SSDM-1529: PAPER - OPENBIS - Migrate Manage Properties YeastLab Continuation

SVN: 33471

plasmid/source/core-plugins/stellingmigration/1/compatibility/disabled_managed.py

+def configureUI():
+    tableBuilder = createTableBuilder()
+    
+    ##
+    ## Headers
+    ##
+    tableBuilder.addHeader("message")
+    usedTableHeaders = {"message" : True}
+    samples = list(propertyConverter().convertToElements(property))
+    for sample in samples:
+        for annotation in sample.getAttributes():
+            if annotation not in usedTableHeaders:
+                tableBuilder.addHeader(annotation)
+                usedTableHeaders[annotation] = True
+    
+    property.setOwnTab(True)
+    uiDescription = property.getUiDescription()
+    uiDescription.useTableOutput(tableBuilder.getTableModel())
+    
+    ##
+    ## Data
+    ## 
+    row = tableBuilder.addRow()
+    row.setCell("message", "Please use the new managed properties annotations, legacy functionality is disabled.")
+    
+    for sample in samples:
+        row = tableBuilder.addRow()
+        for annotation in sample.getAttributes():
+            row.setCell(annotation, sample.getAttribute(annotation))
+    
+
+def updateFromUI(action):
+    raise Exception("Please use the new managed properties annotations, legacy functionality is disabled.")
+
+##
+## Batch Import Methods
+##
+def batchColumnNames():
+    allTypes = []
+    return allTypes
+
+def updateFromBatchInput(bindings):
+    elements = []
+    input = bindings.get('')
+    if input is not None:
+        raise Exception("Please use the new managed properties annotations, legacy functionality is disabled.")
\ No newline at end of file

plasmid/source/core-plugins/stellingmigration/1/compatibility/overrided/plasmid parents.py

+""" 
+Managed Property Script for handling PLASMID parents of YEAST samples.
+
+@author: Piotr Buczek
+"""
+
+import re
+
+
+print "###################"
+"""space that all parents come from (fixed)"""
+SPACE = "YEAST_LAB"
+
+"""input pattern matching one plasmid, e.g.: 
+- 'FRP1 (DEL:URA3)', 
+- 'FRP2 (INT)', 
+- 'FRP3(MOD:URA3)', 
+- 'FRP4'
+"""
+INPUT_PATTERN = """
+                 # no '^': allow whitespace at the beginning
+    ([^ (]*)     # 1st group: match code of a sample, everything before a space or '(' (e.g. 'FRP')
+    (\ *\(       # start of 2nd group (matches an optional relationship type with annotation) 
+                 # any spaces followed by a '('
+    ([^:]*)      # 3rd group: match relationship type, any character but ':' (e.g. 'DEL', 'INT', 'MOD')
+    :?           # optional ':' separator
+    (.*)         # 4th group: match annotation, any text (e.g. 'URA3')
+    \))?         # end of 2nd (optional) group: closing bracket of relationship details
+                 # no '$': allow whitespace at the end
+"""
+
+""" due to some weird jython threading issue, we need to compile the pattern outside the function body """
+inputPattern = re.compile(INPUT_PATTERN, re.VERBOSE)
+
+"""relationship types shortcuts"""
+
+DEL_REL_TYPE = 'DEL'
+INT_REL_TYPE = 'INT'
+MOD_REL_TYPE = 'MOD'
+
+"""tuple of supported relationship types as shortcuts"""
+REL_TYPES = (DEL_REL_TYPE, INT_REL_TYPE, MOD_REL_TYPE)
+"""dictionary from relationship type shortcut to its 'character' representation"""
+REL_TYPE_CHARS = {
+    DEL_REL_TYPE: u'\u0394', # unicode '∆'
+    INT_REL_TYPE: '::', 
+    MOD_REL_TYPE: '_' 
+}
+"""dictionary from relationship type shortcut to its full name/label"""
+REL_TYPE_LABELS = {
+    DEL_REL_TYPE: 'deletion', 
+    INT_REL_TYPE: 'integration', 
+    MOD_REL_TYPE: 'modification' 
+}
+
+REL_TYPE_LABEL_OTHER = '(other)'
+REL_TYPE_LABELS_WITH_NONE = tuple([REL_TYPE_LABEL_OTHER] + REL_TYPE_LABELS.values())
+
+"""names of additional sample XML element attributes"""
+
+ATR_CODE = "code"
+ATR_RELATIONSHIP = "rel"
+ATR_ANNOTATION = "annotation"
+
+"""labels of table columns"""
+
+CONNECTION_LABEL = "connection"
+LINK_LABEL = "link"
+CODE_LABEL = "code"
+RELATIONSHIP_LABEL = "relationship"
+ANNOTATION_LABEL = "annotation"
+
+"""action labels"""
+
+ADD_ACTION_LABEL = "Add"
+EDIT_ACTION_LABEL = "Edit"
+DELETE_ACTION_LABEL = "Delete"
+
+"""helper functions"""
+
+def _group(pattern, input):
+    """@return: groups returned by performing pattern search with given @pattern on given @input"""
+    return pattern.search(input).groups()
+
+
+def _translateToChar(relationship):
+    """
+       @param relationship: relationship type as a shortcut (@see REL_TYPES), may be null
+       @return: character representation of given @relationship, 
+                empty string for null
+                '[<relationship>]' for unknown relationship
+    """
+    if relationship:
+        if relationship in REL_TYPE_CHARS:
+            return REL_TYPE_CHARS[relationship]
+        else:
+            return "[" + relationship + "]"
+    else:
+        return ""
+    
+    
+def _translateToLabel(relationship):
+    """
+       @param relationship: relationship type as a shortcut (@see REL_TYPES), may be null
+       @return: full name of given @relationship, 
+                empty string for null, 
+                '[<relationship>]' for unknown relationship
+    """
+    if relationship:
+        if relationship in REL_TYPE_LABELS:
+            return REL_TYPE_LABELS[relationship]
+        else:
+            return "[" + relationship + "]"
+    else:
+        return REL_TYPE_LABEL_OTHER    
+
+def _translateFromLabel(relationshipLabel):
+    """
+       @param relationshipLabel: relationship type as label (@see REL_TYPE_LABELS_WITH_NONE)
+       @return: type of given @relationshipLabel, None for REL_TYPE_LABEL_OTHER, 
+    """
+    if relationshipLabel == REL_TYPE_LABEL_OTHER:
+        return None
+    elif relationshipLabel == 'deletion':
+        return DEL_REL_TYPE
+    elif relationshipLabel == 'integration':
+        return INT_REL_TYPE
+    elif relationshipLabel == 'modification':
+        return MOD_REL_TYPE    
+
+def _createConnectionString(code, relationship, annotation):
+    """
+       @param code: code of a sample
+       @param relationship: relationship type as a shortcut (@see REL_TYPES), may be null
+       @param annotation: annotation of the relationship, may be null
+       @return: string representation of a connection with @relationship translated to a 'character'
+    """
+    result = code
+    if relationship:
+        result += _translateToChar(relationship)
+    if annotation:
+        result += annotation
+    return result
+
+
+def _createSampleLink(code, relationship, annotation):
+    """
+       Creates sample link XML element for sample with specified @code. The element will contain
+       given @code as 'code' attribute apart from standard 'permId' attribute. If specified 
+       @relationship or @annotation are not null they will also be contained as attributes.
+       
+       If the sample doesn't exist in DB a fake link will be created with @code as permId.
+       
+       @param code: code of a sample
+       @param relationship: relationship type as a shortcut (@see REL_TYPES), may be null
+       @param annotation: annotation of the relationship, may be null
+       @return: sample link XML element as string, e.g.:
+       - '<Sample code="FRP1" permId="20110309154532868-4219"/>'
+       - '<Sample code="FRP2" permId="20110309154532868-4219" relationship="DEL" annotation="URA3"/>'
+       - '<Sample code="FAKE_SAMPLE_CODE" permId="FAKE_SAMPLE_CODE"/>
+       - '<Sample code="FRP4" permId="20110309154532868-4219" relationship="INT"/>'
+       @raise ValidationException: if the specified relationship type is unknown
+    """
+    permId = entityInformationProvider().getSamplePermId(SPACE, code)
+    if not permId:
+        permId = code
+    sampleLink = elementFactory().createSampleLink(permId)
+    sampleLink.addAttribute(ATR_CODE, code)
+    if relationship:
+        sampleLink.addAttribute(ATR_RELATIONSHIP, relationship)
+        if relationship in REL_TYPES:
+            connectionString = _createConnectionString(code, relationship, annotation)
+        else:
+            raise ValidationException("Unknown relationship: '" + relationship + 
+                                      "'. Expected one of: " + REL_TYPES)
+    if annotation:
+        sampleLink.addAttribute(ATR_ANNOTATION, annotation)
+    return sampleLink    
+
+""" MAIN FUNCTIONS """
+
+"""Example input:
+
+FRP1 (DEL:URA3), FRP2 (INT), FRP3 (MOD:URA3), FRP4
+
+Relationship types:
+- DEL: deletion
+- INT: integration
+- MOD: modification
+"""
+
+#def showRawValueInForms():
+ #   return False
+ 
+#def batchColumnNames():
+#    return [CODE_LABEL, RELATIONSHIP_LABEL, ANNOTATION_LABEL]
+
+
+
+ 
+#def updateFromRegistrationForm(bindings):
+#    elements = []
+#    for item in bindings:
+#        code = item.get("CODE")
+#        relationship = item.get("RELATIONSHIP")
+#        annotation=item.get("ANNOTATION")
+#        print "code is", code
+#    if code:
+#        print "bindings", bindings, "+", code, "+", relationship, "+", annotation
+
+#        sampleLink = _createSampleLink(code, relationship, annotation)
+ #       elements.append(sampleLink)
+            
+#    property.value = propertyConverter().convertToString(elements)
+ 
+
+
+def updateFromBatchInput(bindings):
+    elements = []
+    input = bindings.get('')
+    if input is not None:
+        plasmids = input.split(',')
+        for p in plasmids:
+            (code, g, relationship, annotation) = _group(inputPattern, p.strip())
+            sampleLink = _createSampleLink(code, relationship, annotation)
+            elements.append(sampleLink)
+    
+    parentsInput = bindings.get(originalColumnNameBindingKey('YEAST_PARENTS'))
+    if parentsInput is not None:
+        parents = parentsInput.split(',')
+        for parent in parents:
+            permId = entityInformationProvider().getSamplePermId(SPACE, parent.strip())
+            parentPlasmids = entityInformationProvider().getSamplePropertyValue(permId, 'PLASMIDS')
+            if parentPlasmids is None:
+                continue
+            parentElements = list(propertyConverter().convertStringToElements(parentPlasmids))
+            for parentLink in parentElements:
+                elements.append(parentLink)     
+        
+    property.value = propertyConverter().convertToString(elements)
+
+
+def configureUI():
+    
+    """Create table builder and add columns."""
+    tableBuilder = createTableBuilder()
+    tableBuilder.addHeader(LINK_LABEL)
+    tableBuilder.addHeader(CONNECTION_LABEL)
+    tableBuilder.addHeader(CODE_LABEL)
+    tableBuilder.addHeader(RELATIONSHIP_LABEL)
+    tableBuilder.addHeader(ANNOTATION_LABEL)
+
+    """The property value should contain XML with list of samples. Add a new row for every sample."""
+    elements = list(propertyConverter().convertToElements(property))
+    for plasmid in elements:
+        code = plasmid.getAttribute(ATR_CODE, "")
+        relationship = plasmid.getAttribute(ATR_RELATIONSHIP, "")
+        annotation = plasmid.getAttribute(ATR_ANNOTATION, "")
+   
+        row = tableBuilder.addRow()
+        row.setCell(CONNECTION_LABEL, _createConnectionString(code, relationship, annotation))
+        row.setCell(LINK_LABEL, plasmid, code)
+        row.setCell(CODE_LABEL, code)
+        row.setCell(RELATIONSHIP_LABEL, _translateToLabel(relationship))
+        row.setCell(ANNOTATION_LABEL, annotation)
+        
+    """Specify that the property should be shown in a tab and set the table output."""
+    property.setOwnTab(True)
+    uiDescription = property.getUiDescription()
+    uiDescription.useTableOutput(tableBuilder.getTableModel())
+    
+    """
+       Define and add actions with input fields used to:
+       1. specify attributes of new plasmid relationship,
+    """
+    addAction = uiDescription.addTableAction(ADD_ACTION_LABEL)\
+                             .setDescription('Add new plasmid relationship:')
+    widgets = [
+        inputWidgetFactory().createTextInputField(CODE_LABEL)\
+                            .setMandatory(True)\
+                            .setValue('FRP')\
+                            .setDescription('Code of plasmid sample, e.g. "FRP1"'),
+        inputWidgetFactory().createComboBoxInputField(RELATIONSHIP_LABEL, REL_TYPE_LABELS_WITH_NONE)\
+                            .setMandatory(False)\
+                            .setValue(REL_TYPE_LABEL_OTHER),
+        inputWidgetFactory().createTextInputField(ANNOTATION_LABEL)\
+                            .setMandatory(False)\
+                            .setDescription('Relationship annotation, e.g. "URA3"'),
+    ]
+    addAction.addInputWidgets(widgets)
+      
+    """
+       2. modify attributes of a selected plasmid relationship,
+    """
+    editAction = uiDescription.addTableAction(EDIT_ACTION_LABEL)\
+                              .setDescription('Edit selected plasmid relationship:')
+    # Exactly 1 row needs to be selected to enable action.
+    editAction.setRowSelectionRequiredSingle()            
+    widgets = [
+        inputWidgetFactory().createTextInputField(CODE_LABEL)\
+                            .setMandatory(True)\
+                            .setDescription('Code of plasmid sample, e.g. "FRP1"'),
+        inputWidgetFactory().createComboBoxInputField(RELATIONSHIP_LABEL, REL_TYPE_LABELS_WITH_NONE)\
+                            .setMandatory(False),
+        inputWidgetFactory().createTextInputField(ANNOTATION_LABEL)\
+                            .setMandatory(False)\
+                            .setDescription('Relationship annotation, e.g. "URA3"'),
+    ]
+    editAction.addInputWidgets(widgets)
+    # Bind field name with column name.
+    editAction.addBinding(CODE_LABEL, CODE_LABEL)
+    editAction.addBinding(RELATIONSHIP_LABEL, RELATIONSHIP_LABEL)
+    editAction.addBinding(ANNOTATION_LABEL, ANNOTATION_LABEL)
+  
+    """
+       3. delete selected plasmid relationships.
+    """
+    deleteAction = uiDescription.addTableAction(DELETE_ACTION_LABEL)\
+                                .setDescription('Are you sure you want to delete selected plasmid relationships?')
+    # 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 plasmid relationship element with values from input fields
+           and add it to existing elements.
+        """
+        code = action.getInputValue(CODE_LABEL)
+        relationshipLabel = action.getInputValue(RELATIONSHIP_LABEL)
+        relationship = _translateFromLabel(relationshipLabel)
+        annotation = action.getInputValue(ANNOTATION_LABEL)
+        sampleLink = _createSampleLink(code, relationship, annotation)
+        
+        elements.append(sampleLink)
+    elif action.name == EDIT_ACTION_LABEL:
+        """
+           For 'edit' action find the plasmid relationship element corresponding to selected row
+           and replace it with an element with values from input fields.
+        """
+        code = action.getInputValue(CODE_LABEL)
+        relationshipLabel = action.getInputValue(RELATIONSHIP_LABEL)
+        relationship = _translateFromLabel(relationshipLabel)
+        annotation = action.getInputValue(ANNOTATION_LABEL)
+        sampleLink = _createSampleLink(code, relationship, annotation)
+        
+        selectedRowId = action.getSelectedRows()[0]
+        elements[selectedRowId] = sampleLink
+    elif action.name == DELETE_ACTION_LABEL:
+        """
+           For 'delete' action delete the relationships 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:
+            elements.pop(rowId)      
+    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)

plasmid/source/core-plugins/stellingmigration/1/compatibility/overrided/yeast parents.py

+""" 
+Managed Property Script for handling YEAST parents of YEAST samples.
+
+@author: Piotr Buczek
+"""
+
+import re
+
+""""space that all parents come from (fixed)"""
+SPACE = "YEAST_LAB"
+
+"""plasmid_list attribute name"""
+ATR_CODE = "code"
+
+"""labels of table columns"""
+LINK_LABEL = "link"
+CODE_LABEL = "code"
+
+"""action labels"""
+
+ADD_ACTION_LABEL = "Add"
+EDIT_ACTION_LABEL = "Edit"
+DELETE_ACTION_LABEL = "Delete"
+
+"""helper functions"""
+
+def _createSampleLink(plasmid_list):
+    """
+       Creates sample link XML element for sample with specified 'plasmid_list'. The element will contain
+       given plasmid_list as 'plasmid_list' attribute apart from standard 'permId' attribute.
+       
+       If the sample doesn't exist in DB a fake link will be created with the 'plasmid_list' as permId.
+       
+       @return: sample link XML element as string, e.g.:
+       - '<Sample plasmid_list="FRP1" permId="20110309154532868-4219"/>'
+       - '<Sample plasmid_list="FAKE_SAMPLE_CODE" permId="FAKE_SAMPLE_CODE"/>
+    """
+    plasmidPath= "/YEAST_LAB/" + plasmid_list
+    permId = entityInformationProvider().getSamplePermId(SPACE, plasmid_list)
+    if not permId:
+        permId = plasmid_list
+    sampleLink = elementFactory().createSampleLink(permId)
+    
+    sampleLink.addAttribute(ATR_CODE, plasmid_list)
+    
+    return sampleLink    
+
+
+"""
+Example input:
+
+FRY1, FRY2, FRY3, FRY4
+"""
+
+#def showRawValueInForms():
+ #   return False
+ 
+#def batchColumnNames():
+#    return [CODE_LABEL]
+
+#def updateFromRegistrationForm(bindings):
+#    elements = []
+#    for item in bindings:
+#        plasmid_list = item.get('CODE')
+#        sampleLink = _createSampleLink(plasmid_list)
+ #       elements.append(sampleLink)
+            
+#    property.value = propertyConverter().convertToString(elements)
+
+ 
+
+
+
+def updateFromBatchInput(bindings):
+    elements = []
+    input = bindings.get('')
+    if input is not None:
+        samples = input.split(',')
+        for plasmid_list in samples:
+            sampleLink = _createSampleLink(plasmid_list.strip())
+            elements.append(sampleLink)
+    property.value = propertyConverter().convertToString(elements)
+
+
+def configureUI():
+    """Create table builder and add columns."""
+    tableBuilder = createTableBuilder()
+    tableBuilder.addHeader(LINK_LABEL)
+    tableBuilder.addHeader(CODE_LABEL)
+
+    """The property value should contain XML with list of samples. Add a new row for every sample."""
+    elements = list(propertyConverter().convertToElements(property))
+    for plasmid in elements:
+        plasmid_list = plasmid.getAttribute(ATR_CODE, "")
+   
+        row = tableBuilder.addRow()
+        row.setCell(LINK_LABEL, plasmid, plasmid_list)
+        row.setCell(CODE_LABEL, plasmid_list)
+        
+    """Specify that the property should be shown in a tab and set the table output."""
+    property.setOwnTab(True)
+    uiDescription = property.getUiDescription()
+    uiDescription.useTableOutput(tableBuilder.getTableModel())
+    
+    """
+       Define and add actions with input fields used to:
+       1. specify attributes of new yeast parent,
+    """
+    addAction = uiDescription.addTableAction(ADD_ACTION_LABEL)\
+                             .setDescription('Add new plasmid relationship:')
+    widgets = [
+        inputWidgetFactory().createTextInputField(CODE_LABEL)\
+                            .setMandatory(True)\
+                            .setValue('FRY')\
+                            .setDescription('Code of yeast parent sample, e.g. "FRY1"')
+    ]
+    addAction.addInputWidgets(widgets)
+      
+    """
+       2. modify attributes of a selected yeast parent,
+    """
+    editAction = uiDescription.addTableAction(EDIT_ACTION_LABEL)\
+                              .setDescription('Edit selected plasmid relationship:')
+    # Exactly 1 row needs to be selected to enable action.
+    editAction.setRowSelectionRequiredSingle()            
+    widgets = [
+        inputWidgetFactory().createTextInputField(CODE_LABEL)\
+                            .setMandatory(True)\
+                            .setDescription('Code of yeast parent sample, e.g. "FRY1"')
+    ]
+    editAction.addInputWidgets(widgets)
+    # Bind field name with column name.
+    editAction.addBinding(CODE_LABEL, CODE_LABEL)
+  
+    """
+       3. delete selected yeast parents.
+    """
+    deleteAction = uiDescription.addTableAction(DELETE_ACTION_LABEL)\
+                                .setDescription('Are you sure you want to delete selected yeast parent relationships?')
+    # 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 yeast parent element with values from input fields
+           and add it to existing elements.
+        """
+        plasmid_list = action.getInputValue(CODE_LABEL)
+        sampleLink = _createSampleLink(plasmid_list)
+        
+        elements.append(sampleLink)
+    elif action.name == EDIT_ACTION_LABEL:
+        """
+           For 'edit' action find the yeast parent element corresponding to selected row
+           and replace it with an element with values from input fields.
+        """
+        plasmid_list = action.getInputValue(CODE_LABEL)
+        sampleLink = _createSampleLink(plasmid_list)
+        
+        selectedRowId = action.getSelectedRows()[0]
+        elements[selectedRowId] = sampleLink
+    elif action.name == DELETE_ACTION_LABEL:
+        """
+           For 'delete' action delete yeast parents 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:
+            elements.pop(rowId)      
+    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)    
\ No newline at end of file