def list_narratives(self, ws_id=None):
# self.log.debug("Listing Narratives")
# self.log.debug("kbase_session = %s" % str(self.kbase_session))
"""
By default, this searches for Narrative types in any workspace that the
current token has read access to. Works anonymously as well.
If the ws_id field is not None, it will only look up Narratives in that
particular workspace (by its numerical id).
Returns a list of dictionaries of object descriptions, one for each Narrative.
The keys in each dictionary are those from the list_objects_fields list above.
This is just a wrapper around the Workspace list_objects command.
Raises: WorkspaceError, if access is denied; ValueError is ws_id is not
numeric.
"""
log_event(g_log, 'list_narratives start', {'ws_id': ws_id})
list_obj_params = {'type': self.nar_type, 'includeMetadata': 1}
if ws_id:
try:
int(ws_id) # will throw an exception if ws_id isn't an int
list_obj_params['ids'] = [ws_id]
except ValueError:
raise
try:
ws = self.ws_client()
res = ws.list_objects(list_obj_params)
except ServerError as err:
raise WorkspaceError(err, ws_id)
my_narratives = [dict(zip(list_objects_fields, obj)) for obj in res]
for nar in my_narratives:
# Look first for the name in the object metadata. if it's not there, use
# the object's name. If THAT'S not there, use Untitled.
# This gives support for some rather old narratives that don't
# have their name stashed in the metadata.
nar['name'] = nar['meta'].get('name', nar.get('name', 'Untitled'))
return my_narratives
def _ws_id_to_name(self, wsid):
try:
ws_info = self.ws_client().get_workspace_info({'id': wsid})
return ws_info[1]
except ServerError as err:
raise WorkspaceError(err, wsid)
def write_narrative(self, ref, nb, cur_user):
"""
:param ref: a NarrativeRef
:param nb: a notebook model
:cur_user: the current user id
Given a notebook, break this down into a couple parts:
1. Figure out what ws and obj to save to
2. Build metadata object
3. Save the narrative object (write_narrative)
4. Return any notebook changes as a list-
(narrative, ws_id, obj_id, ver)
"""
assert isinstance(
ref,
NarrativeRef), "write_narrative must use a NarrativeRef as input!"
if 'worksheets' in nb:
# it's an old version. update it by replacing the 'worksheets' key with
# the 'cells' subkey
# the old version only uses the first 'worksheet', so if it's there,
# copy it out
if (isinstance(nb['worksheets'], list)
and len(nb['worksheets']) > 0
and 'cells' in nb['worksheets'][0]):
nb['cells'] = nb['worksheets'][0]['cells']
else:
nb['cells'] = list()
del (nb['worksheets'])
nb['nbformat'] = 4
ws_id = ref.wsid
obj_id = ref.objid
# make sure the metadata's up to date.
try:
meta = nb['metadata']
if 'name' not in meta:
meta['name'] = 'Untitled'
if 'ws_name' not in meta:
meta[
'ws_name'] = util.kbase_env.workspace or self._ws_id_to_name(
ws_id)
if 'creator' not in meta:
meta['creator'] = cur_user
if 'type' not in meta:
meta['type'] = self.nar_type
if 'description' not in meta:
meta['description'] = ''
if 'data_dependencies' not in meta:
meta['data_dependencies'] = list()
if 'job_ids' not in meta:
meta['job_ids'] = {
'methods': [],
'apps': [],
'job_usage': {
'queue_time': 0,
'run_time': 0
}
}
if 'methods' not in meta['job_ids']:
meta['job_ids']['methods'] = list()
if 'apps' not in meta['job_ids']:
meta['job_ids']['apps'] = list()
if 'job_usage' not in meta['job_ids']:
meta['job_ids']['job_usage'] = {'queue_time': 0, 'run_time': 0}
meta['is_temporary'] = 'false'
meta['format'] = 'ipynb'
if len(meta['name']) > MAX_METADATA_STRING_BYTES - len('name'):
meta['name'] = meta['name'][0:MAX_METADATA_STRING_BYTES -
len('name')]
nb['metadata'] = meta
except Exception as e:
raise HTTPError(
400, 'Unexpected error setting Narrative attributes: %s' % e)
# With that set, update the workspace metadata with the new info.
perms = self.narrative_permissions(ref, user=cur_user)
if perms[cur_user] == 'a':
try:
updated_metadata = {
u'is_temporary': u'false',
u'narrative_nice_name': nb[u'metadata'][u'name']
}
self.ws_client().alter_workspace_metadata({
u'wsi': {
u'id': ws_id
},
u'new':
updated_metadata
})
except ServerError as err:
raise WorkspaceError(
err,
ws_id,
message="Error adjusting Narrative metadata",
http_code=500)
# Now we can save the Narrative object.
try:
ws_save_obj = {
'type':
self.nar_type,
'data':
nb,
'objid':
obj_id,
'meta':
nb['metadata'].copy(),
'provenance': [{
'service': 'narrative',
'description': 'Saved by KBase Narrative Interface',
'service_ver': str(biokbase.narrative.version())
}]
}
# no non-strings allowed in metadata!
ws_save_obj['meta']['data_dependencies'] = json.dumps(
ws_save_obj['meta']['data_dependencies'])
# Sort out job info we want to keep
# Gonna look like this, so init it that way
nb_job_usage = nb['metadata']['job_ids'].get(
'job_usage', {
'queue_time': 0,
'run_time': 0
})
job_info = {
'queue_time': nb_job_usage.get('queue_time', 0),
'run_time': nb_job_usage.get('run_time', 0),
'running': 0,
'completed': 0,
'error': 0
}
for job in nb['metadata']['job_ids']['methods'] + nb['metadata'][
'job_ids']['apps']:
status = job.get('status', 'running')
if status.startswith('complete'):
job_info['completed'] += 1
elif 'error' in status:
job_info['error'] += 1
else:
job_info['running'] += 1
ws_save_obj['meta']['job_info'] = json.dumps(job_info)
if 'job_ids' in ws_save_obj['meta']:
ws_save_obj['meta'].pop('job_ids')
# clear out anything from metadata that doesn't have a string value
# This flushes things from IPython that we don't need as KBase object metadata
ws_save_obj['meta'] = {
k: v
for k, v in ws_save_obj['meta'].items() if isinstance(v, str)
}
ws_save_obj['meta'] = self._process_cell_usage(
nb, ws_save_obj['meta'])
# Actually do the save now!
obj_info = self.ws_client().save_objects({
'id': ws_id,
'objects': [ws_save_obj]
})[0]
return (nb, obj_info[6], obj_info[0], obj_info[4])
except ServerError as err:
raise WorkspaceError(err, ws_id)
except Exception as e:
raise HTTPError(500, '%s saving Narrative: %s' % (type(e), e))
def write_narrative(self, ref, nb, cur_user):
"""
:param ref: a NarrativeRef
:param nb: a notebook model
:cur_user: the current user id
Given a notebook, break this down into a couple parts:
1. Figure out what ws and obj to save to
2. Build metadata object
3. Save the narrative object (write_narrative)
4. Return any notebook changes as a list-
(narrative, ws_id, obj_id, ver)
"""
assert isinstance(
ref, NarrativeRef
), "write_narrative must use a NarrativeRef as input!"
if "worksheets" in nb:
# it's an old version. update it by replacing the 'worksheets' key with
# the 'cells' subkey
# the old version only uses the first 'worksheet', so if it's there,
# copy it out
if (
isinstance(nb["worksheets"], list)
and len(nb["worksheets"]) > 0
and "cells" in nb["worksheets"][0]
):
nb["cells"] = nb["worksheets"][0]["cells"]
else:
nb["cells"] = list()
del nb["worksheets"]
nb["nbformat"] = 4
ws_id = ref.wsid
obj_id = ref.objid
# make sure the metadata's up to date.
try:
meta = nb["metadata"]
if "name" not in meta:
meta["name"] = "Untitled"
if "ws_name" not in meta:
meta["ws_name"] = util.kbase_env.workspace or self._ws_id_to_name(ws_id)
if "creator" not in meta:
meta["creator"] = cur_user
if "type" not in meta:
meta["type"] = self.nar_type
if "description" not in meta:
meta["description"] = ""
if "data_dependencies" not in meta:
meta["data_dependencies"] = list()
if "job_ids" not in meta:
meta["job_ids"] = {
"methods": [],
"apps": [],
"job_usage": {"queue_time": 0, "run_time": 0},
}
if "methods" not in meta["job_ids"]:
meta["job_ids"]["methods"] = list()
if "apps" not in meta["job_ids"]:
meta["job_ids"]["apps"] = list()
if "job_usage" not in meta["job_ids"]:
meta["job_ids"]["job_usage"] = {"queue_time": 0, "run_time": 0}
meta["is_temporary"] = "false"
meta["format"] = "ipynb"
if len(meta["name"]) > MAX_METADATA_STRING_BYTES - len("name"):
meta["name"] = meta["name"][0 : MAX_METADATA_STRING_BYTES - len("name")]
nb["metadata"] = meta
except Exception as e:
raise HTTPError(
400, "Unexpected error setting Narrative attributes: %s" % e
)
# With that set, update the workspace metadata with the new info.
perms = self.narrative_permissions(ref, user=cur_user)
if perms[cur_user] == "a":
try:
updated_metadata = {
"is_temporary": "false",
"narrative_nice_name": nb["metadata"]["name"],
"searchtags": "narrative",
}
self.ws_client().alter_workspace_metadata(
{"wsi": {"id": ws_id}, "new": updated_metadata}
)
except ServerError as err:
raise WorkspaceError(
err,
ws_id,
message="Error adjusting Narrative metadata",
http_code=500,
)
# Now we can save the Narrative object.
try:
ws_save_obj = {
"type": self.nar_type,
"data": nb,
"objid": obj_id,
"meta": nb["metadata"].copy(),
"provenance": [
{
"service": "narrative",
"description": "Saved by KBase Narrative Interface",
"service_ver": str(biokbase.narrative.version()),
}
],
}
# no non-strings allowed in metadata!
ws_save_obj["meta"]["data_dependencies"] = json.dumps(
ws_save_obj["meta"]["data_dependencies"]
)
# Sort out job info we want to keep
# Gonna look like this, so init it that way
nb_job_usage = nb["metadata"]["job_ids"].get(
"job_usage", {"queue_time": 0, "run_time": 0}
)
job_info = {
"queue_time": nb_job_usage.get("queue_time", 0),
"run_time": nb_job_usage.get("run_time", 0),
"running": 0,
"completed": 0,
"error": 0,
}
for job in (
nb["metadata"]["job_ids"]["methods"] + nb["metadata"]["job_ids"]["apps"]
):
status = job.get("status", "running")
if status.startswith("complete"):
job_info["completed"] += 1
elif "error" in status:
job_info["error"] += 1
else:
job_info["running"] += 1
ws_save_obj["meta"]["job_info"] = json.dumps(job_info)
if "job_ids" in ws_save_obj["meta"]:
ws_save_obj["meta"].pop("job_ids")
# clear out anything from metadata that doesn't have a string value
# This flushes things from IPython that we don't need as KBase object metadata
ws_save_obj["meta"] = {
k: v for k, v in ws_save_obj["meta"].items() if isinstance(v, str)
}
ws_save_obj["meta"] = self._process_cell_usage(nb, ws_save_obj["meta"])
# Actually do the save now!
obj_info = self.ws_client().save_objects(
{"id": ws_id, "objects": [ws_save_obj]}
)[0]
return (nb, obj_info[6], obj_info[0], obj_info[4])
except ServerError as err:
raise WorkspaceError(err, ws_id)
except Exception as e:
raise HTTPError(500, "%s saving Narrative: %s" % (type(e), e))