From 3b05e12161d55fbfc342f0b78a7d3d0ee7bf6d2b Mon Sep 17 00:00:00 2001
From: pkupczyk <pkupczyk>
Date: Tue, 21 Jan 2014 10:14:58 +0000
Subject: [PATCH] SP-1118 / BIS-628 : iPad App for Aebersold Lab
SVN: 30400
---
.../ipad-tag-browser-service/ipad_read.py | 182 ++++++++++++++----
1 file changed, 146 insertions(+), 36 deletions(-)
diff --git a/openbis-ipad/source/core-plugins/ipad-ui-tag-browser/1/dss/reporting-plugins/ipad-tag-browser-service/ipad_read.py b/openbis-ipad/source/core-plugins/ipad-ui-tag-browser/1/dss/reporting-plugins/ipad-tag-browser-service/ipad_read.py
index 04b7f3ebda0..edacba5e33a 100644
--- a/openbis-ipad/source/core-plugins/ipad-ui-tag-browser/1/dss/reporting-plugins/ipad-tag-browser-service/ipad_read.py
+++ b/openbis-ipad/source/core-plugins/ipad-ui-tag-browser/1/dss/reporting-plugins/ipad-tag-browser-service/ipad_read.py
@@ -7,16 +7,30 @@ 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, SearchSubCriteria
from java.util import Date
+from java.util import HashMap
from datetime import datetime
+##########
+# Request
+##########
+
+def getEntitiesParameter(handler):
+ entities = handler.getEntitiesParameter();
+ for entity in entities:
+ refcon = entity['REFCON']
+ if type(refcon) == str or type(refcon) == unicode:
+ refconMap = ObjectMapper().readValue(refcon, HashMap().getClass())
+ entity['REFCON'] = refconMap
+ return entities
+
###############
# Dictionaries
###############
def createTagDictionary(name, children):
dictionary = {}
- dictionary['PERM_ID'] = 'TAG#' + name.upper()
+ dictionary['PERM_ID'] = 'TAG.' + name.upper()
dictionary['CATEGORY'] = 'Navigation'
dictionary['SUMMARY_HEADER'] = name
dictionary['SUMMARY'] = None
@@ -29,41 +43,41 @@ def createTagDictionary(name, children):
return dictionary
-def createMaterialDictionary(material):
+def createExperimentDictionary(experiment):
dictionary = {}
- dictionary['PERM_ID'] = 'MATERIAL#' + material.getMaterialIdentifier()
- dictionary['CATEGORY'] = 'Material ' + material.getMaterialType()
- dictionary['SUMMARY_HEADER'] = material.getCode()
- dictionary['SUMMARY'] = material.getPropertyValue("DESC")
- dictionary['IDENTIFIER'] = material.getMaterialIdentifier()
- dictionary['IMAGES'] = []
- dictionary['CHILDREN'] = []
+ dictionary['PERM_ID'] = 'EXPERIMENT.' + experiment.getPermId()
+ dictionary['CATEGORY'] = 'Experiment ' + experiment.getExperimentType()
+ dictionary['SUMMARY_HEADER'] = experiment.getExperimentIdentifier()
+ dictionary['SUMMARY'] = None
+ dictionary['IDENTIFIER'] = experiment.getExperimentIdentifier()
+ dictionary['IMAGES'] = IpadServiceUtilities.jsonEncodedValue([])
+ dictionary['CHILDREN'] = IpadServiceUtilities.jsonEncodedValue([])
dictionary['ROOT_LEVEL'] = None
refcon = {}
- refcon['ENTITY_TYPE'] = 'MATERIAL'
- refcon['CODE'] = material.getCode()
- refcon['TYPE_CODE'] = material.getMaterialType();
+ refcon['ENTITY_TYPE'] = 'EXPERIMENT'
+ # there is no way to get an experiment by a permanent id
+ refcon['IDENTIFIER'] = experiment.getExperimentIdentifier()
dictionary['REFCON'] = IpadServiceUtilities.jsonEncodedValue(refcon)
return dictionary
-
-def createMaterialDetailedDictionary(material):
- dictionary = createMaterialDictionary(material)
- propertyDefinitions = getPropertyDefinitions(material.getMaterialType(), searchService.listPropertiesDefinitionsForMaterialType)
- properties = getProperties(material, propertyDefinitions)
+
+def createExperimentDetailedDictionary(experiment):
+ dictionary = createExperimentDictionary(experiment)
+ propertyDefinitions = getPropertyDefinitions(experiment.getExperimentType(), searchService.listPropertiesDefinitionsForExperimentType)
+ properties = getProperties(experiment, propertyDefinitions)
dictionary['PROPERTIES'] = IpadServiceUtilities.jsonEncodedValue(properties)
return dictionary
def createSampleDictionary(sample):
dictionary = {}
- dictionary['PERM_ID'] = 'SAMPLE#' + sample.getPermId()
+ dictionary['PERM_ID'] = 'SAMPLE.' + sample.getPermId()
dictionary['CATEGORY'] = 'Sample ' + sample.getSampleType()
- dictionary['SUMMARY_HEADER'] = sample.getCode()
- dictionary['SUMMARY'] = sample.getPropertyValue("DESC")
+ dictionary['SUMMARY_HEADER'] = sample.getSampleIdentifier()
+ dictionary['SUMMARY'] = None
dictionary['IDENTIFIER'] = sample.getSampleIdentifier()
- dictionary['IMAGES'] = []
- dictionary['CHILDREN'] = []
+ dictionary['IMAGES'] = IpadServiceUtilities.jsonEncodedValue([])
+ dictionary['CHILDREN'] = IpadServiceUtilities.jsonEncodedValue([])
dictionary['ROOT_LEVEL'] = None
refcon = {}
@@ -79,14 +93,67 @@ def createSampleDetailedDictionary(sample):
properties = getProperties(sample, propertyDefinitions)
dictionary['PROPERTIES'] = IpadServiceUtilities.jsonEncodedValue(properties)
return dictionary
+
+def createDataSetDictionary(dataSet):
+ dictionary = {}
+ dictionary['PERM_ID'] = 'DATA_SET.' + dataSet.getDataSetCode()
+ dictionary['CATEGORY'] = 'Data set ' + dataSet.getDataSetType()
+ dictionary['SUMMARY_HEADER'] = dataSet.getDataSetCode()
+ dictionary['SUMMARY'] = None
+ dictionary['IDENTIFIER'] = dataSet.getDataSetCode()
+ dictionary['IMAGES'] = IpadServiceUtilities.jsonEncodedValue([])
+ dictionary['CHILDREN'] = IpadServiceUtilities.jsonEncodedValue([])
+ dictionary['ROOT_LEVEL'] = None
+
+ refcon = {}
+ refcon['ENTITY_TYPE'] = 'DATA_SET'
+ refcon['CODE'] = dataSet.getDataSetCode()
+ dictionary['REFCON'] = IpadServiceUtilities.jsonEncodedValue(refcon)
+
+ return dictionary
+def createDataSetDetailedDictionary(dataSet):
+ dictionary = createDataSetDictionary(dataSet)
+ propertyDefinitions = getPropertyDefinitions(dataSet.getDataSetType(), searchService.listPropertiesDefinitionsForDataSetType)
+ properties = getProperties(dataSet, propertyDefinitions)
+ dictionary['PROPERTIES'] = IpadServiceUtilities.jsonEncodedValue(properties)
+ return dictionary
+
+def createMaterialDictionary(material):
+ dictionary = {}
+ dictionary['PERM_ID'] = 'MATERIAL.' + material.getMaterialIdentifier()
+ dictionary['CATEGORY'] = 'Material ' + material.getMaterialType()
+ dictionary['SUMMARY_HEADER'] = material.getMaterialIdentifier()
+ dictionary['SUMMARY'] = None
+ dictionary['IDENTIFIER'] = material.getMaterialIdentifier()
+ dictionary['IMAGES'] = IpadServiceUtilities.jsonEncodedValue([])
+ dictionary['CHILDREN'] = IpadServiceUtilities.jsonEncodedValue([])
+ dictionary['ROOT_LEVEL'] = None
+
+ refcon = {}
+ refcon['ENTITY_TYPE'] = 'MATERIAL'
+ refcon['CODE'] = material.getCode()
+ refcon['TYPE_CODE'] = material.getMaterialType();
+ dictionary['REFCON'] = IpadServiceUtilities.jsonEncodedValue(refcon)
+
+ return dictionary
+
+def createMaterialDetailedDictionary(material):
+ dictionary = createMaterialDictionary(material)
+ propertyDefinitions = getPropertyDefinitions(material.getMaterialType(), searchService.listPropertiesDefinitionsForMaterialType)
+ properties = getProperties(material, propertyDefinitions)
+ dictionary['PROPERTIES'] = IpadServiceUtilities.jsonEncodedValue(properties)
+ return dictionary
+
+
#########
# Entity
#########
-def getExperiment(permId):
- pass
-
+def getExperiment(identifier):
+ # there is no way to get an experiment by a permanent id
+ return searchService.getExperiment(identifier)
+
def getSample(permId):
criteria = SearchCriteria()
criteria.setOperator(criteria.SearchOperator.MATCH_ANY_CLAUSES)
@@ -98,10 +165,17 @@ def getSample(permId):
return None
def getDataSet(code):
- pass
+ criteria = SearchCriteria()
+ criteria.setOperator(criteria.SearchOperator.MATCH_ANY_CLAUSES)
+ criteria.addMatchClause(criteria.MatchClause.createAttributeMatch(criteria.MatchClauseAttribute.CODE, code))
+ datasets = searchService.searchForDataSets(criteria)
+ if datasets:
+ return datasets[0]
+ else:
+ return None
def getMaterial(code, typeCode):
- pass
+ return searchService.getMaterial(code, typeCode)
####################
# Entity Properties
@@ -115,11 +189,13 @@ def getPropertyDefinitions(typeCode, searchFunction):
def getProperties(entity, propertyDefinitions):
properties = []
for propertyDefinition in propertyDefinitions:
- properties.append({
- 'key' : propertyDefinition.getPropertyTypeCode(),
- 'label' : propertyDefinition.getPropertyTypeLabel(),
- 'value' : entity.getPropertyValue(propertyDefinition.getPropertyTypeCode())
- })
+ propertyValue = entity.getPropertyValue(propertyDefinition.getPropertyTypeCode())
+ if propertyValue:
+ properties.append({
+ 'key' : propertyDefinition.getPropertyTypeCode(),
+ 'label' : propertyDefinition.getPropertyTypeLabel(),
+ 'value' : propertyValue
+ })
return properties
###################
@@ -137,13 +213,33 @@ class TagRootRequestHandler(RootRequestHandler):
"""Handler for the ROOT request."""
def addDataRows(self):
- tagsPermIdsAndRefcons = self.getEntitiesParameter()
+ tagsPermIdsAndRefcons = getEntitiesParameter(self)
if tagsPermIdsAndRefcons:
tagName = tagsPermIdsAndRefcons[0]['REFCON']['NAME']
- samples = self.searchService.getMetaprojectAssignments(tagName).getSamples();
- self.addRows([createTagDictionary(tagName, [sample.getPermId() for sample in samples])])
+ tagAssignments = self.searchService.getMetaprojectAssignments(tagName)
+
+ experiments = tagAssignments.getExperiments();
+ samples = tagAssignments.getSamples();
+ dataSets = tagAssignments.getDataSets();
+ materials = tagAssignments.getMaterials();
+
+ tagChildren = []
+
+ for experiment in experiments:
+ tagChildren.append('EXPERIMENT.' + experiment.getPermId())
+ for sample in samples:
+ tagChildren.append('SAMPLE.' + sample.getPermId())
+ for dataSet in dataSets:
+ tagChildren.append('DATA_SET.' + dataSet.getDataSetCode())
+ for material in materials:
+ tagChildren.append('MATERIAL.' + material.getMaterialIdentifier())
+
+ self.addRows([createTagDictionary(tagName, tagChildren)])
+ self.addRows([createExperimentDictionary(experiment) for experiment in experiments])
self.addRows([createSampleDictionary(sample) for sample in samples])
+ self.addRows([createDataSetDictionary(dataSet) for dataSet in dataSets])
+ self.addRows([createMaterialDictionary(material) for material in materials])
class TagDrillRequestHandler(DrillRequestHandler):
"""Handler for the DRILL request."""
@@ -152,15 +248,24 @@ class TagDetailRequestHandler(DetailRequestHandler):
"""Handler for the DETAIL request."""
def addDataRows(self):
- entitiesPermIdsAndRefcons = self.getEntitiesParameter()
+ entitiesPermIdsAndRefcons = getEntitiesParameter(self)
if entitiesPermIdsAndRefcons:
entityRefcon = entitiesPermIdsAndRefcons[0]['REFCON']
entityType = entityRefcon['ENTITY_TYPE'];
+ if 'EXPERIMENT' == entityType:
+ experiment = getExperiment(entityRefcon['IDENTIFIER'])
+ self.addRows([createExperimentDetailedDictionary(experiment)])
if 'SAMPLE' == entityType:
sample = getSample(entityRefcon['PERM_ID'])
self.addRows([createSampleDetailedDictionary(sample)])
+ if 'DATA_SET' == entityType:
+ dataSet = getDataSet(entityRefcon['CODE'])
+ self.addRows([createDataSetDetailedDictionary(dataSet)])
+ if 'MATERIAL' == entityType:
+ material = getMaterial(entityRefcon['CODE'], entityRefcon['TYPE_CODE'])
+ self.addRows([createMaterialDetailedDictionary(material)])
class TagSearchRequestHandler(SearchRequestHandler):
"""Handler for the SEARCH request"""
@@ -168,8 +273,13 @@ class TagSearchRequestHandler(SearchRequestHandler):
def addDataRows(self):
criteria = self.trySearchCriteria()
if criteria:
+ # there is no way to search for experiments and materials
+
samples = self.searchService.searchForSamples(criteria)
self.addRows([createSampleDictionary(sample) for sample in samples])
+
+ dataSets = self.searchService.searchForDataSets(criteria)
+ self.addRows([createDataSetDictionary(dataSet) for dataSet in dataSets])
####################
# Request Factories
--
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