From 6cedbd6204838f1b7f43b66acd96bb0daa64826e Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Thu, 8 Aug 2019 17:42:59 +0200
Subject: [PATCH] re-implemented get_material_type, get_experiment_type,
get_dataset_type
---
pybis/src/python/pybis/pybis.py | 51 +++++++++++++++++++--------------
1 file changed, 29 insertions(+), 22 deletions(-)
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index f9b5316657e..a528693ab9a 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -2592,28 +2592,6 @@ class Openbis:
totalCount = resp.get('totalCount'),
)
-
- def get_experiment_type(self, type):
- try:
- return self._get_types_of(
- method_name = "searchExperimentTypes",
- entity = "Experiment",
- type_name = type
- )
- except Exception:
- raise ValueError("No such experiment type: {}".format(type))
- get_collection_type = get_experiment_type # Alias
-
- def get_material_type(self, type):
- try:
- return self._get_types_of(
- method_name = "searchMaterialTypes",
- entity = "Material",
- type_name = type
- )
- except Exception:
- raise ValueError("No such material type: {}".format(type))
-
def get_dataset_type(self, type):
return self._get_types_of(
method_name = "searchDataSetTypes",
@@ -2633,6 +2611,14 @@ class Openbis:
count = count
)
+ def get_material_type(self, type, only_data=False):
+ return self.get_entity_type(
+ entity = 'materialType',
+ cls = MaterialType,
+ identifier = type,
+ only_data = only_data,
+ )
+
def get_experiment_types(self, type=None, start_with=None, count=None):
""" Returns a list of all available experiment types
"""
@@ -2645,6 +2631,15 @@ class Openbis:
)
get_collection_types = get_experiment_types # Alias
+ def get_experiment_type(self, type, only_data=False):
+ return self.get_entity_type(
+ entity = 'experimentType',
+ cls = ExperimentType,
+ identifier = type,
+ only_data = only_data,
+ )
+ get_collection_type = get_experiment_type # Alias
+
def get_dataset_types(self, type=None, start_with=None, count=None):
""" Returns a list of all available dataSet types
"""
@@ -2656,6 +2651,14 @@ class Openbis:
count = count
)
+ def get_dataset_type(self, type, only_data=False):
+ return self.get_entity_type(
+ entity = 'dataSetType',
+ identifier = type,
+ cls = DataSetType,
+ only_data = only_data,
+ )
+
def get_sample_types(self, type=None, start_with=None, count=None):
""" Returns a list of all available sample types
"""
@@ -2673,6 +2676,7 @@ class Openbis:
entity = 'sampleType',
identifier = type,
cls = SampleType,
+ only_data = only_data,
)
get_object_type = get_sample_type # Alias
@@ -2712,11 +2716,14 @@ class Openbis:
entity_types = DataFrame(objects)
entity_types['permId'] = entity_types['permId'].map(extract_permid)
entity_types['modificationDate'] = entity_types['modificationDate'].map(format_timestamp)
+
+ single_item_method = getattr(self, cls._single_item_method_name)
return Things(
openbis_obj = self,
entity = entity,
df = entity_types[attrs],
start_with = start_with,
+ single_item_method = single_item_method,
count = count,
totalCount = resp.get('totalCount'),
)
--
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