def __init__(self, url, key=None, email=None, password=None):
"""
A base representation of an instance of Galaxy, identified by a
URL and a user's API key.
After you have created an ``GalaxyInstance`` object, access various
modules via the class fields (see the source for the most up-to-date
list): ``libraries``, ``histories``, ``workflows``, ``datasets``,
and ``users`` are the minimum set supported. For example, to work with
histories, and get a list of all the user's histories, the following
should be done::
from bioblend import galaxy
gi = galaxy.GalaxyInstance(url='http://127.0.0.1:8000', key='your_api_key')
hl = gi.histories.get_histories()
:type url: str
:param url: A FQDN or IP for a given instance of Galaxy. For example:
http://127.0.0.1:8080. If a Galaxy instance is served under
a prefix (e.g., http://127.0.0.1:8080/galaxy/), supply the
entire URL including the prefix (note that the prefix must
end with a slash).
:type key: str
:param key: User's API key for the given instance of Galaxy, obtained
from the user preferences. If a key is not supplied, an
email address and password must be and key will
automatically be created for the user.
:type email: str
:param email: Galaxy e-mail address corresponding to the user.
Ignored if key is supplied directly.
:type password: str
:param password: Password of Galaxy account corresponding to the above
e-mail address. Ignored if key is supplied directly.
"""
super(GalaxyInstance, self).__init__(url, key, email, password)
self.libraries = libraries.LibraryClient(self)
self.histories = histories.HistoryClient(self)
self.workflows = workflows.WorkflowClient(self)
self.datasets = datasets.DatasetClient(self)
self.users = users.UserClient(self)
self.genomes = genomes.GenomeClient(self)
self.tools = tools.ToolClient(self)
self.toolShed = toolshed.ToolShedClient(self)
self.config = config.ConfigClient(self)
self.visual = visual.VisualClient(self)
self.quotas = quotas.QuotaClient(self)
self.groups = groups.GroupsClient(self)
self.roles = roles.RolesClient(self)
self.datatypes = datatypes.DatatypesClient(self)
self.jobs = jobs.JobsClient(self)
self.forms = forms.FormsClient(self)
self.ftpfiles = ftpfiles.FTPFilesClient(self)
self.tool_data = tool_data.ToolDataClient(self)
self.folders = folders.FoldersClient(self)
def __init__(self, url, key):
"""
A base representation of an instance of Galaxy, identified by a
URL and a user's API key.
After you have created an ``GalaxyInstance`` object, access various
modules via the class fields (see the source for the most up-to-date
list): ``libraries``, ``histories``, ``workflows``, ``datasets``,
and ``users`` are the minimum set supported. For example, to work with
histories, and get a list of all the user's histories, the following
should be done::
from bioblend import galaxy
gi = galaxy.GalaxyInstance(url='http://127.0.0.1:8000', key='your_api_key')
hl = gi.histories.get_histories()
print "List of histories:", hl
:type url: string
:param url: A FQDN or IP for a given instance of Galaxy. For example:
http://127.0.0.1:8080
:type key: string
:param key: User's API key for the given instance of Galaxy, obtained
from the user preferences.
"""
# Make sure the url scheme is defined (otherwise requests will not work)
if not urlparse.urlparse(url).scheme:
url = "http://" + url
# All of Galaxy's API's are rooted at <url>/api so make that the base url
self.base_url = url
self.url = urlparse.urljoin(url, 'api')
self.key = key
self.default_params = {'key': key}
self.json_headers = {'Content-Type': 'application/json'}
self.verify = False # Should SSL verification be done
self.libraries = libraries.LibraryClient(self)
self.histories = histories.HistoryClient(self)
self.workflows = workflows.WorkflowClient(self)
self.datasets = datasets.DatasetClient(self)
self.users = users.UserClient(self)
self.genomes = genomes.GenomeClient(self)
self.tools = tools.ToolClient(self)
self.toolShed = toolshed.ToolShedClient(self)
self.config = config.ConfigClient(self)
self.visual = visual.VisualClient(self)
self.quotas = quotas.QuotaClient(self)
self.groups = groups.GroupsClient(self)
self.datatypes = datatypes.DatatypesClient(self)
self.jobs = jobs.JobsClient(self)
self.forms = forms.FormsClient(self)
self.ftpfiles = ftpfiles.FTPFilesClient(self)
def __init__(self, name=None, galaxy_instance=None, id=None, check_by="id", timestamp_new=True):
# initialize bioblend History client
self._hist = histories.HistoryClient(galaxy_instance)
self._data = None
self._datasets = []
self._dataset_collections = []
if id:
# check if its already created
raise Exception("Not implemented") # this should not happen
elif name:
# create unique string from name + date/time
nonce=""
if timestamp_new:
nonce=str(datetime.utcnow()).split('.')[0]
name += " @ {}".format(nonce)
_info = self._hist.create_history(name=name)
self.dbg("Created history:\n{}".format(_info))
self._data = _info
else:
self.err("Need either a name to create a new history or an id to find existent")
def __init__(self, url, key=None, email=None, password=None, verify=True):
"""
A base representation of a connection to a Galaxy instance, identified
by the server URL and user credentials.
After you have created a ``GalaxyInstance`` object, access various
modules via the class fields. For example, to work with histories and
get a list of all the user's histories, the following should be done::
from bioblend import galaxy
gi = galaxy.GalaxyInstance(url='http://127.0.0.1:8000', key='your_api_key')
hl = gi.histories.get_histories()
:type url: str
:param url: A FQDN or IP for a given instance of Galaxy. For example:
http://127.0.0.1:8080 . If a Galaxy instance is served under
a prefix (e.g., http://127.0.0.1:8080/galaxy/), supply the
entire URL including the prefix (note that the prefix must
end with a slash). If a Galaxy instance has HTTP Basic
authentication with username and password, then the
credentials should be included in the URL, e.g.
http://user:pass@host:port/galaxy/
:type key: str
:param key: User's API key for the given instance of Galaxy, obtained
from the user preferences. If a key is not supplied, an
email address and password must be and the key will
automatically be created for the user.
:type email: str
:param email: Galaxy e-mail address corresponding to the user.
Ignored if key is supplied directly.
:type password: str
:param password: Password of Galaxy account corresponding to the above
e-mail address. Ignored if key is supplied directly.
:param verify: Whether to verify the server's TLS certificate
:type verify: bool
"""
super().__init__(url, key, email, password, verify=verify)
self.libraries = libraries.LibraryClient(self)
self.histories = histories.HistoryClient(self)
self.workflows = workflows.WorkflowClient(self)
self.invocations = invocations.InvocationClient(self)
self.datasets = datasets.DatasetClient(self)
self.dataset_collections = dataset_collections.DatasetCollectionClient(
self)
self.users = users.UserClient(self)
self.genomes = genomes.GenomeClient(self)
self.tools = tools.ToolClient(self)
self.toolshed = toolshed.ToolShedClient(self)
self.toolShed = self.toolshed # historical alias
self.config = config.ConfigClient(self)
self.visual = visual.VisualClient(self)
self.quotas = quotas.QuotaClient(self)
self.groups = groups.GroupsClient(self)
self.roles = roles.RolesClient(self)
self.datatypes = datatypes.DatatypesClient(self)
self.jobs = jobs.JobsClient(self)
self.forms = forms.FormsClient(self)
self.ftpfiles = ftpfiles.FTPFilesClient(self)
self.tool_data = tool_data.ToolDataClient(self)
self.folders = folders.FoldersClient(self)
self.tool_dependencies = tool_dependencies.ToolDependenciesClient(self)
def __init__(self, url, key=None, email=None, password=None):
"""
A base representation of an instance of Galaxy, identified by a
URL and a user's API key.
After you have created an ``GalaxyInstance`` object, access various
modules via the class fields (see the source for the most up-to-date
list): ``libraries``, ``histories``, ``workflows``, ``datasets``,
and ``users`` are the minimum set supported. For example, to work with
histories, and get a list of all the user's histories, the following
should be done::
from bioblend import galaxy
gi = galaxy.GalaxyInstance(url='http://127.0.0.1:8000', key='your_api_key')
hl = gi.histories.get_histories()
:type url: string
:param url: A FQDN or IP for a given instance of Galaxy. For example:
http://127.0.0.1:8080
:type key: string
:param key: User's API key for the given instance of Galaxy, obtained
from the user preferences. If a key is not supplied, an
email address and password must be and key will
automatically be created for the user.
:type email: string
:param email: Galaxy e-mail address corresponding to the user.
Ignored if key is supplied directly.
:type password: string
:param password: Password of Galaxy account corresponding to the above
e-mail address. Ignored if key is supplied directly.
"""
# Make sure the url scheme is defined (otherwise requests will not work)
if not urlparse(url).scheme:
url = "http://" + url
# All of Galaxy's API's are rooted at <url>/api so make that the base url
self.base_url = url
self.url = urljoin(url, 'api')
self._init_auth(key, email, password)
self.json_headers = {'Content-Type': 'application/json'}
self.verify = True # Should SSL verification be done
self.libraries = libraries.LibraryClient(self)
self.histories = histories.HistoryClient(self)
self.workflows = workflows.WorkflowClient(self)
self.datasets = datasets.DatasetClient(self)
self.users = users.UserClient(self)
self.genomes = genomes.GenomeClient(self)
self.tools = tools.ToolClient(self)
self.toolShed = toolshed.ToolShedClient(self)
self.config = config.ConfigClient(self)
self.visual = visual.VisualClient(self)
self.quotas = quotas.QuotaClient(self)
self.groups = groups.GroupsClient(self)
self.roles = roles.RolesClient(self)
self.datatypes = datatypes.DatatypesClient(self)
self.jobs = jobs.JobsClient(self)
self.forms = forms.FormsClient(self)
self.ftpfiles = ftpfiles.FTPFilesClient(self)
self.tool_data = tool_data.ToolDataClient(self)
self.folders = folders.FoldersClient(self)
