From 343ad6780e9ba820f302ea4e454271aa7097f6b7 Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <chandrasekhar.ramakrishnan@id.ethz.ch>
Date: Wed, 5 Apr 2017 17:22:12 +0200
Subject: [PATCH] SSDM-4670: Moving functionality for creating git data sets to
a separate module.
---
src/python/PyBis/pybis/data_set.py | 95 ++++++++++++++++++++++++++++++
src/python/PyBis/pybis/pybis.py | 63 ++------------------
2 files changed, 99 insertions(+), 59 deletions(-)
create mode 100644 src/python/PyBis/pybis/data_set.py
diff --git a/src/python/PyBis/pybis/data_set.py b/src/python/PyBis/pybis/data_set.py
new file mode 100644
index 00000000000..b53c039ee7a
--- /dev/null
+++ b/src/python/PyBis/pybis/data_set.py
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+data_set.py
+
+Module with functions for operating on data sets.
+
+
+Created by Chandrasekhar Ramakrishnan on 2017-04-05.
+Copyright (c) 2017 Chandrasekhar Ramakrishnan. All rights reserved.
+"""
+
+
+class GitDataSetCreation(object):
+ def __init__(self, openbis):
+ """Initialize the object with an openbis reference
+ :param openbis: The openBIS API object.
+ """
+ self.openbis = openbis
+
+ def new_git_data_set(self, data_set_type, path, commit_id, dms, sample=None, properties={},
+ dss_code=None, parents=None, data_set_code=None):
+ """ Create a link data set.
+ :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 dms: An external data managment system object or external_dms_id
+ :param sample: A sample object or sample id.
+ :param dss_code: Code for the DSS -- defaults to the first dss if none is supplied.
+ :param properties: Properties for the data set.
+ :param parents: Parents for the data set.
+ :param data_set_code: A data set code -- used if provided, otherwise generated on the server
+ :return: A DataSet object
+ """
+
+ if dss_code is None:
+ dss_code = self.openbis.get_datastores()['code'][0]
+
+ # if a sample identifier was given, use it as a string.
+ # if a sample object was given, take its identifier
+ sample_id = self.openbis.sample_to_sample_id(sample)
+ dms_id = self.openbis.external_data_managment_system_to_dms_id(dms)
+
+ parentIds = []
+ if parents is not None:
+ if not isinstance(parents, list):
+ parents = [parents]
+ parentIds = [self.openbis.data_set_to_data_set_id(parent) for parent in parents]
+
+ data_set_creation = {
+ "linkedData": {
+ "@type": "as.dto.dataset.create.LinkedDataCreation",
+ "contentCopies": [
+ {
+ "@type": "as.dto.dataset.create.ContentCopyCreation",
+ "path": path,
+ "gitCommitHash": commit_id,
+ "externalDmsId": dms_id
+ }
+ ]
+ },
+ "typeId": {
+ "@type": "as.dto.entitytype.id.EntityTypePermId",
+ "permId": data_set_type
+ },
+ "sampleId": sample_id,
+ "dataStoreId": {
+ "permId": dss_code,
+ "@type": "as.dto.datastore.id.DataStorePermId"
+ },
+ "parentIds": parentIds,
+ "measured": False,
+ "properties": properties,
+ "@type": "as.dto.dataset.create.DataSetCreation"
+ }
+ if data_set_code is not None:
+ data_set_creation['code'] = data_set_code
+ data_set_creation["autoGeneratedCode"] = False
+ else:
+ data_set_creation["autoGeneratedCode"] = True
+
+ # register the files in openBIS
+ request = {
+ "method": "createDataSets",
+ "params": [
+ self.openbis.token,
+ [data_set_creation]
+ ]
+ }
+
+ # noinspection PyProtectedMember
+ resp = self.openbis._post_request(self.openbis.as_v3, request)
+ return self.openbis.get_dataset(resp[0]['permId'])
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index 530a01578ce..7fead8c7f89 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -30,6 +30,7 @@ from tabulate import tabulate
from pybis.utils import parse_jackson, check_datatype, split_identifier, format_timestamp, is_identifier, is_permid, nvl
from pybis.property import PropertyHolder, PropertyAssignments
from pybis.masterdata import Vocabulary
+from . import data_set as pbds
import pandas as pd
from pandas import DataFrame, Series
@@ -1760,70 +1761,14 @@ class Openbis:
:param commit_id: The git commit id
:param dms: An external data managment system object or external_dms_id
:param sample: A sample object or sample id.
- :param dss_code: Code for the DSS -- defaults to the first dss if noe is supplied.
+ :param dss_code: Code for the DSS -- defaults to the first dss if none is supplied.
:param properties: Properties for the data set.
:param parents: Parents for the data set.
:param data_set_code: A data set code -- used if provided, otherwise generated on the server
:return: A DataSet object
"""
-
- if dss_code is None:
- dss_code = self.get_datastores()['code'][0]
-
- # if a sample identifier was given, use it as a string.
- # if a sample object was given, take its identifier
- sample_id = self.sample_to_sample_id(sample)
- dms_id = self.external_data_managment_system_to_dms_id(dms)
-
- parentIds = []
- if parents is not None:
- if not isinstance(parents, list):
- parents = [parents]
- parentIds = [self.data_set_to_data_set_id(parent) for parent in parents]
-
- data_set_creation = {
- "linkedData": {
- "@type": "as.dto.dataset.create.LinkedDataCreation",
- "contentCopies": [
- {
- "@type": "as.dto.dataset.create.ContentCopyCreation",
- "path": path,
- "gitCommitHash": commit_id,
- "externalDmsId": dms_id
- }
- ]
- },
- "typeId": {
- "@type": "as.dto.entitytype.id.EntityTypePermId",
- "permId": data_set_type
- },
- "sampleId": sample_id,
- "dataStoreId": {
- "permId": dss_code,
- "@type": "as.dto.datastore.id.DataStorePermId"
- },
- "parentIds": parentIds,
- "measured": False,
- "properties": properties,
- "@type": "as.dto.dataset.create.DataSetCreation"
- }
- if data_set_code is not None:
- data_set_creation['code'] = data_set_code
- data_set_creation["autoGeneratedCode"] = False
- else:
- data_set_creation["autoGeneratedCode"] = True
-
- # register the files in openBIS
- request = {
- "method": "createDataSets",
- "params": [
- self.token,
- [data_set_creation]
- ]
- }
-
- resp = self._post_request(self.as_v3, request)
- return self.get_dataset(resp[0]['permId'])
+ return pbds.GitDataSetCreation(self).new_git_data_set(data_set_type, path, commit_id, dms, sample,
+ properties, dss_code, parents, data_set_code)
@staticmethod
def sample_to_sample_id(sample):
--
GitLab