From dae3cefa56f250eda1672a0a52840fb8be0f36d6 Mon Sep 17 00:00:00 2001
From: "Fuentes Serna Juan Mariano (ID SIS)" <juanf@bs-mbpr28.d.ethz.ch>
Date: Tue, 11 Dec 2018 15:47:34 +0100
Subject: [PATCH] SSDM-6975 : Dynamic properties
---
.../1/as/master-data/data-model.xls | Bin 103424 -> 102912 bytes
.../scripts}/genetic_modifications.py | 8 +-
.../1/as/webapps/eln-lims/html/index.html | 2 +-
.../eln-lims/html/js/config/Profile.js | 2 +-
...echnology.js => LifeSciencesTechnology.js} | 12 +-
.../eln-lims/1/compatibility/comments.py | 183 ------------
.../eln-lims/1/compatibility/managed.py | 267 ------------------
.../1/compatibility/requests_children_code.py | 14 -
8 files changed, 12 insertions(+), 476 deletions(-)
rename openbis_standard_technologies/dist/core-plugins/{eln-lims/1/compatibility => eln-lims-life-sciences/1/as/master-data/scripts}/genetic_modifications.py (92%)
rename openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/{BiologyTechnology.js => LifeSciencesTechnology.js} (88%)
delete mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/comments.py
delete mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/managed.py
delete mode 100644 openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/requests_children_code.py
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls
index fcb9ea57fb21fb635024372cb7a862d01a076864..e48c6791cc01af5e22d312990581b33b826836ad 100644
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diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/genetic_modifications.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/scripts/genetic_modifications.py
similarity index 92%
rename from openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/genetic_modifications.py
rename to openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/scripts/genetic_modifications.py
index b91679ab633..0739e95afae 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/genetic_modifications.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/scripts/genetic_modifications.py
@@ -37,7 +37,7 @@ def calculate():
parentCode = parent.code()
#Add the code
annotationMap = getAnnotationsForParent(parent, child)
- if(annotationMap["PLASMID_RELATIONSHIP"] == "LOT"):
+ if(annotationMap["ANNOTATION.SYSTEM.PLASMID_RELATIONSHIP"] == "LOT"):
newLostList.append(parent.entityPE().getPermId())
elif parent.entityPE().getPermId() not in lostList:
#Check if is the first to add the separator or not
@@ -58,16 +58,16 @@ def calculate():
return genotypeResult
def getAnnotationString(annotationMap):
- return annotationMap["PLASMID_RELATIONSHIP"] + " " + annotationMap["PLASMID_ANNOTATION"]
+ return annotationMap["ANNOTATION.SYSTEM.PLASMID_RELATIONSHIP"] + " " + annotationMap["ANNOTATION.SYSTEM.PLASMID_ANNOTATION"]
def getAnnotationsForParent(parent, child):
permId = parent.entityPE().getPermId()
annotations = child.propertyValue("ANNOTATIONS_STATE")
if (annotations is not None) and ('<root' in annotations):
- relationshipValue = getAnnotationFromPermId(annotations, permId, "PLASMID_RELATIONSHIP")
+ relationshipValue = getAnnotationFromPermId(annotations, permId, "ANNOTATION.SYSTEM.PLASMID_RELATIONSHIP")
if relationshipValue is None:
relationshipValue = "None"
- annotationValue = getAnnotationFromPermId(annotations, permId, "PLASMID_ANNOTATION");
+ annotationValue = getAnnotationFromPermId(annotations, permId, "ANNOTATION.SYSTEM.PLASMID_ANNOTATION");
if annotationValue is None:
annotationValue = ""
annotation = "\"" + str(annotationValue) + "\""
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html
index cd590405472..50c5bd15300 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html
@@ -262,7 +262,7 @@
<script type="text/javascript" src="./js/plugins/ELNLIMSPlugin.js"></script>
<script type="text/javascript" src="./js/plugins/GenericTechnology.js"></script>
- <script type="text/javascript" src="./js/plugins/BiologyTechnology.js"></script>
+ <script type="text/javascript" src="./js/plugins/LifeSciencesTechnology.js"></script>
<script type="text/javascript" src="./js/plugins/MicroscopyTechnology.js"></script>
<script type="text/javascript">
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
index 1350c50b9cc..53fb5118d6c 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
@@ -133,7 +133,7 @@ $.extend(DefaultProfile.prototype, {
// "ADMIN-BS-MBPR28.D.ETHZ.CH-E96954A7" : "http://localhost:8080/download"
}
- this.plugins = [new GenericTechnology(), new BiologyTechnology(), new MicroscopyTechnology()];
+ this.plugins = [new GenericTechnology(), new LifeSciencesTechnology(), new MicroscopyTechnology()];
this.sampleFormTop = function($container, model) {
for(var i = 0; i < this.plugins.length; i++) {
this.plugins[i].sampleFormTop($container, model);
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/BiologyTechnology.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/LifeSciencesTechnology.js
similarity index 88%
rename from openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/BiologyTechnology.js
rename to openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/LifeSciencesTechnology.js
index c7dfec2ec05..d064fe15a72 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/BiologyTechnology.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/plugins/LifeSciencesTechnology.js
@@ -1,8 +1,8 @@
-function BiologyTechnology() {
+function LifeSciencesTechnology() {
this.init();
}
-$.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
+$.extend(LifeSciencesTechnology.prototype, ELNLIMSPlugin.prototype, {
init: function() {
},
@@ -151,7 +151,7 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Plasmid",
"TYPE": "PLASMID",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.PLASMID.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.PLASMID.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
}
],
},
@@ -169,7 +169,7 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Plasmid",
"TYPE": "PLASMID",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.PLASMID.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.PLASMID.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
}
],
},
@@ -187,7 +187,7 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Plasmid",
"TYPE": "PLASMID",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.PLASMID.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.PLASMID.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
},
{
"LABEL" : "Parental fly",
@@ -211,7 +211,7 @@ $.extend(BiologyTechnology.prototype, ELNLIMSPlugin.prototype, {
"LABEL" : "Plasmid",
"TYPE": "PLASMID",
"MIN_COUNT" : 0,
- "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.PLASMID.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.PLASMID.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
+ "ANNOTATION_PROPERTIES" : [{"TYPE" : "ANNOTATION.SYSTEM.PLASMID_RELATIONSHIP", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.PLASMID_ANNOTATION", "MANDATORY" : false },{"TYPE" : "ANNOTATION.SYSTEM.COMMENTS", "MANDATORY" : false }]
}
],
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/comments.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/comments.py
deleted file mode 100644
index 396f3acb179..00000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/comments.py
+++ /dev/null
@@ -1,183 +0,0 @@
-from java.util import Date
-
-"""
-Example XML property value handled by this script:
-<root>
- <commentEntry date="2011-02-20 14:15:28 GMT+01:00" person="buczekp">Here is the 1st entry text.<commentEntry>
- <commentEntry date="2011-02-20 14:16:28 GMT+01:00" person="kohleman">Here is the 2nd entry text - a warning!<commentEntry>
- <commentEntry date="2011-02-20 14:17:28 GMT+01:00" person="tpylak">Here is the 3rd entry text - an error!!!<commentEntry>
- <commentEntry date="2011-02-20 14:18:28 GMT+01:00" person="brinn">Here is the 4th entry text - an error!!!<commentEntry>
- <commentEntry date="2011-02-20 14:19:28 GMT+01:00" person="felmer">Here is the 5th entry text - a warning!<commentEntry>
-</root>
-"""
-##
-## Configuration
-##
-COMMENT_ENTRY_ELEMENT_LABEL = 'commentEntry'
-
-""" labels of table columns and corresponding input fields """
-DATE_LABEL = 'Date'
-PERSON_LABEL = 'Person'
-COMMENT_TEXT_LABEL = 'Comment Text'
-
-""" names of attributes of XML elements for comment entries """
-DATE_ATTRIBUTE = 'date'
-PERSON_ATTRIBUTE = 'person'
-
-""" action labels (shown as button labels in UI) """
-ADD_ACTION_LABEL = 'Add Comment Entry'
-EDIT_ACTION_LABEL = 'Edit'
-DELETE_ACTION_LABEL = 'Delete'
-
-##
-## Main Methods
-##
-def configureUI():
- """Create table builder and add headers of columns."""
- builder = createTableBuilder()
- builder.addHeader(DATE_LABEL, 250) # date and comment text values are long, override default width (150)
- builder.addHeader(PERSON_LABEL)
- builder.addHeader(COMMENT_TEXT_LABEL, 400)
-
- """
- Extract XML elements from property value to a Python list.
- For each element (comment entry) add add a row to the table.
- """
- elements = list(propertyConverter().convertToElements(property))
- for commentEntry in elements:
- row = builder.addRow()
- row.setCell(DATE_LABEL, Date(long(commentEntry.getAttribute(DATE_ATTRIBUTE))))
- row.setCell(PERSON_LABEL, commentEntry.getAttribute(PERSON_ATTRIBUTE))
- row.setCell(COMMENT_TEXT_LABEL, commentEntry.getData())
-
- """Specify that the property should be shown in a tab and set the table output."""
- property.setOwnTab(True)
- uiDescription = property.getUiDescription()
- uiDescription.useTableOutput(builder.getTableModel())
-
- """
- Define and add actions with input fields used to:
- 1. specify attributes of new comment entry,
- """
- addAction = uiDescription.addTableAction(ADD_ACTION_LABEL)\
- .setDescription('Add a new comment entry:')
- widgets = [
- inputWidgetFactory().createMultilineTextInputField(COMMENT_TEXT_LABEL)\
- .setMandatory(True)
- ]
- addAction.addInputWidgets(widgets)
-
- """
- 2. modify attributes of a selected comment entry,
- """
- editAction = uiDescription.addTableAction(EDIT_ACTION_LABEL)\
- .setDescription('Edit selected comment entry:')
- # Exactly 1 row needs to be selected to enable action.
- editAction.setRowSelectionRequiredSingle()
- widgets = [
- inputWidgetFactory().createMultilineTextInputField(COMMENT_TEXT_LABEL).setMandatory(True)
- ]
- editAction.addInputWidgets(widgets)
- # Bind field name with column name.
- editAction.addBinding(COMMENT_TEXT_LABEL, COMMENT_TEXT_LABEL)
-
- """
- 3. delete selected comment entries.
- """
- deleteAction = uiDescription.addTableAction(DELETE_ACTION_LABEL)\
- .setDescription('Are you sure you want to delete selected comment entry?')
- # Delete is enabled when at least 1 row is selected.
- deleteAction.setRowSelectionRequired()
-
-
-def updateFromUI(action):
- """Extract list of elements from old value of the property."""
- converter = propertyConverter()
- elements = list(converter.convertToElements(property))
-
- """Implement behaviour of user actions."""
- if action.name == ADD_ACTION_LABEL:
- """
- For 'add' action create new comment entry element with values from input fields
- and add it to existing elements.
- """
- element = elementFactory().createElement(COMMENT_ENTRY_ELEMENT_LABEL)
- """Fill element attributes with appropriate values."""
- element.addAttribute(DATE_ATTRIBUTE, str(Date().getTime())) # current date
- element.addAttribute(PERSON_ATTRIBUTE, action.getPerson().getUserId()) # invoker the action
- """Retrieve values from input fields filled by user on the client side."""
-
- """Set comment text as a text element, not an attribute."""
- element.setData(action.getInputValue(COMMENT_TEXT_LABEL))
- """Add the new entry to the end of the element list."""
- elements.append(element)
- elif action.name == EDIT_ACTION_LABEL:
- """
- For 'edit' action find the comment entry element corresponding to selected row
- and replace it with an element with values from input fields.
- """
-
- selectedRowId = action.getSelectedRows()[0]
- xmlUser = elements[selectedRowId].getAttribute(PERSON_ATTRIBUTE)
- if action.getPerson().getUserId() == xmlUser:
- elements[selectedRowId].setData(action.getInputValue(COMMENT_TEXT_LABEL))
- else:
- raise ValidationException('Comment creator and current user differ:\n' + str(xmlUser) + "!=" + str(action.getPerson().getUserId()) )
- elif action.name == DELETE_ACTION_LABEL:
- """
- For 'delete' action delete the entries that correspond to selected rows.
- NOTE: As many rows can be deleted at once it is easier to delete them in reversed order.
- """
- rowIds = list(action.getSelectedRows())
- rowIds.reverse()
- for rowId in rowIds:
- xmlUser = elements[rowId].getAttribute(PERSON_ATTRIBUTE)
- if action.getPerson().getUserId() == xmlUser:
- elements.pop(rowId)
- else:
- raise ValidationException('Comment creator and current user differ:\n' + str(xmlUser) + "!=" + str(action.getPerson().getUserId()) )
- else:
- raise ValidationException('action not supported')
-
- """Update value of the managed property to XML string created from modified list of elements."""
- property.value = converter.convertToString(elements)
-
-##
-## Form Methods
-##
-def showRawValueInForms():
- return False
-
-def updateFromRegistrationForm(bindings):
- elements = []
- for item in bindings:
- comment_text_list = item.get('COMMENTENTRY')
- sampleLink = _createCommentEntry(comment_text_list)
- elements.append(sampleLink)
-
- property.value = propertyConverter().convertToString(elements)
-
-##
-## Batch Import Methods
-##
-def batchColumnNames():
- return [COMMENT_ENTRY_ELEMENT_LABEL]
-
-def updateFromBatchInput(bindings):
- elements = []
- input = bindings.get('COMMENTENTRY')
- if input is not None:
- commentEntry = _createCommentEntry(input)
- elements.append(commentEntry)
- property.value = propertyConverter().convertToString(elements)
-
-##
-## Help Methods
-##
-def _createCommentEntry(comment_text_list):
- #if comment_text_list is not None:
- commentEntry = elementFactory().createElement(COMMENT_ENTRY_ELEMENT_LABEL)
- commentEntry.addAttribute(PERSON_ATTRIBUTE, person.getUserId())
- commentEntry.addAttribute(DATE_ATTRIBUTE,str(Date().getTime()))
- commentEntry.setData(comment_text_list)
- return commentEntry
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/managed.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/managed.py
deleted file mode 100644
index 848a92850e0..00000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/managed.py
+++ /dev/null
@@ -1,267 +0,0 @@
-from ch.systemsx.cisd.openbis.generic.server import CommonServiceProvider
-
-##
-## Configuration
-##
-
-# This needs to be edited for each sample type to match the Profile.js ANNOTATION_PROPERTIES map.
-configuration = {}
-configuration["MEDIA"] = {
- "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
- "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
- "MEDIA" : {"QUANTITY" : False, "COMMENTS" : False }
- };
-
-configuration["SOLUTION_BUFFER"] = {
- "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
- "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
- "MEDIA" : {"QUANTITY" : False, "COMMENTS" : False }
- };
-
-configuration["GENERAL_PROTOCOL"] = {
- "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
- "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
- "MEDIA" : {"QUANTITY" : False, "COMMENTS" : False },
- "ENZYME" : {"QUANTITY" : False, "COMMENTS" : False },
- "GENERAL_PROTOCOL" : {"COMMENTS" : False }
- };
-
-configuration["PCR_PROTOCOL"] = {
- "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
- "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
- "ENZYME" : {"QUANTITY" : False, "COMMENTS" : False }
- };
-
-configuration["WESTERN_BLOTTING_PROTOCOL"] = {
- "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
- "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
- "ANTIBODY" : {"QUANTITY" : False, "COMMENTS" : False }
- };
-
-configuration["PLASMID"] = {
- "PLASMID" : {"COMMENTS" : False }
- };
-
-configuration["BACTERIA"] = {
- "BACTERIA" : {"COMMENTS" : False },
- "PLASMID" : {"PLASMID_RELATIONSHIP" : False, "PLASMID_ANNOTATION" : False, "COMMENTS" : False }
- };
-
-configuration["YEAST"] = {
- "YEAST" : {"COMMENTS" : False },
- "PLASMID" : {"PLASMID_RELATIONSHIP" : False, "PLASMID_ANNOTATION" : False, "COMMENTS" : False, "CONTAINED" : False }
- };
-
-configuration["CELL_LINE"] = {
- "CELL_LINE" : {"COMMENTS" : False },
- "PLASMID" : {"PLASMID_RELATIONSHIP" : False, "PLASMID_ANNOTATION" : False, "COMMENTS" : False },
- "FLY" : {"COMMENTS" : False }
- };
-
-configuration["FLY"] = {
- "FLY" : {"COMMENTS" : False },
- "PLASMID" : {"PLASMID_RELATIONSHIP" : False, "PLASMID_ANNOTATION" : False, "COMMENTS" : False }
- };
-
-configuration["EXPERIMENTAL_STEP"] = {
- "ANTIBODY" : {"QUANTITY" : False, "COMMENTS" : False },
- "BACTERIA" : {"COMMENTS" : False },
- "CELL_LINE" : {"COMMENTS" : False },
- "CHEMICAL" : {"QUANTITY" : False, "COMMENTS" : False },
- "ENZYME" : {"QUANTITY" : False, "COMMENTS" : False },
- "FLY" : {"COMMENTS" : False },
- "MEDIA" : {"QUANTITY" : False, "COMMENTS" : False },
- "OLIGO" : {"COMMENTS" : False },
- "PLASMID" : {"COMMENTS" : False },
- "RNA" : {"COMMENTS" : False },
- "SOLUTION_BUFFER" : {"QUANTITY" : False, "COMMENTS" : False },
- "YEAST" : {"COMMENTS" : False },
- "GENERAL_PROTOCOL" : {"COMMENTS" : False },
- "PCR_PROTOCOL" : {"COMMENTS" : False },
- "WESTERN_BLOTTING_PROTOCOL" : {"COMMENTS" : False }
- };
-
-#Global Variables
-annotableType = "<REPLACE_WITH_ANNOTABLE_TYPE>"
-propertyTypes = None
-def getPropertyTypes():
- global propertyTypes
- if propertyTypes is None:
- server = CommonServiceProvider.getCommonServer()
- contextOrNull = server.tryToAuthenticateAsSystem()
- propertyTypes = server.listPropertyTypes(contextOrNull.getSessionToken(), False)
- return propertyTypes;
-
-##
-## Help Methods
-##
-def getAllAnnotableSampleTypesForType(fromAnnotableType):
- allTypes = {};
- for sampleTypeWithAnnotations in configuration:
- if (fromAnnotableType == None) or (fromAnnotableType == sampleTypeWithAnnotations):
- for sampleTypeWithAnnotationsForType in configuration[sampleTypeWithAnnotations]:
- allTypes[sampleTypeWithAnnotationsForType] = True;
- return allTypes;
-
-def getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCodeToFind, fromAnnotableType):
- for sampleTypeWithAnnotations in configuration:
- if (fromAnnotableType == None) or (fromAnnotableType == sampleTypeWithAnnotations):
- for sampleTypeWithAnnotationsForType in configuration[sampleTypeWithAnnotations]:
- if sampleTypeWithAnnotationsForType == sampleTypeCodeToFind:
- return configuration[sampleTypeWithAnnotations][sampleTypeWithAnnotationsForType];
- return None;
-
-def getPropertyType(propertyTypeCode):
- for propertyType in getPropertyTypes():
- if propertyType.code == propertyTypeCode:
- return propertyType
- return None;
-
-def createAnnotationsFor(identifier, annotations, sampleType):
- permId = entityInformationProvider().getSamplePermId(identifier);
- newAnnotation = elementFactory().createSampleLink(permId)
-
- newAnnotation.addAttribute("identifier", identifier)
- newAnnotation.addAttribute("sampleType", sampleType)
- for annotation in annotations:
- newAnnotation.addAttribute(annotation, annotations[annotation])
- return newAnnotation
-
-def getWidgetForAdd(sampleTypeCode, annotableType):
- #print "sampleTypeCode:" + sampleTypeCode + " - " + annotableType #Deleting this comment causes the thing to break
- widgets = []
- widgetIdentifier = inputWidgetFactory().createTextInputField("identifier")\
- .setMandatory(True)\
- .setValue("")\
- .setDescription("")
- widgets.append(widgetIdentifier)
- for propertyTypeCode in getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType):
- propertyType = getPropertyType(propertyTypeCode)
- widget = inputWidgetFactory().createTextInputField(propertyType.label)\
- .setMandatory(getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType)[propertyTypeCode])\
- .setValue("")\
- .setDescription(propertyType.description)
- widgets.append(widget)
- return widgets;
-
-def isValid(dataType, value):
- return True
-
-##
-## Main Methods
-##
-def configureUI():
- # Add Headers
- tableBuilder = createTableBuilder()
- tableBuilder.addHeader("identifier")
- tableBuilder.addHeader("sampleType")
- tableBuilder.addHeader("name")
-
- usedTableHeaders = {"identifier" : True, "sampleType" : True, "name" : True }
-
- for sampleTypeCode in getAllAnnotableSampleTypesForType(annotableType):
- for propertyTypeCode in getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType):
- if propertyTypeCode not in usedTableHeaders:
- tableBuilder.addHeader(propertyTypeCode)
- usedTableHeaders[propertyTypeCode] = True
-
- property.setOwnTab(True)
- uiDescription = property.getUiDescription()
- uiDescription.useTableOutput(tableBuilder.getTableModel())
-
- # Add Rows
- samples = list(propertyConverter().convertToElements(property))
- for sample in samples:
- row = tableBuilder.addRow()
- permId = sample.getAttribute("permId")
-
- nameValue = entityInformationProvider().getSamplePropertyValue(permId, "NAME")
- if nameValue is not None:
- row.setCell("name", nameValue)
-
- for annotation in sample.getAttributes():
- if annotation != "permId":
- if annotation == "identifier":
- row.setCell(annotation, sample, sample.getAttribute(annotation))
- else:
- row.setCell(annotation, sample.getAttribute(annotation))
-
- # Add Create buttons
- for sampleTypeCode in getAllAnnotableSampleTypesForType(annotableType):
- title = "Add " + sampleTypeCode;
- addAction = uiDescription.addTableAction(title).setDescription(title)
- widgets = getWidgetForAdd(sampleTypeCode, annotableType)
- addAction.addInputWidgets(widgets)
-
- # Add Delete button
- deleteAction = uiDescription.addTableAction("Delete")\
- .setDescription('Are you sure you want to delete selected annotation?')
- deleteAction.setRowSelectionRequired() # Delete is enabled when at least 1 row is selected.
-
-def updateFromUI(action):
- converter = propertyConverter()
- elements = list(converter.convertToElements(property))
-
- if action.name.startswith("Add"):
- sampleTypeCode = action.name[4:]
- identifier = action.getInputValue("identifier")
- annotations = { }
- for propertyTypeCode in getPropertyTypesForSampleTypeFromAnnotableType(sampleTypeCode, annotableType):
- propertyType = getPropertyType(propertyTypeCode)
- propertyTypeValue = action.getInputValue(propertyType.label)
- if not isValid(propertyType.dataType, propertyTypeValue):
- raise ValidationException("Property " + str(propertyType.label) + " with invalid value " + str(propertyTypeValue))
- if propertyTypeValue is None:
- propertyTypeValue = ""
- annotations[propertyTypeCode] = propertyTypeValue
- newAnnotation = createAnnotationsFor(identifier, annotations, sampleTypeCode)
- elements.append(newAnnotation)
-
- if action.name.startswith("Delete"):
- rowIds = list(action.getSelectedRows())
- rowIds.reverse()
- for rowId in rowIds:
- elements.pop(rowId)
-
- property.value = converter.convertToString(elements)
-
-##
-## Batch Import Methods
-##
-def batchColumnNames():
- allTypes = []
- for sampleTypeCode in getAllAnnotableSampleTypesForType(annotableType):
- allTypes.append(sampleTypeCode)
- return allTypes
-
-def updateFromBatchInput(bindings):
- #print "--------> UPDATE FROM BATCH INPUT: "
- elements = []
-
- for annotableSampleType in getAllAnnotableSampleTypesForType(annotableType):
- annotatedSamples = bindings.get(annotableSampleType)
- #print "-----> TYPE: " + str(annotableSampleType) + " BINDINGS: " + str(annotatedSamples)
- if (annotatedSamples != None and annotatedSamples != ""):
- #Annotations
- for sampleLine in annotatedSamples.split("\\"):
- propertyTypes = getPropertyTypesForSampleTypeFromAnnotableType(annotableSampleType, annotableType)
- identifier = None
- permId = None
- sampleLink = None
- for sampleProperty in sampleLine.split(";"):
- propertyName = sampleProperty.split(":")[0]
- propertyValue = sampleProperty.split(":")[1]
- if propertyName == "identifier":
- identifier = propertyValue
- permId = entityInformationProvider().getSamplePermId(propertyValue)
- sampleLink = elementFactory().createSampleLink(permId)
- sampleLink.addAttribute(propertyName, propertyValue)
- sampleLink.addAttribute('sampleType', annotableSampleType)
- elif propertyName in propertyTypes:
- sampleLink.addAttribute(propertyName, propertyValue)
- else:
- raise NameError('Found invalid property: ' + propertyName + " on type " + annotableSampleType)
- if identifier is not None:
- elements.append(sampleLink)
- #Links
- property.value = propertyConverter().convertToString(elements)
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/requests_children_code.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/requests_children_code.py
deleted file mode 100644
index c79ad63402a..00000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/compatibility/requests_children_code.py
+++ /dev/null
@@ -1,14 +0,0 @@
-def retrieve_childrenCode():
-
- sample= entity.samplePE()
- children=sample.children
- if len(children) != 0:
- children_code = children[0].getCode()
- else:
- children_code="n.a."
-
-
- return children_code
-
-def calculate():
- return retrieve_childrenCode()
--
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