diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index dee45c91ecef50594578945f56267c74baaf84a6..6fd62dbc4bb697d841622a01de5513370ab2e7e8 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -12,6 +12,7 @@ from __future__ import print_function
import os
import requests
from requests.packages.urllib3.exceptions import InsecureRequestWarning
+
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)
import time
@@ -28,13 +29,13 @@ from pybis.utils import parse_jackson, check_datatype, split_identifier, format_
from pybis.property import PropertyHolder, PropertyAssignments
from pybis.masterdata import Vocabulary
-
import pandas as pd
from pandas import DataFrame, Series
import threading
from threading import Thread
from queue import Queue
+
DROPBOX_PLUGIN = "jupyter-uploader-api"
@@ -43,7 +44,8 @@ def _definitions(entity):
"Space": {
"attrs_new": "code description".split(),
"attrs_up": "description".split(),
- "attrs": "code permId description registrator registrationDate modificationDate".split(), "identifier": "spaceId",
+ "attrs": "code permId description registrator registrationDate modificationDate".split(),
+ "identifier": "spaceId",
},
"Project": {
"attrs_new": "code description space attachments".split(),
@@ -64,9 +66,9 @@ def _definitions(entity):
"attrs_up": "space experiment tags attachments".split(),
"attrs": "code permId identifier type space experiment tags attachments".split(),
"ids2type": {
- 'parentIds': { 'permId': { '@type': 'as.dto.sample.id.SamplePermId' } },
- 'childIds': { 'permId': { '@type': 'as.dto.sample.id.SamplePermId' } },
- 'componentIds': { 'permId': {'@type': 'as.dto.sample.id.SamplePermId' } },
+ 'parentIds': {'permId': {'@type': 'as.dto.sample.id.SamplePermId'}},
+ 'childIds': {'permId': {'@type': 'as.dto.sample.id.SamplePermId'}},
+ 'componentIds': {'permId': {'@type': 'as.dto.sample.id.SamplePermId'}},
},
"identifier": "sampleId",
"cre_type": "as.dto.sample.create.SampleCreation",
@@ -76,107 +78,107 @@ def _definitions(entity):
"attrs_new": "type experiment sample parents children container components tags".split(),
"attrs_up": "experiment sample parents children container components tags".split(),
"attrs": "code permId type experiment sample parents children container components tags accessDate dataProducer dataProductionDate registrator registrationDate modifier modificationDate dataStore measured".split(),
-
+
"ids2type": {
- 'parentIds': { 'permId': { '@type': 'as.dto.dataset.id.DataSetPermId' } },
- 'childIds': { 'permId': { '@type': 'as.dto.dataset.id.DataSetPermId' } },
- 'componentIds': { 'permId': { '@type': 'as.dto.dataset.id.DataSetPermId' } },
- 'containerIds': { 'permId': { '@type': 'as.dto.dataset.id.DataSetPermId' } },
+ 'parentIds': {'permId': {'@type': 'as.dto.dataset.id.DataSetPermId'}},
+ 'childIds': {'permId': {'@type': 'as.dto.dataset.id.DataSetPermId'}},
+ 'componentIds': {'permId': {'@type': 'as.dto.dataset.id.DataSetPermId'}},
+ 'containerIds': {'permId': {'@type': 'as.dto.dataset.id.DataSetPermId'}},
},
"multi": "".split(),
"identifier": "dataSetId",
},
"Material": {
"attrs_new": "code description type creation tags".split(),
- "attrs" : "code description type creation registrator tags".split()
+ "attrs": "code description type creation registrator tags".split()
},
"Tag": {
"attrs_new": "code description experiments samples dataSets materials".split(),
"attrs": "code description experiments samples dataSets materials registrationDate".split(),
},
"attr2ids": {
- "space" : "spaceId",
- "project" : "projectId",
- "sample" : "sampleId",
- "samples" : "sampleIds",
- "dataSet" : "dataSetId",
- "dataSets" : "dataSetIds",
- "experiment" : "experimentId",
+ "space": "spaceId",
+ "project": "projectId",
+ "sample": "sampleId",
+ "samples": "sampleIds",
+ "dataSet": "dataSetId",
+ "dataSets": "dataSetIds",
+ "experiment": "experimentId",
"experiments": "experimentIds",
- "material" : "materialId",
- "materials" : "materialIds",
- "container" : "containerId",
- "component" : "componentId",
- "components" : "componentIds",
- "parents" : "parentIds",
- "children" : "childIds",
- "tags" : "tagIds",
+ "material": "materialId",
+ "materials": "materialIds",
+ "container": "containerId",
+ "component": "componentId",
+ "components": "componentIds",
+ "parents": "parentIds",
+ "children": "childIds",
+ "tags": "tagIds",
},
"ids2type": {
- 'spaceId': { 'permId': { '@type': 'as.dto.space.id.SpacePermId' } },
- 'projectId': { 'permId': { '@type': 'as.dto.project.id.ProjectPermId' } },
- 'experimentId': { 'permId': { '@type': 'as.dto.experiment.id.ExperimentPermId' } },
- 'tagIds': { 'code': { '@type': 'as.dto.tag.id.TagCode' } },
+ 'spaceId': {'permId': {'@type': 'as.dto.space.id.SpacePermId'}},
+ 'projectId': {'permId': {'@type': 'as.dto.project.id.ProjectPermId'}},
+ 'experimentId': {'permId': {'@type': 'as.dto.experiment.id.ExperimentPermId'}},
+ 'tagIds': {'code': {'@type': 'as.dto.tag.id.TagCode'}},
},
}
return entities[entity]
search_criteria = {
- "space": "as.dto.space.search.SpaceSearchCriteria",
- "project": "as.dto.project.search.ProjectSearchCriteria",
+ "space": "as.dto.space.search.SpaceSearchCriteria",
+ "project": "as.dto.project.search.ProjectSearchCriteria",
"experiment": "as.dto.experiment.search.ExperimentSearchCriteria",
- "sample": "as.dto.sample.search.SampleSearchCriteria",
- "dataset": "as.dto.dataset.search.DataSetSearchCriteria",
- "code": "as.dto.common.search.CodeSearchCriteria",
- "sample_type":"as.dto.sample.search.SampleTypeSearchCriteria",
+ "sample": "as.dto.sample.search.SampleSearchCriteria",
+ "dataset": "as.dto.dataset.search.DataSetSearchCriteria",
+ "code": "as.dto.common.search.CodeSearchCriteria",
+ "sample_type": "as.dto.sample.search.SampleTypeSearchCriteria",
}
fetch_option = {
- "space": { "@type": "as.dto.space.fetchoptions.SpaceFetchOptions" },
- "project": { "@type": "as.dto.project.fetchoptions.ProjectFetchOptions" },
- "experiment": {
+ "space": {"@type": "as.dto.space.fetchoptions.SpaceFetchOptions"},
+ "project": {"@type": "as.dto.project.fetchoptions.ProjectFetchOptions"},
+ "experiment": {
"@type": "as.dto.experiment.fetchoptions.ExperimentFetchOptions",
- "type": { "@type": "as.dto.experiment.fetchoptions.ExperimentTypeFetchOptions" }
+ "type": {"@type": "as.dto.experiment.fetchoptions.ExperimentTypeFetchOptions"}
},
- "sample": {
+ "sample": {
"@type": "as.dto.sample.fetchoptions.SampleFetchOptions",
- "type": { "@type": "as.dto.sample.fetchoptions.SampleTypeFetchOptions" }
+ "type": {"@type": "as.dto.sample.fetchoptions.SampleTypeFetchOptions"}
},
- "samples": { "@type": "as.dto.sample.fetchoptions.SampleFetchOptions" },
- "dataSets": {
+ "samples": {"@type": "as.dto.sample.fetchoptions.SampleFetchOptions"},
+ "dataSets": {
"@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions",
- "properties": { "@type": "as.dto.property.fetchoptions.PropertyFetchOptions" },
- "type": { "@type": "as.dto.dataset.fetchoptions.DataSetTypeFetchOptions" },
+ "properties": {"@type": "as.dto.property.fetchoptions.PropertyFetchOptions"},
+ "type": {"@type": "as.dto.dataset.fetchoptions.DataSetTypeFetchOptions"},
},
- "physicalData": { "@type": "as.dto.dataset.fetchoptions.PhysicalDataFetchOptions" },
- "linkedData": { "@type": "as.dto.dataset.fetchoptions.LinkedDataFetchOptions" },
-
+ "physicalData": {"@type": "as.dto.dataset.fetchoptions.PhysicalDataFetchOptions"},
+ "linkedData": {"@type": "as.dto.dataset.fetchoptions.LinkedDataFetchOptions"},
- "properties": { "@type": "as.dto.property.fetchoptions.PropertyFetchOptions" },
- "propertyAssignments" : {
- "@type" : "as.dto.property.fetchoptions.PropertyAssignmentFetchOptions",
+ "properties": {"@type": "as.dto.property.fetchoptions.PropertyFetchOptions"},
+ "propertyAssignments": {
+ "@type": "as.dto.property.fetchoptions.PropertyAssignmentFetchOptions",
"propertyType": {
"@type": "as.dto.property.fetchoptions.PropertyTypeFetchOptions"
}
},
- "tags": { "@type": "as.dto.tag.fetchoptions.TagFetchOptions" },
+ "tags": {"@type": "as.dto.tag.fetchoptions.TagFetchOptions"},
- "registrator": { "@type": "as.dto.person.fetchoptions.PersonFetchOptions" },
- "modifier": { "@type": "as.dto.person.fetchoptions.PersonFetchOptions" },
- "leader": { "@type": "as.dto.person.fetchoptions.PersonFetchOptions" },
+ "registrator": {"@type": "as.dto.person.fetchoptions.PersonFetchOptions"},
+ "modifier": {"@type": "as.dto.person.fetchoptions.PersonFetchOptions"},
+ "leader": {"@type": "as.dto.person.fetchoptions.PersonFetchOptions"},
- "attachments": { "@type": "as.dto.attachment.fetchoptions.AttachmentFetchOptions" },
+ "attachments": {"@type": "as.dto.attachment.fetchoptions.AttachmentFetchOptions"},
"attachmentsWithContent": {
"@type": "as.dto.attachment.fetchoptions.AttachmentFetchOptions",
"content": {
"@type": "as.dto.common.fetchoptions.EmptyFetchOptions"
},
},
- "history": { "@type": "as.dto.history.fetchoptions.HistoryEntryFetchOptions" },
- "dataStore": { "@type": "as.dto.datastore.fetchoptions.DataStoreFetchOptions" },
+ "history": {"@type": "as.dto.history.fetchoptions.HistoryEntryFetchOptions"},
+ "dataStore": {"@type": "as.dto.datastore.fetchoptions.DataStoreFetchOptions"},
}
+
def search_request_for_identifier(ident, entity):
search_request = {}
@@ -192,11 +194,13 @@ def search_request_for_identifier(ident, entity):
}
return search_request
+
def extract_code(obj):
if not isinstance(obj, dict):
return str(obj)
return obj['code']
+
def extract_deletion(obj):
del_objs = []
for deleted_object in obj['deletedObjects']:
@@ -207,26 +211,31 @@ def extract_deletion(obj):
})
return del_objs
+
def extract_identifier(ident):
- if not isinstance(ident, dict):
+ if not isinstance(ident, dict):
return str(ident)
return ident['identifier']
+
def extract_nested_identifier(ident):
- if not isinstance(ident, dict):
+ if not isinstance(ident, dict):
return str(ident)
return ident['identifier']['identifier']
+
def extract_permid(permid):
if not isinstance(permid, dict):
return str(permid)
return permid['permId']
+
def extract_nested_permid(permid):
if not isinstance(permid, dict):
return str(permid)
return permid['permId']['permId']
+
def extract_property_assignments(pas):
pa_strings = []
for pa in pas:
@@ -236,19 +245,22 @@ def extract_property_assignments(pas):
pa_strings.append(pa['propertyType']['label'])
return pa_strings
+
def extract_person(person):
if not isinstance(person, dict):
return str(person)
return person['userId']
+
def crc32(fileName):
"""since Python3 the zlib module returns unsigned integers (2.7: signed int)
"""
prev = 0
- for eachLine in open(fileName,"rb"):
+ for eachLine in open(fileName, "rb"):
prev = zlib.crc32(eachLine, prev)
# return as hex
- return "%x"%(prev & 0xFFFFFFFF)
+ return "%x" % (prev & 0xFFFFFFFF)
+
def _create_tagIds(tags=None):
if tags is None:
@@ -257,9 +269,10 @@ def _create_tagIds(tags=None):
tags = [tags]
tagIds = []
for tag in tags:
- tagIds.append({ "code": tag, "@type": "as.dto.tag.id.TagCode" })
+ tagIds.append({"code": tag, "@type": "as.dto.tag.id.TagCode"})
return tagIds
+
def _tagIds_for_tags(tags=None, action='Add'):
"""creates an action item to add or remove tags. Action is either 'Add', 'Remove' or 'Set'
"""
@@ -286,6 +299,7 @@ def _tagIds_for_tags(tags=None, action='Add'):
}
return tagIds
+
def _list_update(ids=None, entity=None, action='Add'):
"""creates an action item to add, set or remove ids.
"""
@@ -310,7 +324,8 @@ def _list_update(ids=None, entity=None, action='Add'):
],
"@type": "as.dto.common.update.IdListUpdateValue"
}
- return list_update
+ return list_update
+
def _create_typeId(type):
return {
@@ -327,21 +342,23 @@ def _create_projectId(ident):
"@type": "as.dto.project.id.ProjectIdentifier"
}
else:
- return {
+ return {
"permId": ident,
"@type": "as.dto.project.id.ProjectPermId"
}
+
def _common_search(search_type, value, comparison="StringEqualToValue"):
sreq = {
- "@type": search_type,
+ "@type": search_type,
"fieldValue": {
"value": value,
- "@type": "as.dto.common.search.{}".format(comparison)
- }
- }
+ "@type": "as.dto.common.search.{}".format(comparison)
+ }
+ }
return sreq
+
def _criteria_for_code(code):
return {
"fieldValue": {
@@ -351,21 +368,22 @@ def _criteria_for_code(code):
"@type": "as.dto.common.search.CodeSearchCriteria"
}
-def _subcriteria_for_type(code, entity):
+def _subcriteria_for_type(code, entity):
return {
"@type": "as.dto.{}.search.{}TypeSearchCriteria".format(entity.lower(), entity),
- "criteria": [
+ "criteria": [
{
- "@type": "as.dto.common.search.CodeSearchCriteria",
- "fieldValue": {
- "value": code.upper(),
- "@type": "as.dto.common.search.StringEqualToValue"
- }
+ "@type": "as.dto.common.search.CodeSearchCriteria",
+ "fieldValue": {
+ "value": code.upper(),
+ "@type": "as.dto.common.search.StringEqualToValue"
+ }
}
- ]
+ ]
}
+
def _subcriteria_for_status(status_value):
status_value = status_value.upper()
valid_status = "AVAILABLE LOCKED ARCHIVED UNARCHIVE_PENDING ARCHIVE_PENDING BACKUP_PENDING".split()
@@ -377,13 +395,14 @@ def _subcriteria_for_status(status_value):
"operator": "AND",
"criteria": [{
"@type":
- "as.dto.dataset.search.StatusSearchCriteria",
- "fieldName" : "status",
+ "as.dto.dataset.search.StatusSearchCriteria",
+ "fieldName": "status",
"fieldType": "ATTRIBUTE",
- "fieldValue" : status_value
+ "fieldValue": status_value
}]
}
+
def _gen_search_criteria(req):
sreq = {}
for key, val in req.items():
@@ -405,7 +424,7 @@ def _gen_search_criteria(req):
sreq["criteria"] = []
if "space" in si:
sreq["criteria"].append(
- _gen_search_criteria({ "space": "Space", "code": si["space"] })
+ _gen_search_criteria({"space": "Space", "code": si["space"]})
)
if "experiment" in si:
pass
@@ -414,15 +433,16 @@ def _gen_search_criteria(req):
sreq["criteria"].append(
_common_search(
"as.dto.common.search.CodeSearchCriteria", si["code"].upper()
- )
+ )
)
elif key == "operator":
- sreq["operator"] = val.upper()
+ sreq["operator"] = val.upper()
else:
sreq["@type"] = "as.dto.{}.search.{}SearchCriteria".format(key, val)
return sreq
+
def _subcriteria_for_tags(tags):
if not isinstance(tags, list):
tags = [tags]
@@ -445,6 +465,7 @@ def _subcriteria_for_tags(tags):
"criteria": criterias
}
+
def _subcriteria_for_is_finished(is_finished):
return {
"@type": "as.dto.common.search.StringPropertySearchCriteria",
@@ -456,6 +477,7 @@ def _subcriteria_for_is_finished(is_finished):
}
}
+
def _subcriteria_for_properties(prop, val):
return {
"@type": "as.dto.common.search.StringPropertySearchCriteria",
@@ -467,14 +489,14 @@ def _subcriteria_for_properties(prop, val):
}
}
-def _subcriteria_for_permid(permids, entity, parents_or_children=''):
+def _subcriteria_for_permid(permids, entity, parents_or_children=''):
if not isinstance(permids, list):
permids = [permids]
criterias = []
for permid in permids:
- criterias.append( {
+ criterias.append({
"@type": "as.dto.common.search.PermIdSearchCriteria",
"fieldValue": {
"value": permid,
@@ -482,7 +504,7 @@ def _subcriteria_for_permid(permids, entity, parents_or_children=''):
},
"fieldType": "ATTRIBUTE",
"fieldName": "code"
- } )
+ })
criteria = {
"criteria": criterias,
@@ -493,6 +515,7 @@ def _subcriteria_for_permid(permids, entity, parents_or_children=''):
}
return criteria
+
def _subcriteria_for_code(code, object_type):
if code is not None:
if is_permid(code):
@@ -511,7 +534,7 @@ def _subcriteria_for_code(code, object_type):
"value": code.upper(),
"@type": "as.dto.common.search.StringEqualToValue"
},
- "@type": fieldtype
+ "@type": fieldtype
}
],
"@type": search_criteria[object_type.lower()],
@@ -519,7 +542,7 @@ def _subcriteria_for_code(code, object_type):
}
return criteria
else:
- criteria = { "@type": search_criteria[object_type.lower()] }
+ criteria = {"@type": search_criteria[object_type.lower()]}
return criteria
@@ -534,13 +557,13 @@ class Openbis:
:param host:
"""
url_obj = urlparse(url)
- if url_obj.netloc is None:
+ if url_obj.netloc is None:
raise ValueError("please provide the url in this format: https://openbis.host.ch:8443")
if url_obj.hostname is None:
raise ValueError("hostname is missing")
- self.url = url_obj.geturl()
- self.port = url_obj.port
+ self.url = url_obj.geturl()
+ self.port = url_obj.port
self.hostname = url_obj.hostname
self.as_v3 = '/openbis/openbis/rmi-application-server-v3.json'
self.as_v1 = '/openbis/openbis/rmi-general-information-v1.json'
@@ -561,12 +584,10 @@ class Openbis:
def spaces(self):
return self.get_spaces()
-
@property
def projects(self):
return self.get_projects()
-
def _get_cached_token(self):
"""Read the token from the cache, and set the token ivar to it, if there, otherwise None.
If the token is not valid anymore, delete it.
@@ -585,7 +606,6 @@ class Openbis:
except FileNotFoundError:
return None
-
def gen_token_path(self, parent_folder=None):
"""generates a path to the token file.
The token is usually saved in a file called
@@ -600,7 +620,6 @@ class Openbis:
path = os.path.join(parent_folder, self.hostname + '.token')
return path
-
def save_token(self, token=None, parent_folder=None):
""" saves the session token to the disk, usually here: ~/.pybis/hostname.token. When a new Openbis instance is created, it tries to read this saved token by default.
"""
@@ -619,7 +638,6 @@ class Openbis:
f.write(token)
self.token_path = token_path
-
def delete_token(self, token_path=None):
""" deletes a stored session token.
"""
@@ -627,7 +645,6 @@ class Openbis:
token_path = self.token_path
os.remove(token_path)
-
def _post_request(self, resource, request):
""" internal method, used to handle all post requests and serializing / deserializing
data
@@ -639,8 +656,8 @@ class Openbis:
if request["params"][0] is None:
raise ValueError("Your session expired, please log in again")
resp = requests.post(
- self.url + resource,
- json.dumps(request),
+ self.url + resource,
+ json.dumps(request),
verify=self.verify_certificates
)
@@ -648,7 +665,7 @@ class Openbis:
resp = resp.json()
if 'error' in resp:
print(json.dumps(request))
- raise ValueError('an error has occured: ' + resp['error']['message'] )
+ raise ValueError('an error has occured: ' + resp['error']['message'])
elif 'result' in resp:
return resp['result']
else:
@@ -656,7 +673,6 @@ class Openbis:
else:
raise ValueError('general error while performing post request')
-
def logout(self):
""" Log out of openBIS. After logout, the session token is no longer valid.
"""
@@ -664,15 +680,14 @@ class Openbis:
return
logout_request = {
- "method":"logout",
- "params":[self.token],
+ "method": "logout",
+ "params": [self.token],
}
resp = self._post_request(self.as_v3, logout_request)
self.token = None
self.token_path = None
return resp
-
def login(self, username=None, password=None, save_token=False):
"""Log into openBIS.
Expects a username and a password and updates the token (session-ID).
@@ -682,8 +697,8 @@ class Openbis:
"""
login_request = {
- "method":"login",
- "params":[username, password],
+ "method": "login",
+ "params": [username, password],
}
result = self._post_request(self.as_v3, login_request)
if result is None:
@@ -694,8 +709,6 @@ class Openbis:
self.save_token()
return self.token
-
-
def get_datastores(self):
""" Get a list of all available datastores. Usually there is only one, but in some cases
there might be multiple servers. If you upload a file, you need to specifiy the datastore you want
@@ -704,34 +717,33 @@ class Openbis:
request = {
"method": "listDataStores",
- "params": [ self.token ],
+ "params": [self.token],
}
resp = self._post_request(self.as_v1, request)
if resp is not None:
- return DataFrame(resp)[['code','downloadUrl', 'hostUrl']]
+ return DataFrame(resp)[['code', 'downloadUrl', 'hostUrl']]
else:
raise ValueError("No datastore found!")
-
def get_spaces(self, code=None):
""" Get a list of all available spaces (DataFrame object). To create a sample or a
dataset, you need to specify in which space it should live.
"""
-
+
criteria = {}
options = {}
request = {
"method": "searchSpaces",
- "params": [ self.token,
- criteria,
- options,
- ],
+ "params": [self.token,
+ criteria,
+ options,
+ ],
}
resp = self._post_request(self.as_v3, request)
if resp is not None:
spaces = DataFrame(resp['objects'])
- spaces['registrationDate']= spaces['registrationDate'].map(format_timestamp)
- spaces['modificationDate']= spaces['modificationDate'].map(format_timestamp)
+ spaces['registrationDate'] = spaces['registrationDate'].map(format_timestamp)
+ spaces['modificationDate'] = spaces['modificationDate'].map(format_timestamp)
sp = Things(
self,
'space',
@@ -741,33 +753,31 @@ class Openbis:
else:
raise ValueError("No spaces found!")
-
def get_space(self, spaceId):
""" Returns a Space object for a given identifier (spaceId).
"""
spaceId = str(spaceId).upper()
- fetchopts = { "@type": "as.dto.space.fetchoptions.SpaceFetchOptions" }
+ fetchopts = {"@type": "as.dto.space.fetchoptions.SpaceFetchOptions"}
for option in ['registrator']:
fetchopts[option] = fetch_option[option]
request = {
- "method": "getSpaces",
- "params": [
- self.token,
- [{
- "permId": spaceId,
- "@type": "as.dto.space.id.SpacePermId"
- }],
- fetchopts
+ "method": "getSpaces",
+ "params": [
+ self.token,
+ [{
+ "permId": spaceId,
+ "@type": "as.dto.space.id.SpacePermId"
+ }],
+ fetchopts
],
- }
+ }
resp = self._post_request(self.as_v3, request)
if len(resp) == 0:
raise ValueError("No such space: %s" % spaceId)
return Space(self, None, resp[spaceId])
-
def get_samples(self, code=None, permId=None, space=None, project=None, experiment=None, type=None,
withParents=None, withChildren=None, tags=None, **properties):
""" Get a list of all samples for a given space/project/experiment (or any combination)
@@ -779,7 +789,7 @@ class Openbis:
"space": "Space",
"operator": "AND",
"code": space
- })
+ })
)
if project:
exp_crit = _subcriteria_for_code(experiment, 'experiment')
@@ -799,13 +809,13 @@ class Openbis:
if code:
sub_criteria.append(_criteria_for_code(code))
if permId:
- sub_criteria.append(_common_search("as.dto.common.search.PermIdSearchCriteria",permId))
+ sub_criteria.append(_common_search("as.dto.common.search.PermIdSearchCriteria", permId))
if withParents:
if not isinstance(withParents, list):
withParents = [withParents]
for parent in withParents:
sub_criteria.append(
- _gen_search_criteria({
+ _gen_search_criteria({
"sample": "SampleParents",
"identifier": parent
})
@@ -815,7 +825,7 @@ class Openbis:
withChildren = [withChildren]
for child in withChildren:
sub_criteria.append(
- _gen_search_criteria({
+ _gen_search_criteria({
"sample": "SampleChildren",
"identifier": child
})
@@ -827,16 +837,16 @@ class Openbis:
"operator": "AND"
}
- fetchopts = fetch_option['sample']
+ fetchopts = fetch_option['sample']
for option in ['tags', 'properties', 'registrator', 'modifier', 'experiment']:
fetchopts[option] = fetch_option[option]
request = {
"method": "searchSamples",
- "params": [ self.token,
- criteria,
- fetchopts,
- ],
+ "params": [self.token,
+ criteria,
+ fetchopts,
+ ],
}
resp = self._post_request(self.as_v3, request)
@@ -848,8 +858,8 @@ class Openbis:
if len(samples) is 0:
raise ValueError("No samples found!")
- samples['registrationDate']= samples['registrationDate'].map(format_timestamp)
- samples['modificationDate']= samples['modificationDate'].map(format_timestamp)
+ samples['registrationDate'] = samples['registrationDate'].map(format_timestamp)
+ samples['modificationDate'] = samples['modificationDate'].map(format_timestamp)
samples['registrator'] = samples['registrator'].map(extract_person)
samples['modifier'] = samples['modifier'].map(extract_person)
samples['identifier'] = samples['identifier'].map(extract_identifier)
@@ -857,12 +867,15 @@ class Openbis:
samples['experiment'] = samples['experiment'].map(extract_nested_identifier)
samples['sample_type'] = samples['type'].map(extract_nested_permid)
- ss = samples[['identifier', 'permId', 'experiment', 'sample_type', 'registrator', 'registrationDate', 'modifier', 'modificationDate']]
+ ss = samples[
+ ['identifier', 'permId', 'experiment', 'sample_type', 'registrator', 'registrationDate', 'modifier',
+ 'modificationDate']]
return Things(self, 'sample', ss, 'identifier')
else:
raise ValueError("No samples found!")
- def get_experiments(self, code=None, type=None, space=None, project=None, tags=None, is_finished=None, **properties):
+ def get_experiments(self, code=None, type=None, space=None, project=None, tags=None, is_finished=None,
+ **properties):
""" Get a list of all experiment for a given space or project (or any combination)
"""
@@ -888,16 +901,16 @@ class Openbis:
"@type": "as.dto.experiment.search.ExperimentSearchCriteria",
"operator": "AND"
}
- fetchopts = fetch_option['experiment']
+ fetchopts = fetch_option['experiment']
for option in ['tags', 'properties', 'registrator', 'modifier', 'project']:
fetchopts[option] = fetch_option[option]
request = {
"method": "searchExperiments",
- "params": [ self.token,
- criteria,
- fetchopts,
- ],
+ "params": [self.token,
+ criteria,
+ fetchopts,
+ ],
}
resp = self._post_request(self.as_v3, request)
if len(resp['objects']) == 0:
@@ -907,24 +920,23 @@ class Openbis:
parse_jackson(objects)
experiments = DataFrame(objects)
- experiments['registrationDate']= experiments['registrationDate'].map(format_timestamp)
- experiments['modificationDate']= experiments['modificationDate'].map(format_timestamp)
- experiments['project']= experiments['project'].map(extract_code)
+ experiments['registrationDate'] = experiments['registrationDate'].map(format_timestamp)
+ experiments['modificationDate'] = experiments['modificationDate'].map(format_timestamp)
+ experiments['project'] = experiments['project'].map(extract_code)
experiments['registrator'] = experiments['registrator'].map(extract_person)
experiments['modifier'] = experiments['modifier'].map(extract_person)
experiments['identifier'] = experiments['identifier'].map(extract_identifier)
experiments['permId'] = experiments['permId'].map(extract_permid)
experiments['type'] = experiments['type'].map(extract_code)
- exps = experiments[['identifier', 'permId', 'project', 'type', 'registrator',
- 'registrationDate', 'modifier', 'modificationDate']]
+ exps = experiments[['identifier', 'permId', 'project', 'type', 'registrator',
+ 'registrationDate', 'modifier', 'modificationDate']]
return Things(self, 'experiment', exps, 'identifier')
-
- def get_datasets(self,
- code=None, type=None, withParents=None, withChildren=None, status=None,
- sample=None, experiment=None, project=None, tags=None
- ):
+ def get_datasets(self,
+ code=None, type=None, withParents=None, withChildren=None, status=None,
+ sample=None, experiment=None, project=None, tags=None
+ ):
sub_criteria = []
@@ -959,8 +971,8 @@ class Openbis:
}
fetchopts = {
- "containers": { "@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions" },
- "type": { "@type": "as.dto.dataset.fetchoptions.DataSetTypeFetchOptions" }
+ "containers": {"@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions"},
+ "type": {"@type": "as.dto.dataset.fetchoptions.DataSetTypeFetchOptions"}
}
for option in ['tags', 'properties', 'sample', 'experiment']:
@@ -968,10 +980,10 @@ class Openbis:
request = {
"method": "searchDataSets",
- "params": [ self.token,
- criteria,
- fetchopts,
- ],
+ "params": [self.token,
+ criteria,
+ fetchopts,
+ ],
}
resp = self._post_request(self.as_v3, request)
objects = resp['objects']
@@ -980,21 +992,21 @@ class Openbis:
else:
parse_jackson(objects)
datasets = DataFrame(objects)
- datasets['registrationDate']= datasets['registrationDate'].map(format_timestamp)
- datasets['modificationDate']= datasets['modificationDate'].map(format_timestamp)
- datasets['experiment']= datasets['experiment'].map(extract_nested_identifier)
- datasets['sample']= datasets['sample'].map(extract_nested_identifier)
- datasets['type']= datasets['type'].map(extract_code)
+ datasets['registrationDate'] = datasets['registrationDate'].map(format_timestamp)
+ datasets['modificationDate'] = datasets['modificationDate'].map(format_timestamp)
+ datasets['experiment'] = datasets['experiment'].map(extract_nested_identifier)
+ datasets['sample'] = datasets['sample'].map(extract_nested_identifier)
+ datasets['type'] = datasets['type'].map(extract_code)
datasets['permId'] = datasets['code']
ds = Things(
self,
'dataset',
- datasets[['permId', 'properties', 'type', 'experiment', 'sample', 'registrationDate', 'modificationDate']],
+ datasets[
+ ['permId', 'properties', 'type', 'experiment', 'sample', 'registrationDate', 'modificationDate']],
'permId'
)
return ds
-
def get_experiment(self, expId, withAttachments=False):
""" Returns an experiment object for a given identifier (expId).
"""
@@ -1014,28 +1026,26 @@ class Openbis:
fetchopts['attachments'] = fetch_option['attachmentsWithContent']
request = {
- "method": "getExperiments",
- "params": [
+ "method": "getExperiments",
+ "params": [
self.token,
- [ search_request ],
+ [search_request],
fetchopts
],
- }
+ }
resp = self._post_request(self.as_v3, request)
if len(resp) == 0:
raise ValueError("No such experiment: %s" % expId)
- return Experiment(self,
- self.get_experiment_type(resp[expId]["type"]["code"]),
- resp[expId]
- )
-
+ return Experiment(self,
+ self.get_experiment_type(resp[expId]["type"]["code"]),
+ resp[expId]
+ )
def new_experiment(self, type, **kwargs):
""" Creates a new experiment of a given experiment type.
"""
return Experiment(self, self.get_experiment_type(type), None, **kwargs)
-
def update_experiment(self, experimentId, properties=None, tagIds=None, attachments=None):
params = {
"experimentId": {
@@ -1045,7 +1055,7 @@ class Openbis:
"@type": "as.dto.experiment.update.ExperimentUpdate"
}
if properties is not None:
- params["properties"]= properties
+ params["properties"] = properties
if tagIds is not None:
params["tagIds"] = tagIds
if attachments is not None:
@@ -1055,14 +1065,13 @@ class Openbis:
"method": "updateExperiments",
"params": [
self.token,
- [ params ]
+ [params]
]
}
self._post_request(self.as_v3, request)
-
- def create_sample(self, space_ident, code, type,
- project_ident=None, experiment_ident=None, properties=None, attachments=None, tags=None):
+ def create_sample(self, space_ident, code, type,
+ project_ident=None, experiment_ident=None, properties=None, attachments=None, tags=None):
tagIds = _create_tagIds(tags)
typeId = _create_typeId(type)
@@ -1071,7 +1080,7 @@ class Openbis:
if properties is None:
properties = {}
-
+
request = {
"method": "createSamples",
"params": [
@@ -1080,7 +1089,7 @@ class Openbis:
{
"properties": properties,
"code": code,
- "typeId" : typeId,
+ "typeId": typeId,
"projectId": projectId,
"experimentId": experimentId,
"tagIds": tagIds,
@@ -1093,9 +1102,8 @@ class Openbis:
resp = self._post_request(self.as_v3, request)
return self.get_sample(resp[0]['permId'])
-
def update_sample(self, sampleId, space=None, project=None, experiment=None,
- parents=None, children=None, components=None, properties=None, tagIds=None, attachments=None):
+ parents=None, children=None, components=None, properties=None, tagIds=None, attachments=None):
params = {
"sampleId": {
"permId": sampleId,
@@ -1108,7 +1116,7 @@ class Openbis:
if project is not None:
params['projectId'] = project
if properties is not None:
- params["properties"]= properties
+ params["properties"] = properties
if tagIds is not None:
params["tagIds"] = tagIds
if attachments is not None:
@@ -1118,19 +1126,18 @@ class Openbis:
"method": "updateSamples",
"params": [
self.token,
- [ params ]
+ [params]
]
}
self._post_request(self.as_v3, request)
-
def delete_entity(self, entity, permid, reason):
"""Deletes Spaces, Projects, Experiments, Samples and DataSets
"""
entity_type = "as.dto.{}.id.{}PermId".format(entity.lower(), entity.capitalize())
request = {
- "method": "delete" + entity.capitalize() + 's',
+ "method": "delete" + entity.capitalize() + 's',
"params": [
self.token,
[
@@ -1147,7 +1154,6 @@ class Openbis:
}
self._post_request(self.as_v3, request)
-
def get_deletions(self):
request = {
"method": "searchDeletions",
@@ -1165,7 +1171,7 @@ class Openbis:
objects = resp['objects']
parse_jackson(objects)
- new_objs = []
+ new_objs = []
for value in objects:
del_objs = extract_deletion(value)
if len(del_objs) > 0:
@@ -1173,18 +1179,15 @@ class Openbis:
return DataFrame(new_objs)
-
def new_project(self, space, code, description=None, **kwargs):
return Project(self, None, space=space, code=code, description=description, **kwargs)
-
def _gen_fetchoptions(self, options):
fo = {}
for option in options:
fo[option] = fetch_option[option]
return fo
-
def get_project(self, projectId):
options = ['space', 'registrator', 'modifier', 'attachments']
if is_identifier(projectId):
@@ -1207,7 +1210,6 @@ class Openbis:
}
resp = self._post_request(self.as_v3, request)
return Project(self, resp['objects'][0])
-
def get_projects(self, space=None):
""" Get a list of all available projects (DataFrame object).
@@ -1223,16 +1225,16 @@ class Openbis:
"operator": "AND"
}
- fetchopts = { "@type": "as.dto.project.fetchoptions.ProjectFetchOptions" }
- for option in ['registrator', 'modifier', 'leader' ]:
+ fetchopts = {"@type": "as.dto.project.fetchoptions.ProjectFetchOptions"}
+ for option in ['registrator', 'modifier', 'leader']:
fetchopts[option] = fetch_option[option]
request = {
"method": "searchProjects",
- "params": [ self.token,
- criteria,
- fetchopts,
- ],
+ "params": [self.token,
+ criteria,
+ fetchopts,
+ ],
}
resp = self._post_request(self.as_v3, request)
@@ -1244,21 +1246,20 @@ class Openbis:
if len(projects) is 0:
raise ValueError("No projects found!")
- projects['registrationDate']= projects['registrationDate'].map(format_timestamp)
- projects['modificationDate']= projects['modificationDate'].map(format_timestamp)
+ projects['registrationDate'] = projects['registrationDate'].map(format_timestamp)
+ projects['modificationDate'] = projects['modificationDate'].map(format_timestamp)
projects['leader'] = projects['leader'].map(extract_person)
projects['registrator'] = projects['registrator'].map(extract_person)
projects['modifier'] = projects['modifier'].map(extract_person)
projects['permId'] = projects['permId'].map(extract_permid)
projects['identifier'] = projects['identifier'].map(extract_identifier)
- pros=projects[['identifier', 'permId', 'leader', 'registrator', 'registrationDate',
- 'modifier', 'modificationDate']]
+ pros = projects[['identifier', 'permId', 'leader', 'registrator', 'registrationDate',
+ 'modifier', 'modificationDate']]
return Things(self, 'project', pros, 'identifier')
else:
raise ValueError("No projects found!")
-
def _create_get_request(self, method_name, entity, permids, options):
if not isinstance(permids, list):
@@ -1271,11 +1272,11 @@ class Openbis:
match = re.match('/', permid)
if match:
search_params.append(
- { "identifier" : permid, "@type" : type + 'Identifier' }
+ {"identifier": permid, "@type": type + 'Identifier'}
)
- else:
+ else:
search_params.append(
- { "permId" : permid, "@type": type + 'PermId' }
+ {"permId": permid, "@type": type + 'PermId'}
)
fo = {}
@@ -1292,29 +1293,28 @@ class Openbis:
}
return request
-
def get_terms(self, vocabulary=None):
""" Returns information about vocabulary, including its controlled vocabulary
"""
search_request = {}
if vocabulary is not None:
- search_request = _gen_search_criteria( {
- "vocabulary": "VocabularyTerm",
- "criteria" : [{
+ search_request = _gen_search_criteria({
+ "vocabulary": "VocabularyTerm",
+ "criteria": [{
"vocabulary": "Vocabulary",
"code": vocabulary
}]
})
-
+
fetch_options = {
- "vocabulary" : { "@type" : "as.dto.vocabulary.fetchoptions.VocabularyFetchOptions" },
+ "vocabulary": {"@type": "as.dto.vocabulary.fetchoptions.VocabularyFetchOptions"},
"@type": "as.dto.vocabulary.fetchoptions.VocabularyTermFetchOptions"
}
request = {
"method": "searchVocabularyTerms",
- "params": [ self.token, search_request, fetch_options ]
+ "params": [self.token, search_request, fetch_options]
}
resp = self._post_request(self.as_v3, request)
parse_jackson(resp)
@@ -1325,7 +1325,7 @@ class Openbis:
"""
request = {
"method": "searchTags",
- "params": [ self.token, {}, {} ]
+ "params": [self.token, {}, {}]
}
resp = self._post_request(self.as_v3, request)
parse_jackson(resp)
@@ -1333,21 +1333,20 @@ class Openbis:
objects['registrationDate'] = objects['registrationDate'].map(format_timestamp)
return objects[['code', 'registrationDate']]
-
def get_sample_types(self, type=None):
""" Returns a list of all available sample types
"""
return self._get_types_of(
"searchSampleTypes",
"Sample",
- type,
+ type,
["generatedCodePrefix"]
)
def get_sample_type(self, type):
try:
return self._get_types_of(
- "searchSampleTypes",
+ "searchSampleTypes",
"Sample",
type,
["generatedCodePrefix"]
@@ -1355,27 +1354,25 @@ class Openbis:
except Exception:
raise ValueError("no such sample type: {}".format(type))
-
def get_experiment_types(self, type=None):
""" Returns a list of all available experiment types
"""
return self._get_types_of(
- "searchExperimentTypes",
- "Experiment",
+ "searchExperimentTypes",
+ "Experiment",
type
)
def get_experiment_type(self, type):
- try:
+ try:
return self._get_types_of(
- "searchExperimentTypes",
- "Experiment",
+ "searchExperimentTypes",
+ "Experiment",
type
)
except Exception:
raise ValueError("No such experiment type: {}".format(type))
-
def get_material_types(self, type=None):
""" Returns a list of all available material types
"""
@@ -1387,11 +1384,10 @@ class Openbis:
except Exception:
raise ValueError("No such material type: {}".format(type))
-
def get_dataset_types(self, type=None):
""" Returns a list (DataFrame object) of all currently available dataset types
"""
- return self._get_types_of("searchDataSetTypes", "DataSet", type, ['kind'] )
+ return self._get_types_of("searchDataSetTypes", "DataSet", type, ['kind'])
def get_dataset_type(self, type):
try:
@@ -1399,7 +1395,6 @@ class Openbis:
except Exception:
raise ValueError("No such dataSet type: {}".format(type))
-
def _get_types_of(self, method_name, entity, type_name=None, additional_attributes=None):
""" Returns a list of all available types of an entity.
If the name of the entity-type is given, it returns a PropertyAssignments object
@@ -1426,10 +1421,10 @@ class Openbis:
}
fetch_options['propertyAssignments'] = fetch_option['propertyAssignments']
attributes.append('propertyAssignments')
-
+
request = {
"method": method_name,
- "params": [ self.token, search_request, fetch_options ],
+ "params": [self.token, search_request, fetch_options],
}
resp = self._post_request(self.as_v3, request)
parse_jackson(resp)
@@ -1439,19 +1434,17 @@ class Openbis:
if len(resp['objects']) >= 1:
types = DataFrame(resp['objects'])
types['modificationDate'] = types['modificationDate'].map(format_timestamp)
- return Things(self, entity.lower()+'_type', types[attributes])
+ return Things(self, entity.lower() + '_type', types[attributes])
return types[attributes]
-
+
else:
raise ValueError("Nothing found!")
-
def is_session_active(self):
""" checks whether a session is still active. Returns true or false.
"""
return self.is_token_valid(self.token)
-
def is_token_valid(self, token=None):
"""Check if the connection to openBIS is valid.
This method is useful to check if a token is still valid or if it has timed out,
@@ -1460,18 +1453,17 @@ class Openbis:
"""
if token is None:
token = self.token
-
+
if token is None:
return False
request = {
"method": "isSessionActive",
- "params": [ token ],
+ "params": [token],
}
resp = self._post_request(self.as_v1, request)
return resp
-
def get_dataset(self, permid):
"""fetch a dataset and some metadata attached to it:
- properties
@@ -1491,32 +1483,31 @@ class Openbis:
}]
fetchopts = {
- "parents": { "@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions" },
- "children": { "@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions" },
- "containers": { "@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions" },
- "type": { "@type": "as.dto.dataset.fetchoptions.DataSetTypeFetchOptions" },
+ "parents": {"@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions"},
+ "children": {"@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions"},
+ "containers": {"@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions"},
+ "type": {"@type": "as.dto.dataset.fetchoptions.DataSetTypeFetchOptions"},
}
- for option in ['tags', 'properties', 'dataStore', 'physicalData', 'linkedData',
+ for option in ['tags', 'properties', 'dataStore', 'physicalData', 'linkedData',
'experiment', 'sample']:
fetchopts[option] = fetch_option[option]
request = {
"method": "getDataSets",
- "params": [ self.token,
- criteria,
- fetchopts,
- ],
+ "params": [self.token,
+ criteria,
+ fetchopts,
+ ],
}
resp = self._post_request(self.as_v3, request)
if resp is None or len(resp) == 0:
- raise ValueError('no such dataset found: '+permid)
+ raise ValueError('no such dataset found: ' + permid)
if resp is not None:
for permid in resp:
return DataSet(self, self.get_dataset_type(resp[permid]["type"]["code"]), resp[permid])
-
def get_sample(self, sample_ident, only_data=False, withAttachments=False):
"""Retrieve metadata for the sample.
Get metadata for the sample and any directly connected parents of the sample to allow access
@@ -1524,7 +1515,7 @@ class Openbis:
:param sample_identifiers: A list of sample identifiers to retrieve.
"""
- fetchopts = { "type": { "@type": "as.dto.sample.fetchoptions.SampleTypeFetchOptions" } }
+ fetchopts = {"type": {"@type": "as.dto.sample.fetchoptions.SampleTypeFetchOptions"}}
search_request = search_request_for_identifier(sample_ident, 'sample')
@@ -1534,14 +1525,14 @@ class Openbis:
if withAttachments:
fetchopts['attachments'] = fetch_option['attachmentsWithContent']
- #fetchopts["parents"] = { "@type": "as.dto.sample.fetchoptions.SampleFetchOptions" }
- #fetchopts["children"] = { "@type": "as.dto.sample.fetchoptions.SampleFetchOptions" }
+ # fetchopts["parents"] = { "@type": "as.dto.sample.fetchoptions.SampleFetchOptions" }
+ # fetchopts["children"] = { "@type": "as.dto.sample.fetchoptions.SampleFetchOptions" }
sample_request = {
"method": "getSamples",
"params": [
self.token,
- [ search_request ],
+ [search_request],
fetchopts
],
}
@@ -1550,7 +1541,7 @@ class Openbis:
parse_jackson(resp)
if resp is None or len(resp) == 0:
- raise ValueError('no such sample found: '+sample_ident)
+ raise ValueError('no such sample found: ' + sample_ident)
else:
for sample_ident in resp:
if only_data:
@@ -1558,7 +1549,6 @@ class Openbis:
else:
return Sample(self, self.get_sample_type(resp[sample_ident]["type"]["code"]), resp[sample_ident])
-
def new_space(self, name, description=None):
""" Creates a new space in the openBIS instance.
"""
@@ -1566,19 +1556,18 @@ class Openbis:
"method": "createSpaces",
"params": [
self.token,
- [ {
+ [{
"code": name,
"description": description,
"@type": "as.dto.space.create.SpaceCreation"
- } ]
+ }]
],
}
resp = self._post_request(self.as_v3, request)
return self.get_space(name)
-
def new_analysis(self, name, description=None, sample=None, dss_code=None, result_files=None,
- notebook_files=None, parents=None):
+ notebook_files=None, parents=None):
""" An analysis contains the Jupyter notebook file(s) and some result files.
Technically this method involves uploading files to the session workspace
@@ -1593,17 +1582,17 @@ class Openbis:
sampleId = None
if isinstance(sample, str):
if (is_identifier(sample)):
- sampleId = {
+ sampleId = {
"identifier": sample,
"@type": "as.dto.sample.id.SampleIdentifier"
}
else:
- sampleId = {
+ sampleId = {
"permId": sample,
"@type": "as.dto.sample.id.SamplePermId"
}
else:
- sampleId = {
+ sampleId = {
"identifier": sample.identifier,
"@type": "as.dto.sample.id.SampleIdentifier"
}
@@ -1614,7 +1603,7 @@ class Openbis:
parants = [parents]
for parent in parents:
parentIds.append(parent.permId)
-
+
datastore_url = self._get_dss_url(dss_code)
folder = time.strftime('%Y-%m-%d_%H-%M-%S')
@@ -1623,55 +1612,55 @@ class Openbis:
if notebook_files is not None:
notebooks_folder = os.path.join(folder, 'notebook_files')
self.upload_files(
- datastore_url = datastore_url,
+ datastore_url=datastore_url,
files=notebook_files,
- folder= notebooks_folder,
+ folder=notebooks_folder,
wait_until_finished=True
)
data_sets.append({
- "dataSetType" : "JUPYTER_NOTEBOOk",
+ "dataSetType": "JUPYTER_NOTEBOOk",
"sessionWorkspaceFolder": notebooks_folder,
- "fileNames" : notebook_files,
- "properties" : {}
+ "fileNames": notebook_files,
+ "properties": {}
})
if result_files is not None:
results_folder = os.path.join(folder, 'result_files')
self.upload_files(
- datastore_url = datastore_url,
+ datastore_url=datastore_url,
files=result_files,
folder=results_folder,
wait_until_finished=True
)
data_sets.append({
- "dataSetType" : "JUPYTER_RESULT",
- "sessionWorkspaceFolder" : results_folder,
- "fileNames" : result_files,
- "properties" : {}
+ "dataSetType": "JUPYTER_RESULT",
+ "sessionWorkspaceFolder": results_folder,
+ "fileNames": result_files,
+ "properties": {}
})
# register the files in openBIS
request = {
- "method": "createReportFromAggregationService",
- "params": [
- self.token,
- dss_code,
- DROPBOX_PLUGIN,
- {
- "sample" : { "identifier" : sampleId['identifier'] },
- "sampleId": sampleId,
- "parentIds": parentIds,
- "containers" : [ {
- "dataSetType" : "JUPYTER_CONTAINER",
- "properties" : {
- "NAME" : name,
- "DESCRIPTION" : description
- }
- } ],
- "dataSets" : data_sets,
- }
- ],
+ "method": "createReportFromAggregationService",
+ "params": [
+ self.token,
+ dss_code,
+ DROPBOX_PLUGIN,
+ {
+ "sample": {"identifier": sampleId['identifier']},
+ "sampleId": sampleId,
+ "parentIds": parentIds,
+ "containers": [{
+ "dataSetType": "JUPYTER_CONTAINER",
+ "properties": {
+ "NAME": name,
+ "DESCRIPTION": description
+ }
+ }],
+ "dataSets": data_sets,
+ }
+ ],
}
-
+
resp = self._post_request(self.reg_v1, request)
try:
if resp['rows'][0][0]['value'] == 'OK':
@@ -1679,19 +1668,16 @@ class Openbis:
except:
return resp
-
def new_sample(self, type, **kwargs):
""" Creates a new sample of a given sample type.
"""
return Sample(self, self.get_sample_type(type), None, **kwargs)
-
def new_dataset(self, type, **kwargs):
""" Creates a new dataset of a given sample type.
"""
return DataSet(self, self.get_dataset_type(type.upper()), None, **kwargs)
-
def _get_dss_url(self, dss_code=None):
""" internal method to get the downloadURL of a datastore.
"""
@@ -1700,8 +1686,6 @@ class Openbis:
return dss['downloadUrl'][0]
else:
return dss[dss['code'] == dss_code]['downloadUrl'][0]
-
-
def upload_files(self, datastore_url=None, files=None, folder=None, wait_until_finished=False):
@@ -1720,15 +1704,16 @@ class Openbis:
self.files = files
self.startByte = 0
- self.endByte = 0
-
+ self.endByte = 0
+
# define a queue to handle the upload threads
queue = DataSetUploadQueue()
real_files = []
for filename in files:
if os.path.isdir(filename):
- real_files.extend([os.path.join(dp, f) for dp, dn, fn in os.walk(os.path.expanduser(filename)) for f in fn])
+ real_files.extend(
+ [os.path.join(dp, f) for dp, dn, fn in os.walk(os.path.expanduser(filename)) for f in fn])
else:
real_files.append(os.path.join(filename))
@@ -1738,7 +1723,7 @@ class Openbis:
self.files_in_wsp.append(file_in_wsp)
upload_url = (
datastore_url + '/session_workspace_file_upload'
- + '?filename=' + os.path.join(folder,filename)
+ + '?filename=' + os.path.join(folder, filename)
+ '&id=1'
+ '&startByte=0&endByte=0'
+ '&sessionID=' + self.token
@@ -1754,7 +1739,6 @@ class Openbis:
class DataSetUploadQueue():
-
def __init__(self, workers=20):
# maximum files to be uploaded at once
self.upload_queue = Queue()
@@ -1765,19 +1749,16 @@ class DataSetUploadQueue():
t.daemon = True
t.start()
-
def put(self, things):
""" expects a list [url, filename] which is put into the upload queue
"""
self.upload_queue.put(things)
-
def join(self):
""" needs to be called if you want to wait for all uploads to be finished
"""
self.upload_queue.join()
-
def upload_file(self):
while True:
# get the next item in the queue
@@ -1797,7 +1778,6 @@ class DataSetUploadQueue():
class DataSetDownloadQueue():
-
def __init__(self, workers=20):
# maximum files to be downloaded at once
self.download_queue = Queue()
@@ -1808,19 +1788,16 @@ class DataSetDownloadQueue():
t.daemon = True
t.start()
-
def put(self, things):
""" expects a list [url, filename] which is put into the download queue
"""
self.download_queue.put(things)
-
def join(self):
""" needs to be called if you want to wait for all downloads to be finished
"""
self.download_queue.join()
-
def download_file(self):
while True:
url, filename, file_size, verify_certificates = self.download_queue.get()
@@ -1830,8 +1807,8 @@ class DataSetDownloadQueue():
# request the file in streaming mode
r = requests.get(url, stream=True, verify=verify_certificates)
with open(filename, 'wb') as f:
- for chunk in r.iter_content(chunk_size=1024):
- if chunk: # filter out keep-alive new chunks
+ for chunk in r.iter_content(chunk_size=1024):
+ if chunk: # filter out keep-alive new chunks
f.write(chunk)
assert os.path.getsize(filename) == int(file_size)
@@ -1839,7 +1816,6 @@ class DataSetDownloadQueue():
class OpenBisObject():
-
def __init__(self, openbis_obj, type, data=None, **kwargs):
self.__dict__['openbis'] = openbis_obj
self.__dict__['type'] = type
@@ -1861,32 +1837,32 @@ class OpenBisObject():
return str(self) != str(other)
def _set_data(self, data):
- # assign the attribute data to self.a by calling it
- # (invoking the AttrHolder.__call__ function)
- self.a(data)
- self.__dict__['data'] = data
+ # assign the attribute data to self.a by calling it
+ # (invoking the AttrHolder.__call__ function)
+ self.a(data)
+ self.__dict__['data'] = data
- # put the properties in the self.p namespace (without checking them)
- for key, value in data['properties'].items():
- self.p.__dict__[key.lower()] = value
+ # put the properties in the self.p namespace (without checking them)
+ for key, value in data['properties'].items():
+ self.p.__dict__[key.lower()] = value
@property
def space(self):
- try:
+ try:
return self.openbis.get_space(self._space['permId'])
except Exception:
pass
@property
def project(self):
- try:
+ try:
return self.openbis.get_project(self._project['identifier'])
except Exception:
pass
@property
def experiment(self):
- try:
+ try:
return self.openbis.get_experiment(self._experiment['identifier'])
except Exception:
pass
@@ -1924,9 +1900,9 @@ class PhysicalData():
if data is None:
data = []
self.data = data
- self.attrs = ['speedHint', 'complete', 'shareId', 'size',
- 'fileFormatType', 'storageFormat', 'location', 'presentInArchive',
- 'storageConfirmation', 'locatorType', 'status']
+ self.attrs = ['speedHint', 'complete', 'shareId', 'size',
+ 'fileFormatType', 'storageFormat', 'location', 'presentInArchive',
+ 'storageConfirmation', 'locatorType', 'status']
def __dir__(self):
return self.attrs
@@ -1952,7 +1928,7 @@ class PhysicalData():
for attr in self.attrs:
html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
- attr, getattr(self, attr, '')
+ attr, getattr(self, attr, '')
)
html += """
@@ -2011,15 +1987,15 @@ class DataSet(OpenBisObject):
@type.setter
def type(self, type_name):
- dataset_type = self.openbis.get_dataset_type(type_name.upper())
- self.p.__dict__['_type'] = dataset_type
- self.a.__dict__['_type'] = dataset_type
+ dataset_type = self.openbis.get_dataset_type(type_name.upper())
+ self.p.__dict__['_type'] = dataset_type
+ self.a.__dict__['_type'] = dataset_type
@property
def physicalData(self):
if 'physicalData' in self.data:
return PhysicalData(self.data['physicalData'])
- #return self.data['physicalData']
+ # return self.data['physicalData']
@property
def status(self):
@@ -2031,41 +2007,38 @@ class DataSet(OpenBisObject):
return None
def archive(self, remove_from_data_store=True):
- fetchopts = {
+ fetchopts = {
"removeFromDataStore": remove_from_data_store,
- "@type": "as.dto.dataset.archive.DataSetArchiveOptions"
+ "@type": "as.dto.dataset.archive.DataSetArchiveOptions"
}
self.archive_unarchive('archiveDataSets', fetchopts)
print("DataSet {} archived".format(self.permId))
-
def unarchive(self):
- fetchopts = {
- "@type": "as.dto.dataset.unarchive.DataSetUnarchiveOptions"
+ fetchopts = {
+ "@type": "as.dto.dataset.unarchive.DataSetUnarchiveOptions"
}
self.archive_unarchive('unarchiveDataSets', fetchopts)
print("DataSet {} unarchived".format(self.permId))
-
def archive_unarchive(self, method, fetchopts):
dss = self.get_datastore
payload = {}
request = {
- "method": method,
- "params": [
- self.openbis.token,
- [{
- "permId": self.permId,
- "@type": "as.dto.dataset.id.DataSetPermId"
- }],
- dict(fetchopts)
- ],
+ "method": method,
+ "params": [
+ self.openbis.token,
+ [{
+ "permId": self.permId,
+ "@type": "as.dto.dataset.id.DataSetPermId"
+ }],
+ dict(fetchopts)
+ ],
}
resp = self.openbis._post_request(self._openbis.as_v3, request)
return
-
def set_properties(self, properties):
self.openbis.update_dataset(self.permId, properties=properties)
@@ -2094,7 +2067,7 @@ class DataSet(OpenBisObject):
for filename in files:
file_info = self.get_file_list(start_folder=filename)
file_size = file_info[0]['fileSize']
- download_url = base_url + filename + '?sessionID=' + self.openbis.token
+ download_url = base_url + filename + '?sessionID=' + self.openbis.token
filename_dest = os.path.join(destination, self.permId, filename)
queue.put([download_url, filename_dest, file_size, self.openbis.verify_certificates])
@@ -2102,17 +2075,14 @@ class DataSet(OpenBisObject):
if wait_until_finished:
queue.join()
-
print("Files downloaded to: %s" % os.path.join(destination, self.permId))
-
def get_parents(self):
return self.openbis.get_datasets(withChildren=self.permId)
def get_children(self):
return self.openbis.get_datasets(withParents=self.permId)
-
def file_list(self):
"""returns the list of files including their directories as an array of strings. Just folders are not
listed.
@@ -2125,7 +2095,6 @@ class DataSet(OpenBisObject):
files.append(file['pathInDataSet'])
return files
-
def get_files(self, start_folder='/'):
"""Returns a DataFrame of all files in this dataset
"""
@@ -2142,15 +2111,14 @@ class DataSet(OpenBisObject):
We display the hex number to match with the classic UI
"""
if sig_int < 0:
- sig_int += 2**32
- return "%x"%(sig_int & 0xFFFFFFFF)
-
+ sig_int += 2 ** 32
+ return "%x" % (sig_int & 0xFFFFFFFF)
+
files = self.get_file_list(start_folder=start_folder)
df = DataFrame(files)
df['relativePath'] = df['pathInDataSet'].map(createRelativePath)
df['crc32Checksum'] = df['crc32Checksum'].fillna(0.0).astype(int).map(signed_to_unsigned)
return df[['isDirectory', 'pathInDataSet', 'fileSize', 'crc32Checksum']]
-
def get_file_list(self, recursive=True, start_folder="/"):
"""Lists all files of a given dataset. You can specifiy a start_folder other than "/".
@@ -2158,26 +2126,26 @@ class DataSet(OpenBisObject):
turn off this option by setting recursive=False.
"""
request = {
- "method" : "listFilesForDataSet",
- "params" : [
+ "method": "listFilesForDataSet",
+ "params": [
self.openbis.token,
- self.permId,
+ self.permId,
start_folder,
recursive,
],
- "id":"1"
+ "id": "1"
}
resp = requests.post(
self.data["dataStore"]["downloadUrl"] + '/datastore_server/rmi-dss-api-v1.json',
- json.dumps(request),
+ json.dumps(request),
verify=self.openbis.verify_certificates
)
if resp.ok:
data = resp.json()
if 'error' in data:
- raise ValueError('Error from openBIS: ' + data['error'] )
+ raise ValueError('Error from openBIS: ' + data['error'])
elif 'result' in data:
return data['result']
else:
@@ -2185,7 +2153,6 @@ class DataSet(OpenBisObject):
else:
raise ValueError('internal error while performing post request')
-
def save(self):
if self.is_new:
raise ValueError('not implemented yet.')
@@ -2224,33 +2191,32 @@ class AttrHolder():
self.__dict__['_is_new'] = True
self.__dict__['_tags'] = []
-
def __call__(self, data):
self.__dict__['_is_new'] = False
for attr in self._allowed_attrs:
- if attr in ["code","permId","identifier",
- "type", "container","components"]:
- self.__dict__['_'+attr] = data.get(attr, None)
+ if attr in ["code", "permId", "identifier",
+ "type", "container", "components"]:
+ self.__dict__['_' + attr] = data.get(attr, None)
elif attr in ["space"]:
- d = data.get(attr, None)
+ d = data.get(attr, None)
if d is not None:
d = d['permId']
- self.__dict__['_'+attr] = d
+ self.__dict__['_' + attr] = d
elif attr in ["sample", "experiment", "project"]:
- d = data.get(attr, None)
+ d = data.get(attr, None)
if d is not None:
d = d['identifier']
- self.__dict__['_'+attr] = d
+ self.__dict__['_' + attr] = d
- elif attr in ["parents","children","samples"]:
- self.__dict__['_'+attr] = []
+ elif attr in ["parents", "children", "samples"]:
+ self.__dict__['_' + attr] = []
for item in data[attr]:
if 'identifier' in item:
- self.__dict__['_'+attr].append(item['identifier'])
+ self.__dict__['_' + attr].append(item['identifier'])
elif 'permId' in item:
- self.__dict__['_'+attr].append(item['permId'])
+ self.__dict__['_' + attr].append(item['permId'])
elif attr in ["tags"]:
tags = []
@@ -2263,16 +2229,15 @@ class AttrHolder():
import copy
self.__dict__['_prev_tags'] = copy.deepcopy(tags)
else:
- self.__dict__['_'+attr] = data.get(attr, None)
-
+ self.__dict__['_' + attr] = data.get(attr, None)
def _new_attrs(self):
defs = _definitions(self.entity)
attr2ids = _definitions('attr2ids')
new_obj = {
- "@type" : "as.dto.{}.create.{}Creation".format(self.entity.lower(), self.entity)
- }
+ "@type": "as.dto.{}.create.{}Creation".format(self.entity.lower(), self.entity)
+ }
for attr in defs['attrs_new']:
items = None
@@ -2282,47 +2247,45 @@ class AttrHolder():
continue
elif attr == 'attachments':
- attachments = getattr(self,'_new_attachments')
+ attachments = getattr(self, '_new_attachments')
if attachments is None:
continue
- atts_data = [ attachment.get_data() for attachment in attachments ]
+ atts_data = [attachment.get_data() for attachment in attachments]
items = atts_data
elif attr in defs['multi']:
- items = getattr(self, '_'+attr)
+ items = getattr(self, '_' + attr)
if items is None:
items = []
else:
- items = getattr(self, '_'+attr)
+ items = getattr(self, '_' + attr)
key = None
if attr in attr2ids:
key = attr2ids[attr]
else:
key = attr
-
- new_obj[key] = items
+ new_obj[key] = items
# create a new entity
- request = {
+ request = {
"method": "create{}s".format(self.entity),
"params": [
self.openbis.token,
- [ new_obj ]
+ [new_obj]
]
}
return request
-
def _up_attrs(self):
defs = _definitions(self._entity)
attr2ids = _definitions('attr2ids')
up_obj = {
- "@type" : "as.dto.{}.update.{}Update".format(self.entity.lower(), self.entity),
- defs["identifier"]: self._permId
- }
+ "@type": "as.dto.{}.update.{}Update".format(self.entity.lower(), self.entity),
+ defs["identifier"]: self._permId
+ }
# look at all attributes available for that entity
# that can be updated
@@ -2334,49 +2297,49 @@ class AttrHolder():
attachments = self.__dict__.get('_new_attachments', None)
if attachments is None:
continue
- atts_data = [ attachment.get_data() for attachment in attachments ]
+ atts_data = [attachment.get_data() for attachment in attachments]
if self._is_new:
up_obj['attachments'] = atts_data
else:
up_obj['attachments'] = {
- "actions": [ {
+ "actions": [{
"items": atts_data,
"@type": "as.dto.common.update.ListUpdateActionAdd"
- } ],
+ }],
"@type": "as.dto.attachment.update.AttachmentListUpdateValue"
- }
+ }
elif attr == 'tags':
# look which tags have been added or removed and update them
- if getattr(self,'_prev_tags') is None:
+ if getattr(self, '_prev_tags') is None:
self.__dict__['_prev_tags'] = []
actions = []
for tagId in self._prev_tags:
if tagId not in self._tags:
actions.append({
- "items": [ tagId ],
+ "items": [tagId],
"@type": "as.dto.common.update.ListUpdateActionRemove"
})
for tagId in self._tags:
if tagId not in self._prev_tags:
actions.append({
- "items": [ tagId ],
+ "items": [tagId],
"@type": "as.dto.common.update.ListUpdateActionAdd"
})
-
+
up_obj['tagIds'] = {
"@type": "as.dto.common.update.IdListUpdateValue",
"actions": actions
}
- elif '_'+attr in self.__dict__:
+ elif '_' + attr in self.__dict__:
# handle multivalue attributes (parents, children, tags etc.)
# we only cover the Set mechanism, which means we always update
# all items in a list
if attr in defs['multi']:
- items = self.__dict__.get('_'+attr, [])
+ items = self.__dict__.get('_' + attr, [])
if items == None:
items = []
up_obj[attr2ids[attr]] = {
@@ -2390,49 +2353,48 @@ class AttrHolder():
}
else:
# handle single attributes (space, experiment, project, container, etc.)
- value = self.__dict__.get('_'+attr, {})
+ value = self.__dict__.get('_' + attr, {})
if value is None:
pass
else:
- isModified=False
+ isModified = False
if 'isModified' in value:
- isModified=True
+ isModified = True
del value['isModified']
-
+
up_obj[attr2ids[attr]] = {
- "@type": "as.dto.common.update.FieldUpdateValue",
- "isModified": isModified,
- "value": value,
+ "@type": "as.dto.common.update.FieldUpdateValue",
+ "isModified": isModified,
+ "value": value,
}
# update a new entity
- request = {
+ request = {
"method": "update{}s".format(self.entity),
"params": [
self.openbis.token,
- [ up_obj ]
+ [up_obj]
]
}
return request
-
def __getattr__(self, name):
""" handles all attribute requests dynamically. Values are returned in a sensible way,
for example the identifiers of parents, children and components are returned
as an array of values.
"""
-
- int_name = '_'+name
- if int_name in self.__dict__:
+
+ int_name = '_' + name
+ if int_name in self.__dict__:
if int_name in ['_attachments']:
return [
- {
+ {
"fileName": x['fileName'],
"title": x['title'],
"description": x['description']
- } for x in self._attachments
- ]
- if int_name in ['_registrator','_modifier', '_dataProducer']:
+ } for x in self._attachments
+ ]
+ if int_name in ['_registrator', '_modifier', '_dataProducer']:
return self.__dict__[int_name].get('userId', None)
elif int_name in ['_registrationDate', '_modificationDate', '_accessDate', '_dataProductionDate']:
return format_timestamp(self.__dict__[int_name])
@@ -2464,7 +2426,6 @@ class AttrHolder():
else:
return None
-
def __setattr__(self, name, value):
if name in ["parents", "children", "components"]:
if not isinstance(value, list):
@@ -2472,9 +2433,9 @@ class AttrHolder():
objs = []
for val in value:
# fetch objects in openBIS, make sure they actually exists
- obj = getattr(self._openbis, 'get_'+self._entity.lower())(val)
+ obj = getattr(self._openbis, 'get_' + self._entity.lower())(val)
objs.append(obj)
- self.__dict__['_'+name] = {
+ self.__dict__['_' + name] = {
"@type": "as.dto.common.update.IdListUpdateValue",
"actions": [{
"@type": "as.dto.common.update.ListUpdateActionSet",
@@ -2483,7 +2444,7 @@ class AttrHolder():
}
elif name in ["tags"]:
self.set_tags(value)
-
+
elif name in ["attachments"]:
if isinstance(value, list):
for item in value:
@@ -2499,17 +2460,17 @@ class AttrHolder():
obj = None
if isinstance(value, str):
# fetch object in openBIS, make sure it actually exists
- obj = getattr(self._openbis, "get_"+name)(value)
+ obj = getattr(self._openbis, "get_" + name)(value)
else:
obj = value
- self.__dict__['_'+name] = obj.data['permId']
+ self.__dict__['_' + name] = obj.data['permId']
# mark attribute as modified, if it's an existing entity
if self.is_new:
pass
else:
- self.__dict__['_'+name]['isModified'] = True
+ self.__dict__['_' + name]['isModified'] = True
elif name in ["identifier"]:
raise KeyError("you can not modify the {}".format(name))
@@ -2519,7 +2480,7 @@ class AttrHolder():
raise KeyError("for this {}Type you can not set a code".format(self.entity))
except AttributeError:
pass
-
+
self.__dict__['_code'] = value
elif name == "description":
@@ -2532,16 +2493,16 @@ class AttrHolder():
def get_parents(self):
# e.g. self._openbis.get_samples(withChildren=self.identifier)
- return getattr(self._openbis, 'get_'+self._entity.lower()+'s')(withChildren=self.identifier)
+ return getattr(self._openbis, 'get_' + self._entity.lower() + 's')(withChildren=self.identifier)
def get_children(self):
# e.g. self._openbis.get_samples(withParents=self.identifier)
- return getattr(self._openbis, 'get_'+self._entity.lower()+'s')(withParents=self.identifier)
+ return getattr(self._openbis, 'get_' + self._entity.lower() + 's')(withParents=self.identifier)
@property
def tags(self):
if getattr(self, '_tags') is not None:
- return [ x['code'] for x in self._tags ]
+ return [x['code'] for x in self._tags]
def set_tags(self, tags):
if getattr(self, '_tags') is None:
@@ -2557,7 +2518,7 @@ class AttrHolder():
# add all new tags that are not in the list yet
for tagId in tagIds:
if tagId not in self.__dict__['_tags']:
- self.__dict__['_tags'].append(tagId)
+ self.__dict__['_tags'].append(tagId)
def add_tags(self, tags):
if getattr(self, '_tags') is None:
@@ -2568,7 +2529,7 @@ class AttrHolder():
tagIds = _create_tagIds(tags)
for tagId in tagIds:
if not tagId in self.__dict__['_tags']:
- self.__dict__['_tags'].append(tagId)
+ self.__dict__['_tags'].append(tagId)
def del_tags(self, tags):
if getattr(self, '_tags') is None:
@@ -2579,13 +2540,13 @@ class AttrHolder():
tagIds = _create_tagIds(tags)
for tagId in tagIds:
if tagId in self.__dict__['_tags']:
- self.__dict__['_tags'].remove(tagId)
+ self.__dict__['_tags'].remove(tagId)
def get_attachments(self):
if getattr(self, '_attachments') is None:
return None
else:
- return DataFrame(self._attachments)[['fileName','title','description','version']]
+ return DataFrame(self._attachments)[['fileName', 'title', 'description', 'version']]
def add_attachment(self, fileName, title=None, description=None):
att = Attachment(filename=fileName, title=title, description=description)
@@ -2598,35 +2559,34 @@ class AttrHolder():
self._new_attachments.append(att)
def download_attachments(self):
- method = 'get'+self.entity+'s'
+ method = 'get' + self.entity + 's'
entity = self.entity.lower()
request = {
"method": method,
- "params": [ self._openbis.token,
- [ self._permId ],
- dict(
- attachments= fetch_option['attachmentsWithContent'],
- **fetch_option[entity]
- )
- ]
+ "params": [self._openbis.token,
+ [self._permId],
+ dict(
+ attachments=fetch_option['attachmentsWithContent'],
+ **fetch_option[entity]
+ )
+ ]
}
resp = self._openbis._post_request(self._openbis.as_v3, request)
attachments = resp[self.permId]['attachments']
file_list = []
for attachment in attachments:
filename = os.path.join(
- self._openbis.hostname,
+ self._openbis.hostname,
self.permId,
attachment['fileName']
)
os.makedirs(os.path.dirname(filename), exist_ok=True)
with open(filename, 'wb') as att:
content = base64.b64decode(attachment['content'])
- att.write(content)
+ att.write(content)
file_list.append(filename)
return file_list
-
def _repr_html_(self):
def nvl(val, string=''):
if val is None:
@@ -2643,12 +2603,12 @@ class AttrHolder():
</thead>
<tbody>
"""
-
+
for attr in self._allowed_attrs:
if attr == 'attachments':
continue
html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
- attr, nvl(getattr(self, attr, ''),'')
+ attr, nvl(getattr(self, attr, ''), '')
)
if getattr(self, '_attachments') is not None:
html += "<tr><td>attachments</td><td>"
@@ -2660,7 +2620,6 @@ class AttrHolder():
</table>
"""
return html
-
def __repr__(self):
@@ -2694,20 +2653,20 @@ class Sample():
setattr(self, key, kwargs[key])
def _set_data(self, data):
- # assign the attribute data to self.a by calling it
- # (invoking the AttrHolder.__call__ function)
- self.a(data)
- self.__dict__['data'] = data
+ # assign the attribute data to self.a by calling it
+ # (invoking the AttrHolder.__call__ function)
+ self.a(data)
+ self.__dict__['data'] = data
- # put the properties in the self.p namespace (without checking them)
- for key, value in data['properties'].items():
- self.p.__dict__[key.lower()] = value
+ # put the properties in the self.p namespace (without checking them)
+ for key, value in data['properties'].items():
+ self.p.__dict__[key.lower()] = value
def __dir__(self):
return [
'props', 'get_parents()', 'get_children()',
'get_datasets()', 'get_experiment()',
- 'space', 'project', 'experiment', 'project', 'tags',
+ 'space', 'project', 'experiment', 'project', 'tags',
'set_tags()', 'add_tags()', 'del_tags()',
'add_attachment()', 'get_attachments()', 'download_attachments()'
]
@@ -2722,9 +2681,9 @@ class Sample():
@type.setter
def type(self, type_name):
- sample_type = self.openbis.get_sample_type(type_name)
- self.p.__dict__['_type'] = sample_type
- self.a.__dict__['_type'] = sample_type
+ sample_type = self.openbis.get_sample_type(type_name)
+ self.p.__dict__['_type'] = sample_type
+ self.a.__dict__['_type'] = sample_type
def __getattr__(self, name):
return getattr(self.__dict__['a'], name)
@@ -2759,7 +2718,7 @@ class Sample():
new_sample_data = self.openbis.get_sample(resp[0]['permId'], only_data=True)
self._set_data(new_sample_data)
return self
-
+
else:
request = self._up_attrs()
props = self.p._all_props()
@@ -2767,7 +2726,6 @@ class Sample():
self.openbis._post_request(self.openbis.as_v3, request)
print("Sample successfully updated.")
-
def delete(self, reason):
self.openbis.delete_entity('sample', self.permId, reason)
@@ -2778,18 +2736,18 @@ class Sample():
return self.openbis.get_project(withSamples=[self.permId])
def get_experiment(self):
- try:
+ try:
return self.openbis.get_experiment(self._experiment['identifier'])
except Exception:
pass
@property
def experiment(self):
- try:
+ try:
return self.openbis.get_experiment(self._experiment['identifier'])
except Exception:
pass
-
+
class Space(OpenBisObject):
""" managing openBIS spaces
@@ -2811,8 +2769,8 @@ class Space(OpenBisObject):
"""all the available methods and attributes that should be displayed
when using the autocompletion feature (TAB) in Jupyter
"""
- return['code','permId', 'description', 'registrator', 'registrationDate',
- 'modificationDate', 'get_projects()', 'new_project()', 'get_samples()', 'delete()']
+ return ['code', 'permId', 'description', 'registrator', 'registrationDate',
+ 'modificationDate', 'get_projects()', 'new_project()', 'get_samples()', 'delete()']
def __str__(self):
return self.data.get('code', None)
@@ -2858,17 +2816,17 @@ class Things():
return self.df[key]
else:
# get thing by code
- row = self.df[self.df[self.identifier_name]==key.upper()]
+ row = self.df[self.df[self.identifier_name] == key.upper()]
if row is not None:
# invoke the openbis.get_entity() method
- return getattr(self.openbis, 'get_'+self.entity)(row[self.identifier_name].values[0])
+ return getattr(self.openbis, 'get_' + self.entity)(row[self.identifier_name].values[0])
def __iter__(self):
for item in self.df[[self.identifier_name]][self.identifier_name].iteritems():
- yield getattr(self.openbis, 'get_'+self.entity)(item[1])
+ yield getattr(self.openbis, 'get_' + self.entity)(item[1])
- #return self.df[[self.identifier_name]].to_dict()[self.identifier_name]
+ # return self.df[[self.identifier_name]].to_dict()[self.identifier_name]
class Experiment(OpenBisObject):
@@ -2889,14 +2847,14 @@ class Experiment(OpenBisObject):
setattr(self, key, kwargs[key])
def _set_data(self, data):
- # assign the attribute data to self.a by calling it
- # (invoking the AttrHolder.__call__ function)
- self.a(data)
- self.__dict__['data'] = data
+ # assign the attribute data to self.a by calling it
+ # (invoking the AttrHolder.__call__ function)
+ self.a(data)
+ self.__dict__['data'] = data
- # put the properties in the self.p namespace (without checking them)
- for key, value in data['properties'].items():
- self.p.__dict__[key.lower()] = value
+ # put the properties in the self.p namespace (without checking them)
+ for key, value in data['properties'].items():
+ self.p.__dict__[key.lower()] = value
def __str__(self):
return self.data['code']
@@ -2905,9 +2863,9 @@ class Experiment(OpenBisObject):
# the list of possible methods/attributes displayed
# when invoking TAB-completition
return [
- 'props', 'space', 'project',
- 'project','tags', 'attachments', 'data',
- 'get_datasets()', 'get_samples()',
+ 'props', 'space', 'project',
+ 'project', 'tags', 'attachments', 'data',
+ 'get_datasets()', 'get_samples()',
'set_tags()', 'add_tags()', 'del_tags()',
'add_attachment()', 'get_attachments()', 'download_attachments()'
]
@@ -2922,9 +2880,9 @@ class Experiment(OpenBisObject):
@type.setter
def type(self, type_name):
- experiment_type = self.openbis.get_experiment_type(type_name)
- self.p.__dict__['_type'] = experiment_type
- self.a.__dict__['_type'] = experiment_type
+ experiment_type = self.openbis.get_experiment_type(type_name)
+ self.p.__dict__['_type'] = experiment_type
+ self.a.__dict__['_type'] = experiment_type
def __getattr__(self, name):
return getattr(self.__dict__['a'], name)
@@ -2971,7 +2929,6 @@ class Experiment(OpenBisObject):
class Attachment():
-
def __init__(self, filename, title=None, description=None):
if not os.path.exists(filename):
raise ValueError("File not found: {}".format(filename))
@@ -2981,9 +2938,9 @@ class Attachment():
def get_data_short(self):
return {
- "fileName" : self.fileName,
- "title" : self.title,
- "description" : self.description,
+ "fileName": self.fileName,
+ "title": self.title,
+ "description": self.description,
}
def get_data(self):
@@ -2991,16 +2948,15 @@ class Attachment():
content = att.read()
contentb64 = base64.b64encode(content).decode()
return {
- "fileName" : self.fileName,
- "title" : self.title,
- "description" : self.description,
- "content" : contentb64,
- "@type" : "as.dto.attachment.create.AttachmentCreation",
+ "fileName": self.fileName,
+ "title": self.title,
+ "description": self.description,
+ "content": contentb64,
+ "@type": "as.dto.attachment.create.AttachmentCreation",
}
class Project(OpenBisObject):
-
def __init__(self, openbis_obj, data=None, **kwargs):
self.__dict__['openbis'] = openbis_obj
self.__dict__['a'] = AttrHolder(openbis_obj, 'Project')
@@ -3015,17 +2971,17 @@ class Project(OpenBisObject):
def _modifiable_attrs(self):
return
-
+
def __dir__(self):
"""all the available methods and attributes that should be displayed
when using the autocompletion feature (TAB) in Jupyter
"""
- return['code','permId', 'identifier', 'description', 'space', 'registrator',
- 'registrationDate', 'modifier', 'modificationDate', 'add_attachment()',
- 'get_attachments()', 'download_attachments()',
- 'get_experiments()', 'get_samples()', 'get_datasets()',
- 'delete()'
- ]
+ return ['code', 'permId', 'identifier', 'description', 'space', 'registrator',
+ 'registrationDate', 'modifier', 'modificationDate', 'add_attachment()',
+ 'get_attachments()', 'download_attachments()',
+ 'get_experiments()', 'get_samples()', 'get_datasets()',
+ 'delete()'
+ ]
def get_samples(self):
return self.openbis.get_samples(project=self.permId)
@@ -3037,7 +2993,7 @@ class Project(OpenBisObject):
return self.openbis.get_datasets(project=self.permId)
def delete(self, reason):
- self.openbis.delete_entity('project', self.permId, reason)
+ self.openbis.delete_entity('project', self.permId, reason)
def save(self):
if self.is_new:
@@ -3049,4 +3005,3 @@ class Project(OpenBisObject):
request = self._up_attrs()
self.openbis._post_request(self.openbis.as_v3, request)
print("Project successfully updated.")
-
diff --git a/src/python/pybis/tests/test_openbis.py b/src/python/pybis/tests/test_openbis.py
index 5b2103e84c32cfff1543ee767448a2b2e8e6d1c7..6e6a4f8b7687680e4024c80f3d5920c837463d23 100644
--- a/src/python/pybis/tests/test_openbis.py
+++ b/src/python/pybis/tests/test_openbis.py
@@ -62,7 +62,7 @@ def test_get_sample_parents(openbis_instance):
assert sample.parents[0]['identifier']['identifier'] == '/TEST/TEST-SAMPLE-2-PARENT'
parents = sample.get_parents()
assert isinstance(parents, list)
- assert parents[0].ident == '/TEST/TEST-SAMPLE-2-PARENT'
+ assert parents[0].ident == '/TEST/TEST-SAMPLE-2-PARENT'
def test_get_sample_children(openbis_instance):
@@ -73,7 +73,7 @@ def test_get_sample_children(openbis_instance):
assert sample.children[0]['identifier']['identifier'] == '/TEST/TEST-SAMPLE-2-CHILD-1'
children = sample.get_children()
assert isinstance(children, list)
- assert children[0].ident == '/TEST/TEST-SAMPLE-2-CHILD-1'
+ assert children[0].ident == '/TEST/TEST-SAMPLE-2-CHILD-1'
def test_get_dataset_parents(openbis_instance):
@@ -114,25 +114,22 @@ def test_get_dataset_by_permid(openbis_instance):
def test_dataset_upload(openbis_instance):
datastores = openbis_instance.get_datastores()
assert datastores is not None
-# assert isinstance(datastores, list)
-
- #filename = 'testfile.txt'
- #with open(filename, 'w') as f:
+ # assert isinstance(datastores, list)
+ # filename = 'testfile.txt'
+ # with open(filename, 'w') as f:
# f.write('test-data')
- #ds = openbis_instance.new_dataset(
+ # ds = openbis_instance.new_dataset(
# name = "My Dataset",
# description = "description",
# type = "UNKNOWN",
# sample = sample,
# files = ["testfile.txt"],
- #)
-
-
+ # )
- #analysis = openbis_instance.new_analysis(
+ # analysis = openbis_instance.new_analysis(
# name = "My analysis", # * name of the container
- # description = "a description", #
+ # description = "a description", #
# sample = sample, # my_dataset.sample is the default
# # result files will be registered as JUPYTER_RESULT datatype
@@ -142,8 +139,6 @@ def test_dataset_upload(openbis_instance):
# notebook_files = ["notebook.ipynb"], # specify a specific notebook
# #notebook_files = "~/notebooks/", # path of notebooks
# parents = [parent_dataset], # other parents are optional, my_dataset is the default parent
- #)
-
- #analysis.save # start registering process
-
+ # )
+ # analysis.save # start registering process
\ No newline at end of file