diff env/lib/python3.9/site-packages/bioblend/galaxy/objects/galaxy_instance.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/bioblend/galaxy/objects/galaxy_instance.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,92 @@
+"""
+A representation of a Galaxy instance based on oo wrappers.
+"""
+
+import time
+
+import bioblend
+import bioblend.galaxy
+from bioblend.galaxy.datasets import TERMINAL_STATES
+from . import client
+
+
+def _get_error_info(hda):
+    msg = hda.id
+    try:
+        msg += ' (%s): ' % hda.name
+        msg += hda.wrapped['misc_info']
+    except Exception:  # avoid 'error while generating an error report'
+        msg += ': error'
+    return msg
+
+
+class GalaxyInstance:
+    """
+    A representation of an instance of Galaxy, identified by a URL and
+    a user's API key.
+
+    :type url: str
+    :param url: a FQDN or IP for a given instance of Galaxy. For example:
+      ``http://127.0.0.1:8080``
+
+    :type api_key: str
+    :param api_key: user's API key for the given instance of Galaxy, obtained
+      from the Galaxy web UI.
+
+    This is actually a factory class which instantiates the entity-specific
+    clients.
+
+    Example: get a list of all histories for a user with API key 'foo'::
+
+      from bioblend.galaxy.objects import *
+      gi = GalaxyInstance('http://127.0.0.1:8080', 'foo')
+      histories = gi.histories.list()
+    """
+    def __init__(self, url, api_key=None, email=None, password=None, verify=True):
+        self.gi = bioblend.galaxy.GalaxyInstance(url, api_key, email, password, verify)
+        self.log = bioblend.log
+        self.histories = client.ObjHistoryClient(self)
+        self.libraries = client.ObjLibraryClient(self)
+        self.workflows = client.ObjWorkflowClient(self)
+        self.tools = client.ObjToolClient(self)
+        self.jobs = client.ObjJobClient(self)
+
+    def _wait_datasets(self, datasets, polling_interval, break_on_error=True):
+        """
+        Wait for datasets to come out of the pending states.
+
+        :type datasets: :class:`~collections.Iterable` of
+          :class:`~.wrappers.Dataset`
+        :param datasets: datasets
+
+        :type polling_interval: float
+        :param polling_interval: polling interval in seconds
+
+        :type break_on_error: bool
+        :param break_on_error: if ``True``, raise a RuntimeError exception as
+          soon as at least one of the datasets is in the 'error' state.
+
+        .. warning::
+
+          This is a blocking operation that can take a very long time.
+          Also, note that this method does not return anything;
+          however, each input dataset is refreshed (possibly multiple
+          times) during the execution.
+        """
+        def poll(ds_list):
+            pending = []
+            for ds in ds_list:
+                ds.refresh()
+                if break_on_error and ds.state == 'error':
+                    raise RuntimeError(_get_error_info(ds))
+                if not ds.state:
+                    self.log.warning("Dataset %s has an empty state", ds.id)
+                elif ds.state not in TERMINAL_STATES:
+                    self.log.info("Dataset {0.id} is in non-terminal state {0.state}".format(ds))
+                    pending.append(ds)
+            return pending
+
+        self.log.info('Waiting for datasets')
+        while datasets:
+            datasets = poll(datasets)
+            time.sleep(polling_interval)