From 7b1fe4d90f8b133a9aece0aca9c4a34995e7f92f Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 6 Feb 2013 14:47:59 +0000
Subject: [PATCH] CCS-30 SP-488 : Add connected entities as children of
protocols
SVN: 28306
---
.../ipad-read-service-v1/ipad_read.py | 75 ++++++++++++++++---
1 file changed, 63 insertions(+), 12 deletions(-)
diff --git a/openbis-ipad/ipad-example-data/ipad-ui-ylab/1/dss/reporting-plugins/ipad-read-service-v1/ipad_read.py b/openbis-ipad/ipad-example-data/ipad-ui-ylab/1/dss/reporting-plugins/ipad-read-service-v1/ipad_read.py
index 4e9317dcab7..b893351f5d9 100644
--- a/openbis-ipad/ipad-example-data/ipad-ui-ylab/1/dss/reporting-plugins/ipad-read-service-v1/ipad_read.py
+++ b/openbis-ipad/ipad-example-data/ipad-ui-ylab/1/dss/reporting-plugins/ipad-read-service-v1/ipad_read.py
@@ -3,6 +3,7 @@ from ch.systemsx.cisd.openbis.generic.shared.basic.dto import MaterialIdentifier
from com.fasterxml.jackson.databind import ObjectMapper
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
+from ch.systemsx.cisd.openbis.generic.shared.managed_property import ManagedPropertyFunctions
import codecs
@@ -262,14 +263,16 @@ def retrieve_sample_type_properties_definitions(sample_type):
definitions.sort(lambda x, y: cmp(x.getPositionInForms(), y.getPositionInForms()))
return definitions
-def properties_for_entity(entity, property_definitions, prop_names_set):
- """Extract the properties, in the correct order, for the entity. Restricting them to those in the prop_names_set, if it is non-empty"""
+def properties_for_entity_ignoring(entity, property_definitions, ignored_properties):
+ """Extract the properties, in the correct order, for the entity.
+
+ If ignored_properties is non-empty, do not include those"""
properties = []
- check_prop_names_set = len(prop_names_set) > 0
+ check_ignored_properties = len(ignored_properties) > 0
for propdef in property_definitions:
propcode = propdef.getPropertyTypeCode()
- # Only include the properties we explicitly specify
- if check_prop_names_set and propcode not in prop_names_set:
+ # Skip the properties that are designated to be ignored
+ if check_ignored_properties and propcode in ignored_properties:
continue
value = entity.getPropertyValue(propcode)
if value == u'\ufffd(undefined)':
@@ -278,6 +281,35 @@ def properties_for_entity(entity, property_definitions, prop_names_set):
properties.append(prop)
return properties
+def ordered_properties_for_sample_ignoring(sample, props_to_ignore):
+ property_definitions = retrieve_sample_type_properties_definitions(sample.getSampleType())
+ properties = properties_for_entity_ignoring(sample, property_definitions, props_to_ignore)
+ return properties
+
+def json_encoded_children_from_link_props(entity, link_props):
+ children = []
+ converter = ManagedPropertyFunctions.xmlPropertyConverter()
+ for prop in link_props:
+ elements = converter.convertStringToElements(entity.getPropertyValue(prop))
+ children.extend([element.getAttribute("permId") for element in elements])
+ return json_encoded_value(children)
+
+def replace_link_props_with_desc(entity, props_list, link_props):
+ converter = ManagedPropertyFunctions.xmlPropertyConverter()
+ for prop_key in link_props:
+ lines = []
+ elements = converter.convertStringToElements(entity.getPropertyValue(prop_key))
+ for element in elements:
+ line = u"" + element.getAttribute("name")
+ line = line + " [" + element.getAttribute("code") + "]"
+ line = line + " : " + element.getAttribute("quantity")
+ lines.append(line)
+ desc = u'\n'.join(lines)
+ for prop in props_list:
+ if prop['key'] == prop_key:
+ prop['value'] = desc
+ break
+
def marquee_image_spec_for_url(image_url):
return { 'MARQUEE' : { 'URL' : image_url } }
@@ -349,8 +381,13 @@ def navigation_layer(oligos, antibodies, chemicals, protocols, medias, pcrs, buf
westernBlotting_dict = western_blotting_navigation_layer(westernBlottings)
return [oligo_dict, antibody_dict, chemical_dict, protocol_dict, media_dict, pcr_dict, buffer_dict, plasmid_dict, yeast_dict, bacteria_dict, enzyme_dict, westernBlotting_dict]
-def sample_to_dict_with_props(sample, want_props):
- """Convert a sample to a dictionary. Uses the NAME property to construct the summary. Returns empty children. Callers may need to modify the summary and children as well"""
+def sample_to_dict_with_props_ignoring(sample, want_props, props_to_ignore):
+ """Convert a sample to a dictionary, ignoring the specified properties.
+
+ Uses the NAME property to construct the summary.
+ Returns empty children.
+ Callers may need to modify the summary and children as well
+ """
sample_dict = {}
sample_dict['SUMMARY_HEADER'] = sample.getCode()
name = sample.getPropertyValue("NAME")
@@ -371,13 +408,20 @@ def sample_to_dict_with_props(sample, want_props):
sample_dict['CHILDREN'] = json_encoded_value(children)
if want_props:
- property_definitions = retrieve_sample_type_properties_definitions(sample.getSampleType())
- properties_sample = properties_for_entity(sample, property_definitions, [])
+ properties_sample = ordered_properties_for_sample_ignoring(sample, props_to_ignore)
sample_dict['PROPERTIES'] = json_encoded_value(properties_sample)
- sample_dict['ROOT_LEVEL'] = None
- return sample_dict
+ sample_dict['ROOT_LEVEL'] = None
return sample_dict
+
+def sample_to_dict_with_props(sample, want_props):
+ """Convert a sample to a dictionary.
+
+ Uses the NAME property to construct the summary.
+ Returns empty children.
+ Callers may need to modify the summary and children as well
+ """
+ return sample_to_dict_with_props_ignoring(sample, want_props, [])
def oligo_to_dict(oligo, want_props):
@@ -400,7 +444,14 @@ def chemical_to_dict(chemical, want_props):
return sample_to_dict_with_props(chemical, want_props)
def protocol_to_dict(protocol, want_props):
- return sample_to_dict_with_props(protocol, want_props)
+ protocol_dict = sample_to_dict_with_props(protocol, False)
+ link_props = ["CHEMICALS", "SOLUTIONS_BUFFERS", "MEDIA", "GENERAL_PROTOCOL", "ENZYMES"]
+ protocol_dict['CHILDREN'] = json_encoded_children_from_link_props(protocol, link_props)
+ if want_props:
+ props = ordered_properties_for_sample_ignoring(protocol, [])
+ replace_link_props_with_desc(protocol, props, link_props)
+ protocol_dict['PROPERTIES'] = json_encoded_value(props)
+ return protocol_dict
def media_to_dict(media, want_props):
return sample_to_dict_with_props(media, want_props)
--
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