionError as inst:
if '\"dbkey\": \"An invalid option was selected' in inst.body:
log.error("Galaxy instance does not recognize genome key: %s" % dbkey)
raise
else:
log.info("The dbkey (%s) was specified more than once, skipping additional specification." % ( dbkey ))
gi.make_get_request(urlparse.urljoin(url,'api/tool_data/all_fasta/reload'))
# start indexers
log.info("Start building genome indices.")
indexing_tools = []
while dbkeys:
for dbkey, value in dbkeys.items():
if gi.datasets.show_dataset( value['outputs'][0]['id'] )['state'] in ['ok', 'error']:
# refresh the tool data tables
log.info("Refreshing tool-data tables.")
log.info( gi.make_get_request(urlparse.urljoin(url,'api/tool_data/all_fasta/reload')).text )
time.sleep(2)
for tool_id in index_tools:
log.info("Indexing %s with %s." % (dbkey, tool_id) )
try:
indexing_tools.append(gi.tools.run_tool(history_id=None, tool_id=tool_id, tool_inputs={ 'all_fasta_source':dbkey }))
except ConnectionError as inst:
if '\"text\": \"no tool\",' in inst.body:
log.info("The tool %s cannot be located. Please check it is installed in your galaxy instance." % (tool_id) )
else:
raise
del dbkeys[ dbkey ]
if dbkeys:
time.sleep(sleep_time)
log.info(".")
# Wait for indexers to finish
while indexing_tools:
for i, indexing_tool_value in enumerate( indexing_tools ):
if gi.datasets.show_dataset( indexing_tool_value['outputs'][0]['id'] )['state'] in ['ok', 'error']:
log.info('Finished %s.' % indexing_tool_value)
del indexing_tools[i]
break
if indexing_tools:
time.sleep(sleep_time)
log.info('All indexers have been run, please check results.')
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(os.path.join('$PREFIXDATA', 'yaml_mapping.yaml'))
tools_list = config.tools_default.split(',')
for tool in TOOLS: