From 988a635353215a7b85d930ca592e0da9e148fb0c Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Thu, 28 Feb 2019 16:08:38 +0100
Subject: [PATCH] changed property assignments
---
pybis/src/python/pybis/entity_types.py | 110 ++++++++++++++++++
pybis/src/python/pybis/property_assignment.py | 12 +-
pybis/src/python/pybis/pybis.py | 55 +++++----
3 files changed, 152 insertions(+), 25 deletions(-)
create mode 100644 pybis/src/python/pybis/entity_types.py
diff --git a/pybis/src/python/pybis/entity_types.py b/pybis/src/python/pybis/entity_types.py
new file mode 100644
index 00000000000..aa6207615ec
--- /dev/null
+++ b/pybis/src/python/pybis/entity_types.py
@@ -0,0 +1,110 @@
+from tabulate import tabulate
+from texttable import Texttable
+from pybis.utils import check_datatype, split_identifier, format_timestamp, is_identifier, is_permid, nvl
+from pandas import DataFrame
+
+
+class EntityType():
+ """ holds are properties, that are assigned to an entity, eg. sample or experiment
+ """
+
+ def __init__(self, openbis_obj, data):
+ self.openbis = openbis_obj
+ self.data = data
+
+ def __str__(self):
+ """String representation of this entity type
+ """
+ return self.data['code']
+
+ def _attrs(self):
+ return ['code', 'description', 'autoGeneratedCode', 'subcodeUnique',
+ 'generatedCodePrefix', 'listable', 'showContainer', 'showParents',
+ 'showParentMetadata', 'validationPlugin']
+
+ 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 __eq__(self, other):
+ return str(self) == str(other)
+
+ def __ne__(self, other):
+ return str(self) != str(other)
+
+ def get_propertyAssignments(self):
+ attrs = ['code', 'label', 'description', 'dataType', 'mandatory', 'showInEditView', 'ordinal']
+ pas = [ {**pa['propertyType'], **pa} for pa in self.data['propertyAssignments'] ]
+ return DataFrame(pas, columns=attrs)
+
+ def codes(self):
+ codes = []
+ for pa in self.data['propertyAssignments']:
+ codes.append(pa['propertyType']['code'].lower())
+ return codes
+
+
+ def _repr_html_(self):
+ def nvl(val, string=''):
+ if val is None:
+ return string
+ return val
+
+ html = "<p>{}: <b>{}</b>".format(
+ self.data['@type'].split('.')[-1],
+ self.data['code'],
+ )
+
+ 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():
+ if attr == 'validationPlugin':
+ continue
+ html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
+ attr, nvl(getattr(self, attr, ''), '')
+ )
+
+ html += """
+ </tbody>
+ </table>
+ """
+
+ if self.validationPlugin:
+ html += "<p/><b>Validation Plugin</b>"
+ html += """
+ <table border="1" class="dataframe">
+ <thead>
+ <tr style="text-align: right;">
+ <th>attribute</th>
+ <th>value</th>
+ </tr>
+ </thead>
+ <tbody>
+ """
+ for attr in ['name', 'description', 'pluginType', 'pluginKind',
+ 'available', 'entityKinds']:
+ html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
+ attr, self.validationPlugin.get(attr)
+ )
+ html += """
+ </tbody>
+ </table>
+ """
+
+ return html
+
diff --git a/pybis/src/python/pybis/property_assignment.py b/pybis/src/python/pybis/property_assignment.py
index fd821c05ca9..7b4ca0a1611 100644
--- a/pybis/src/python/pybis/property_assignment.py
+++ b/pybis/src/python/pybis/property_assignment.py
@@ -1,6 +1,7 @@
from tabulate import tabulate
from texttable import Texttable
from pybis.utils import check_datatype, split_identifier, format_timestamp, is_identifier, is_permid, nvl
+from pandas import DataFrame
class PropertyAssignments():
@@ -42,6 +43,10 @@ class PropertyAssignments():
def __ne__(self, other):
return str(self) != str(other)
+ def get_propertyAssignments(self):
+ attrs = ['code', 'dataType', 'description', 'label', 'mandatory', 'ordinal']
+ pas = [ {**pa['propertyType'], **pa} for pa in self.data['propertyAssignments'] ]
+ return DataFrame(pas, columns=attrs)
def codes(self):
codes = []
@@ -109,11 +114,7 @@ class PropertyAssignments():
#if 'autoGeneratedCode' in self.data:
# html += "<p>Code autogenerated: {}</p>".format(
- # self.data['autoGeneratedCode'])
-
- html += """
- <p><b>Property Assignments</b>
-<table border="1" class="dataframe">
+ """
<thead>
<tr style="text-align: right;">
<th>property</th>
@@ -169,3 +170,4 @@ description: {}""".format (
table.set_cols_width([28,28,28,28,9])
table.set_cols_align(['l','l','l','l','l'])
return title + "\n\n" + table.draw()
+
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 2360ab72ebc..7cbd24f3261 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -30,7 +30,7 @@ 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
-from .property_assignment import PropertyAssignments
+from .entity_types import EntityType
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
@@ -2099,7 +2099,9 @@ class Openbis:
return Things(self, 'tag', tags[attrs], 'permId')
- def search_semantic_annotations(self, permId=None, entityType=None, propertyType=None, only_data = False):
+ def search_semantic_annotations(self,
+ permId=None, entityType=None, propertyType=None, only_data=False
+ ):
""" Get a list of semantic annotations for permId, entityType, propertyType or
property type assignment (DataFrame object).
:param permId: permId of the semantic annotation.
@@ -2323,10 +2325,10 @@ class Openbis:
""" Returns a list of all available sample types
"""
return self._get_types_of(
- "searchSampleTypes",
- "Sample",
- type,
- ["generatedCodePrefix"]
+ method_name = "searchSampleTypes",
+ entity = "Sample",
+ type_name = type,
+ optional_attributes = ["generatedCodePrefix"]
)
get_object_types = get_sample_types # Alias
@@ -2334,10 +2336,10 @@ class Openbis:
def get_sample_type(self, type):
try:
property_asignments = self._get_types_of(
- "searchSampleTypes",
- "Sample",
- type,
- ["generatedCodePrefix", "validationPluginId"]
+ method_name = "searchSampleTypes",
+ entity = "Sample",
+ type_name = type,
+ optional_attributes = ["generatedCodePrefix", "validationPluginId"]
)
return SampleType(self, property_asignments.data)
except Exception:
@@ -2349,9 +2351,9 @@ class Openbis:
""" Returns a list of all available experiment types
"""
return self._get_types_of(
- "searchExperimentTypes",
- "Experiment",
- type
+ method_name = "searchExperimentTypes",
+ entity = "Experiment",
+ type_name = type
)
get_collection_types = get_experiment_types # Alias
@@ -2359,9 +2361,9 @@ class Openbis:
def get_experiment_type(self, type):
try:
return self._get_types_of(
- "searchExperimentTypes",
- "Experiment",
- type
+ method_name = "searchExperimentTypes",
+ entity = "Experiment",
+ type_name = type
)
except Exception:
raise ValueError("No such experiment type: {}".format(type))
@@ -2371,11 +2373,19 @@ class Openbis:
def get_material_types(self, type=None):
""" Returns a list of all available material types
"""
- return self._get_types_of("searchMaterialTypes", "Material", type)
+ return self._get_types_of(
+ method_name = "searchMaterialTypes",
+ entity = "Material",
+ type_name = type
+ )
def get_material_type(self, type):
try:
- return self._get_types_of("searchMaterialTypes", "Material", type)
+ return self._get_types_of(
+ method_name = "searchMaterialTypes",
+ entity = "Material",
+ type_name = type
+ )
except Exception:
raise ValueError("No such material type: {}".format(type))
@@ -2386,7 +2396,12 @@ class Openbis:
def get_dataset_type(self, type):
try:
- return self._get_types_of("searchDataSetTypes", "DataSet", type, optional_attributes=['kind'])
+ return self._get_types_of(
+ method_name = "searchDataSetTypes",
+ entity = "DataSet",
+ type_name = type,
+ optional_attributes = ['kind']
+ )
except Exception:
raise ValueError("No such dataSet type: {}".format(type))
@@ -2424,7 +2439,7 @@ class Openbis:
parse_jackson(resp)
if type_name is not None and len(resp['objects']) == 1:
- return PropertyAssignments(
+ return EntityType(
openbis_obj = self,
data = resp['objects'][0]
)
--
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