From aa9d500b6240b8c5b42988c9fd1837978c3e3798 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Fri, 18 Mar 2011 09:39:15 +0000
Subject: [PATCH] [LMS-2145] improved scripts (added actions for plasmids)
SVN: 20391
---
.../jython-scripts/MP-plasmid_parents.py | 146 ++++++++++++++++--
.../jython-scripts/MP-yeast_parents.py | 5 +-
2 files changed, 137 insertions(+), 14 deletions(-)
diff --git a/plasmid/resource/jython-scripts/MP-plasmid_parents.py b/plasmid/resource/jython-scripts/MP-plasmid_parents.py
index 6df558af5c3..d890fd69f3b 100644
--- a/plasmid/resource/jython-scripts/MP-plasmid_parents.py
+++ b/plasmid/resource/jython-scripts/MP-plasmid_parents.py
@@ -1,5 +1,5 @@
"""
-Managed Property Script for handling plasmid parents of yeast samples.
+Managed Property Script for handling PLASMID parents of YEAST samples.
@author: Piotr Buczek
"""
@@ -27,21 +27,30 @@ INPUT_PATTERN = """
# no '$': allow whitespace at the end
"""
+"""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', 'INT', 'MOD')
+REL_TYPES = (DEL_REL_TYPE, INT_REL_TYPE, MOD_REL_TYPE)
"""dictionary from relationship type shortcut to its 'character' representation"""
REL_TYPE_CHARS = {
- 'DEL': '^', # TODO 2011-14-03, Piotr Buczek: use u'\u0394' for '∆', don't encode HTML
- 'INT': '::',
- 'MOD': '_'
+ DEL_REL_TYPE: '^', # TODO 2011-14-03, Piotr Buczek: use u'\u0394' for '∆', don't encode HTML
+ INT_REL_TYPE: '::',
+ MOD_REL_TYPE: '_'
}
"""dictionary from relationship type shortcut to its full name/label"""
REL_TYPE_LABELS = {
- 'DEL': 'deletion',
- 'INT': 'integration',
- 'MOD': 'modification'
+ 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"
@@ -56,6 +65,11 @@ 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"""
@@ -93,8 +107,21 @@ def _translateToLabel(relationship):
else:
return "[" + relationship + "]"
else:
- return ""
+ 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):
"""
@@ -195,5 +222,102 @@ def configureUI():
"""Specify that the property should be shown in a tab and set the table output."""
property.setOwnTab(True)
- uiDesc = property.getUiDescription()
- uiDesc.useTableOutput(tableBuilder.getTableModel())
\ No newline at end of file
+ uiDescription = property.getUiDescription()
+ uiDescription.useTableOutput(tableBuilder.getTableModel())
+
+ """
+ Define and add actions with input fields used to:
+ 1. specify attributes of new log entry,
+ """
+ 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 log entry,
+ """
+ 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 log entries.
+ """
+ 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 entry 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 entry 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 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:
+ 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
diff --git a/plasmid/resource/jython-scripts/MP-yeast_parents.py b/plasmid/resource/jython-scripts/MP-yeast_parents.py
index 876aca43439..7d6e51ca187 100644
--- a/plasmid/resource/jython-scripts/MP-yeast_parents.py
+++ b/plasmid/resource/jython-scripts/MP-yeast_parents.py
@@ -1,5 +1,5 @@
"""
-Managed Property Script for handling yeast parents of yeast samples.
+Managed Property Script for handling YEAST parents of YEAST samples.
@author: Piotr Buczek
"""
@@ -52,11 +52,10 @@ def updateFromBatchInput(bindings):
def configureUI():
-
"""Create table builder and add columns."""
tableBuilder = createTableBuilder()
tableBuilder.addHeader(LINK_LABEL)
- tableBuilder.addHeader(CODE_LABEL, true)
+ 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))
--
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