From fd9b1b9b2d9ca253b47d23ed6f203d32eb342f0e Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Tue, 6 Nov 2018 17:05:32 +0100
Subject: [PATCH] moved PropertyAssignments to file property_assignment.py;
added server_information to openbis object on login; moved class PhyiscalData
to dataset.py
---
pybis/src/python/pybis/pybis.py | 142 ++++++++++++--------------------
1 file changed, 52 insertions(+), 90 deletions(-)
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 6da1ac17112..8e7f8c731f1 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -29,7 +29,8 @@ from tabulate import tabulate
from . import data_set as pbds
from .utils import parse_jackson, check_datatype, split_identifier, format_timestamp, is_identifier, is_permid, nvl, VERBOSE
from .utils import extract_attr, extract_permid, extract_code,extract_deletion,extract_identifier,extract_nested_identifier,extract_nested_permid,extract_property_assignments,extract_role_assignments,extract_person, extract_person_details,extract_id,extract_userId
-from .property import PropertyHolder, PropertyAssignments
+from .property import PropertyHolder
+from .property_assignment import PropertyAssignments
from .vocabulary import Vocabulary, VocabularyTerm
from .openbis_object import OpenBisObject
from .definitions import get_definition_for_entity, fetch_option, get_fetchoption_for_entity, get_type_for_entity, get_method_for_entity
@@ -562,6 +563,7 @@ class Openbis:
return [
'url', 'port', 'hostname',
'login()', 'logout()', 'is_session_active()', 'token', 'is_token_valid("")',
+ "server_information",
"get_server_information()",
"get_dataset('permId')",
"get_datasets()",
@@ -783,6 +785,8 @@ class Openbis:
raise ValueError("login to openBIS failed")
else:
self.token = result
+ self.server_information = self.get_server_information()
+
if save_token:
self.save_token()
# update the OPENBIS_TOKEN environment variable, if OPENBIS_URL is identical to self.url
@@ -1508,32 +1512,6 @@ class Openbis:
return self._dataset_list_for_response(response=resp['objects'], props=props)
- attrs = ['permId', 'type', 'experiment', 'sample',
- 'registrationDate', 'modificationDate', 'location', 'properties'
- ]
-
- if len(resp['objects']) == 0:
- datasets = DataFrame(columns=attrs)
- else:
- objects = resp['objects']
- 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['permId'] = datasets['code']
- datasets['location'] = datasets['physicalData'].map(lambda x: x.get('location') if x else '')
-
- if props is not None:
- for prop in props:
- datasets[prop.upper()] = datasets['properties'].map(lambda x: x.get(prop.upper(), ''))
- attrs.append(prop.upper())
-
- return Things(self, 'dataset', datasets[attrs], 'permId')
-
def get_experiment(self, expId, withAttachments=False, only_data=False):
""" Returns an experiment object for a given identifier (expId).
@@ -1942,7 +1920,7 @@ class Openbis:
return VocabularyTerm(self, resp[ident])
- def get_any_entity(self, identifier, entity, only_data=False, method=None):
+ def _get_any_entity(self, identifier, entity, only_data=False, method=None):
entity_def = get_definition_for_entity(entity)
@@ -2010,7 +1988,7 @@ class Openbis:
def get_vocabulary(self, code, only_data=False):
""" Returns the details of a given vocabulary (including vocabulary terms)
"""
- return self.get_any_entity(code, 'Vocabulary', only_data=only_data, method='getVocabularies')
+ return self._get_any_entity(code, 'Vocabulary', only_data=only_data, method='getVocabularies')
def new_tag(self, code, description=None):
@@ -2409,7 +2387,7 @@ class Openbis:
"code": type_name
})
fetch_options['propertyAssignments'] = fetch_option['propertyAssignments']
- fetch_options['validationPlugin'] = fetch_option['plugin']
+ #fetch_options['validationPlugin'] = fetch_option['plugin']
request = {
"method": method_name,
@@ -2419,7 +2397,10 @@ class Openbis:
parse_jackson(resp)
if type_name is not None and len(resp['objects']) == 1:
- return PropertyAssignments(self, resp['objects'][0])
+ return PropertyAssignments(
+ openbis_obj = self,
+ data = resp['objects'][0]
+ )
types = []
attrs = self._get_attributes(type_name, types, additional_attributes, optional_attributes)
@@ -2537,7 +2518,10 @@ class Openbis:
parse_jackson(response)
attrs = ['permId', 'type', 'experiment', 'sample',
- 'registrationDate', 'modificationDate', 'location', 'properties']
+ 'registrationDate', 'modificationDate',
+ 'location', 'status', 'presentInArchive', 'size',
+ 'properties'
+ ]
if len(response) == 0:
datasets = DataFrame(columns=attrs)
else:
@@ -2548,6 +2532,9 @@ class Openbis:
datasets['sample'] = datasets['sample'].map(extract_nested_identifier)
datasets['type'] = datasets['type'].map(extract_code)
datasets['permId'] = datasets['code']
+ datasets['size'] = datasets['physicalData'].map(lambda x: x.get('size') if x else '')
+ datasets['status'] = datasets['physicalData'].map(lambda x: x.get('status') if x else '')
+ datasets['presentInArchive'] = datasets['physicalData'].map(lambda x: x.get('presentInArchive') if x else '')
datasets['location'] = datasets['physicalData'].map(lambda x: x.get('location') if x else '')
if props is not None:
@@ -2579,7 +2566,11 @@ class Openbis:
)
fetchopts = {"type": {"@type": "as.dto.sample.fetchoptions.SampleTypeFetchOptions"}}
- for option in ['tags', 'properties', 'attachments', 'space', 'experiment', 'registrator', 'dataSets', 'project']:
+
+ options = ['tags', 'properties', 'attachments', 'space', 'experiment', 'registrator', 'dataSets']
+ if self.server_information.project_samples_enabled:
+ options.append('project')
+ for option in options:
fetchopts[option] = fetch_option[option]
if withAttachments:
@@ -2861,59 +2852,6 @@ class LinkedData():
return ''
-class PhysicalData():
- def __init__(self, data=None):
- if data is None:
- data = []
- self.data = data
- self.attrs = ['speedHint', 'complete', 'shareId', 'size',
- 'fileFormatType', 'storageFormat', 'location', 'presentInArchive',
- 'storageConfirmation', 'locatorType', 'status']
-
- def __dir__(self):
- return self.attrs
-
- def __getattr__(self, name):
- if name in self.attrs:
- if name in self.data:
- return self.data[name]
- else:
- return ''
-
- def _repr_html_(self):
- html = """
- <table border="1" class="dataframe">
- <thead>
- <tr style="text-align: right;">
- <th>attribute</th>
- <th>value</th>
- </tr>
- </thead>
- <tbody>
- """
-
- for attr in self.attrs:
- html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
- attr, getattr(self, attr, '')
- )
-
- html += """
- </tbody>
- </table>
- """
- return html
-
- def __repr__(self):
- headers = ['attribute', 'value']
- lines = []
- for attr in self.attrs:
- lines.append([
- attr,
- getattr(self, attr, '')
- ])
- return tabulate(lines, headers=headers)
-
-
class ExternalDMS():
""" managing openBIS external data management systems
"""
@@ -2945,15 +2883,16 @@ class ServerInformation():
def __init__(self, info):
self._info = info
-
- def __dir__(self):
- return [
+ self.attrs = [
'api_version', 'archiving_configured', 'authentication_service',
'enabled_technologies', 'project_samples_enabled'
]
+ def __dir__(self):
+ return self.attrs
+
def __getattr__(self, name):
- return self._info[name.replace('_', '-')]
+ return self._info.get(name.replace('_', '-'))
def get_major_version(self):
return int(self._info["api-version"].split(".")[0]);
@@ -2966,3 +2905,26 @@ class ServerInformation():
def is_openbis_1806(self):
return (self.get_major_version() == 3) and (self.get_minor_version() >= 5);
+
+ def _repr_html_(self):
+ html = """
+ <table border="1" class="dataframe">
+ <thead>
+ <tr style="text-align: right;">
+ <th>attribute</th>
+ <th>value</th>
+ </tr>
+ </thead>
+ <tbody>
+ """
+
+ for attr in self.attrs:
+ html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
+ attr, getattr(self, attr, '')
+ )
+
+ html += """
+ </tbody>
+ </table>
+ """
+ return html
--
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