From 451f581ba31b6a56fd058cd63db377b1f13ff695 Mon Sep 17 00:00:00 2001
From: Yves Noirjean <yves.noirjean@id.ethz.ch>
Date: Wed, 13 Dec 2017 12:48:21 +0100
Subject: [PATCH] pybis: added linkedData support to DataSet; created
GitDataSetUpdate; using parse_jackson in pybis.get_dataset
---
src/python/PyBis/pybis/data_set.py | 84 +++++++++++++++++++++++++++++-
src/python/PyBis/pybis/pybis.py | 37 ++++++++++++-
src/python/PyBis/pybis/utils.py | 3 +-
3 files changed, 120 insertions(+), 4 deletions(-)
diff --git a/src/python/PyBis/pybis/data_set.py b/src/python/PyBis/pybis/data_set.py
index 5f40d21da08..709c1ca79fc 100644
--- a/src/python/PyBis/pybis/data_set.py
+++ b/src/python/PyBis/pybis/data_set.py
@@ -25,7 +25,6 @@ class GitDataSetCreation(object):
"""Initialize the command object with the necessary parameters.
:param openbis: The openBIS API object.
:param data_set_type: The type of the data set
- :param data_set_type: The type of the data set
:param path: The path to the git repository
:param commit_id: The git commit id
:param repository_id: The git repository id - same for copies
@@ -176,3 +175,86 @@ class GitDataSetCreation(object):
transfer_to_file_creation(content, result, 'directory')
transfer_to_file_creation(content, result, 'path')
return result
+
+
+class GitDataSetUpdate(object):
+
+ def __init__(self, openbis, path, commit_id, repository_id, edms_id, data_set_id):
+ """Initialize the command object with the necessary parameters.
+ :param openbis: The openBIS API object.
+ :param path: The path to the git repository
+ :param commit_id: The git commit id
+ :param repository_id: The git repository id - same for copies
+ :param edms_id: If of the external data managment system
+ :param data_set_id: Id of the data set to be updated
+ """
+ self.openbis = openbis
+ self.path = path
+ self.commit_id = commit_id
+ self.repository_id = repository_id
+ self.edms_id =edms_id
+ self.data_set_id = data_set_id
+
+
+ def new_content_copy(self):
+ """ Create a data set update for adding a content copy.
+ :return: A DataSetUpdate object
+ """
+ data_set_update = self.get_data_set_update()
+ self.send_request(data_set_update)
+
+
+ def send_request(self, data_set_update):
+ request = {
+ "method": "updateDataSets",
+ "params": [
+ self.openbis.token,
+ [data_set_update]
+ ]
+ }
+ self.openbis._post_request(self.openbis.as_v3, request)
+
+
+ def get_data_set_update(self):
+ return {
+ "@type": "as.dto.dataset.update.DataSetUpdate",
+ "dataSetId": self.get_data_set_id(),
+ "linkedData": self.get_linked_data()
+ }
+
+
+ def get_data_set_id(self):
+ return {
+ "@type": "as.dto.dataset.id.DataSetPermId",
+ "permId": self.data_set_id
+ }
+
+
+ def get_linked_data(self):
+ return {
+ "@type": "as.dto.common.update.FieldUpdateValue",
+ "isModified": True,
+ "value": {
+ "@type": "as.dto.dataset.update.LinkedDataUpdate",
+ "contentCopies": {
+ "@type": "as.dto.dataset.update.ContentCopyListUpdateValue",
+ "actions": [ {
+ "@type": "as.dto.common.update.ListUpdateActionAdd",
+ "items": [ self.get_content_copy_creation() ]
+ } ]
+ }
+ }
+ }
+
+
+ def get_content_copy_creation(self):
+ return {
+ "@type": "as.dto.dataset.create.ContentCopyCreation",
+ "externalDmsId": {
+ "@type": "as.dto.externaldms.id.ExternalDmsPermId",
+ "permId": self.edms_id
+ },
+ "path": self.path,
+ "gitCommitHash": self.commit_id,
+ "gitRepositoryId" : self.repository_id,
+ }
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index 514481af8ae..314363bc1e1 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -1761,6 +1761,8 @@ class Openbis:
if resp is None or len(resp) == 0:
raise ValueError('no such dataset found: ' + permid)
+ parse_jackson(resp)
+
for permid in resp:
if only_data:
return resp[permid]
@@ -1958,6 +1960,17 @@ class Openbis:
return pbds.GitDataSetCreation(self, data_set_type, path, commit_id, repository_id, dms, sample, experiment,
properties, dss_code, parents, data_set_code, contents).new_git_data_set()
+ def new_content_copy(self, path, commit_id, repository_id, edms_id, data_set_id):
+ """
+ Create a content copy in an existing link data set.
+ :param path: path of the new content copy
+ "param commit_id: commit id of the new content copy
+ "param repository_id: repository id of the content copy
+ "param edms_id: Id of the external data managment system of the content copy
+ "param data_set_id: Id of the data set to which the new content copy belongs
+ """
+ return pbds.GitDataSetUpdate(self, path, commit_id, repository_id, edms_id, data_set_id).new_content_copy()
+
@staticmethod
def sample_to_sample_id(sample):
"""Take sample which may be a string or object and return an identifier for it."""
@@ -2263,6 +2276,22 @@ class OpenBisObject():
return self.a.__repr__()
+class LinkedData():
+ def __init__(self, data=None):
+ self.data = data if data is not None else []
+ self.attrs = ['externalCode', 'contentCopies']
+
+ 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 ''
+
+
class PhysicalData():
def __init__(self, data=None):
if data is None:
@@ -2347,7 +2376,7 @@ class DataSet(OpenBisObject):
return [
'props', 'get_parents()', 'get_children()',
'add_parents()', 'add_children()', 'del_parents()', 'del_children()',
- 'sample', 'experiment', 'physicalData',
+ 'sample', 'experiment', 'physicalData', 'linkedData',
'tags', 'set_tags()', 'add_tags()', 'del_tags()',
'add_attachment()', 'get_attachments()', 'download_attachments()',
"get_files(start_folder='/')", 'file_list',
@@ -2379,7 +2408,11 @@ class DataSet(OpenBisObject):
def physicalData(self):
if 'physicalData' in self.data:
return PhysicalData(self.data['physicalData'])
- # return self.data['physicalData']
+
+ @property
+ def linkedData(self):
+ if 'linkedData' in self.data:
+ return LinkedData(self.data['linkedData'])
@property
def status(self):
diff --git a/src/python/PyBis/pybis/utils.py b/src/python/PyBis/pybis/utils.py
index 7e46c9d4cab..a16f6ac7dda 100644
--- a/src/python/PyBis/pybis/utils.py
+++ b/src/python/PyBis/pybis/utils.py
@@ -9,7 +9,8 @@ def parse_jackson(input_json):
"""
interesting=['tags', 'registrator', 'modifier', 'type', 'parents',
'children', 'containers', 'properties', 'experiment', 'sample',
- 'project', 'space', 'propertyType', 'entityType', 'propertyType', 'propertyAssignment'
+ 'project', 'space', 'propertyType', 'entityType', 'propertyType', 'propertyAssignment',
+ 'externalDms'
]
found = {}
def build_cache(graph):
--
GitLab