From f441643d847bb632b0a9a1c7a5cb9252ecfbf05c Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Mon, 15 May 2017 15:55:08 +0200
Subject: [PATCH] SSDM-5144: using dataset-uploader-api for uploading datasets
---
src/python/PyBis/pybis/pybis.py | 34 ++++++++++++++++++++++++---------
1 file changed, 25 insertions(+), 9 deletions(-)
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index 2b380cef031..6e9e01d841f 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -43,7 +43,7 @@ from queue import Queue
from datetime import datetime
DROPBOX_PLUGIN = "jupyter-uploader-api"
-ELN_PLUGIN = "eln-lims-api"
+DATASET_UPLOADER_PLUGIN = "dataset-uploader-api"
def _definitions(entity):
@@ -566,7 +566,7 @@ def _subcriteria_for_code(code, object_type):
class Openbis:
"""Interface for communicating with openBIS.
A recent version of openBIS is required (minimum 16.05.2).
- For creation of datasets, ELN-LIMS needs to be installed.
+ For creation of datasets, dataset-uploader-api needs to be installed.
"""
__version__ = '1.2.0'
@@ -1546,7 +1546,7 @@ class Openbis:
resp = self._post_request(self.as_v1, request)
return resp
- def get_dataset(self, permid):
+ def get_dataset(self, permid, only_data=False):
"""fetch a dataset and some metadata attached to it:
- properties
- sample
@@ -1588,7 +1588,14 @@ class Openbis:
raise ValueError('no such dataset found: ' + permid)
if resp is not None:
for permid in resp:
- return DataSet(self, type=self.get_dataset_type(resp[permid]["type"]["code"]), data=resp[permid])
+ if only_data:
+ return resp[permid]
+ else:
+ return DataSet(
+ self,
+ type=self.get_dataset_type(resp[permid]["type"]["code"]),
+ data=resp[permid]
+ )
def get_sample(self, sample_ident, only_data=False, withAttachments=False):
"""Retrieve metadata for the sample.
@@ -1840,6 +1847,10 @@ class Openbis:
def new_dataset(self, type=type, files=None, props=None, **kwargs):
""" Creates a new dataset of a given sample type.
+ When working with OpenBIS releases before 16.05.04, updates to the
+ dataset object after newly creating them might not work correctly,
+ because the uploader plugin (for new dataSets) doesn't return the
+ new permId of that object.
"""
if files is None:
raise ValueError('please provide at least one file')
@@ -2340,7 +2351,7 @@ class DataSet(OpenBisObject):
def _generate_plugin_request(self, dss):
- """generates a request to activate the eln-lims ingestion plugin to
+ """generates a request to activate the dataset-uploader ingestion plugin to
register our files as a new dataset
"""
@@ -2361,10 +2372,9 @@ class DataSet(OpenBisObject):
"params": [
self.openbis.token,
dss,
- ELN_PLUGIN,
+ DATASET_UPLOADER_PLUGIN,
{
"method": "insertDataSet",
- "dataSetCode": None,
"sampleIdentifier": sample_identifier,
"experimentIdentifier": experiment_identifier,
"dataSetType": dataset_type,
@@ -2404,8 +2414,14 @@ class DataSet(OpenBisObject):
resp = self.openbis._post_request(self.openbis.reg_v1, request)
if resp['rows'][0][0]['value'] == 'OK':
- print("DataSet successfully created.")
- self
+ permId = resp['rows'][0][2]['value']
+ if permId is None or permId == '':
+ self.__dict__['is_new'] = False
+ print("DataSet successfully created. Because you connected to an openBIS version older than 16.05.04, you cannot update the object.")
+ else:
+ new_dataset_data = self.openbis.get_dataset(permId, only_data=True)
+ self._set_data(new_dataset_data)
+ print("DataSet successfully created.")
else:
raise ValueError('Error while creating the DataSet: ' + resp['rows'][0][1]['value'])
--
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