From b0dfee2df060e227a37b5a403fe30950c76164ca Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Tue, 6 Nov 2018 17:00:42 +0100
Subject: [PATCH] moved class PropertyAssignments to file
property_assignment.py and finally fixed _repr_html_ bug
---
pybis/src/python/pybis/experiment.py | 2 +-
pybis/src/python/pybis/openbis_object.py | 2 +-
pybis/src/python/pybis/plugin.py | 1 -
pybis/src/python/pybis/project.py | 1 -
pybis/src/python/pybis/property.py | 189 ++---------------------
pybis/src/python/pybis/sample_type.py | 2 +-
pybis/src/python/pybis/tag.py | 1 -
7 files changed, 14 insertions(+), 184 deletions(-)
diff --git a/pybis/src/python/pybis/experiment.py b/pybis/src/python/pybis/experiment.py
index eb54dc6fd08..b5102dd8bc2 100644
--- a/pybis/src/python/pybis/experiment.py
+++ b/pybis/src/python/pybis/experiment.py
@@ -1,4 +1,4 @@
-from .property import PropertyHolder, PropertyAssignments
+from .property import PropertyHolder
from .attribute import AttrHolder
from .openbis_object import OpenBisObject
from .definitions import openbis_definitions
diff --git a/pybis/src/python/pybis/openbis_object.py b/pybis/src/python/pybis/openbis_object.py
index d6e683a67f8..1bf0ffedbbb 100644
--- a/pybis/src/python/pybis/openbis_object.py
+++ b/pybis/src/python/pybis/openbis_object.py
@@ -1,4 +1,4 @@
-from .property import PropertyHolder, PropertyAssignments
+from .property import PropertyHolder
from .attribute import AttrHolder
class OpenBisObject():
diff --git a/pybis/src/python/pybis/plugin.py b/pybis/src/python/pybis/plugin.py
index 40cb11891ac..ea8d7e35d91 100644
--- a/pybis/src/python/pybis/plugin.py
+++ b/pybis/src/python/pybis/plugin.py
@@ -1,7 +1,6 @@
from .openbis_object import OpenBisObject
from .definitions import openbis_definitions, fetch_option
from .utils import VERBOSE
-from .property import PropertyHolder, PropertyAssignments
from .attribute import AttrHolder
import json
diff --git a/pybis/src/python/pybis/project.py b/pybis/src/python/pybis/project.py
index c3258740f84..60ee53ba918 100644
--- a/pybis/src/python/pybis/project.py
+++ b/pybis/src/python/pybis/project.py
@@ -1,4 +1,3 @@
-from .property import PropertyHolder, PropertyAssignments
from .attribute import AttrHolder
from .openbis_object import OpenBisObject
from .utils import VERBOSE
diff --git a/pybis/src/python/pybis/property.py b/pybis/src/python/pybis/property.py
index 1eeeebb572b..d8b084e1412 100644
--- a/pybis/src/python/pybis/property.py
+++ b/pybis/src/python/pybis/property.py
@@ -42,15 +42,17 @@ class PropertyHolder():
"""
if name.endswith('_'):
name = name.rstrip('_')
- property_type = self._type.prop[name]['propertyType']
- if property_type['dataType'] == 'CONTROLLEDVOCABULARY':
- return self._get_terms(property_type['vocabulary']['code'])
- else:
- syntax = { property_type["label"] : property_type["dataType"]}
- if property_type["dataType"] == "TIMESTAMP":
- syntax['syntax'] = 'YYYY-MM-DD HH:MIN:SS'
- return syntax
- else: return None
+ if name in self._type.prop:
+ property_type = self._type.prop[name]['propertyType']
+ if property_type['dataType'] == 'CONTROLLEDVOCABULARY':
+ return self._get_terms(property_type['vocabulary']['code'])
+ else:
+ syntax = { property_type["label"] : property_type["dataType"]}
+ if property_type["dataType"] == "TIMESTAMP":
+ syntax['syntax'] = 'YYYY-MM-DD HH:MIN:SS'
+ return syntax
+ return None
+
def __setattr__(self, name, value):
if name not in self._property_names:
@@ -123,172 +125,3 @@ class PropertyHolder():
])
return tabulate(lines, headers=headers)
-
-class PropertyAssignments():
- """ 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
- self.prop = {}
- if self.data['propertyAssignments'] is None:
- self.data['propertyAssignments'] = []
- for pa in self.data['propertyAssignments']:
- self.prop[pa['propertyType']['code'].lower()] = pa
-
- 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 ''
- else:
- return ''
-
- def __eq__(self, other):
- return str(self) == str(other)
-
- def __ne__(self, other):
- return str(self) != str(other)
-
-
- 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>
- """
-
-
- #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>
- <th>label</th>
- <th>description</th>
- <th>dataType</th>
- <th>mandatory</th>
- </tr>
- </thead>
- <tbody>
- """
-
- for pa in self.data['propertyAssignments']:
- html += "<tr> <th>{}</th> <td>{}</td> <td>{}</td> <td>{}</td> <td>{}</td> </tr>".format(
- pa['propertyType']['code'].lower(),
- pa['propertyType']['label'],
- pa['propertyType']['description'],
- pa['propertyType']['dataType'],
- pa['mandatory']
- )
-
- html += """
- </tbody>
- </table>
- """
- return html
-
- def __repr__(self):
- title = """
-{}: {}
-description: {}""".format (
- self.data['@type'].split('.')[-1],
- self.data['code'],
- self.data['description']
- )
-
- table = Texttable()
- table.set_deco(Texttable.HEADER)
-
- headers = ['code', 'label', 'description', 'dataType', 'mandatory']
-
- lines = []
- lines.append(headers)
- for pa in self.data['propertyAssignments']:
- lines.append([
- pa['propertyType']['code'].lower(),
- pa['propertyType']['label'],
- pa['propertyType']['description'],
- pa['propertyType']['dataType'],
- pa['mandatory']
- ])
- table.add_rows(lines)
- 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/sample_type.py b/pybis/src/python/pybis/sample_type.py
index 83491132777..59ca5beb9c7 100644
--- a/pybis/src/python/pybis/sample_type.py
+++ b/pybis/src/python/pybis/sample_type.py
@@ -1,4 +1,4 @@
-from .property import PropertyAssignments
+from .property_assignment import PropertyAssignments
from .semantic_annotation import SemanticAnnotation
class SampleType(PropertyAssignments):
diff --git a/pybis/src/python/pybis/tag.py b/pybis/src/python/pybis/tag.py
index 34e46577117..5f7cd9b1bf7 100644
--- a/pybis/src/python/pybis/tag.py
+++ b/pybis/src/python/pybis/tag.py
@@ -1,6 +1,5 @@
from .openbis_object import OpenBisObject
from .utils import VERBOSE
-from .property import PropertyHolder, PropertyAssignments
from .attribute import AttrHolder
import json
--
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