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Merge pull request #9874 from assuntad23/feature/9669-sort-collection-for-paired-collections
Feature/9669 sort collection for paired collections
This commit is contained in:
Nicola Soranzo
@@ -1852,7 +1852,7 @@ class History(HasTags, Dictifiable, UsesAnnotations, HasName, RepresentById):
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hdas = self.active_datasets
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for hda in hdas:
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# Copy HDA.
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new_hda = hda.copy(force_flush=False)
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new_hda = hda.copy(flush=False)
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new_history.add_dataset(new_hda, set_hid=False, quota=applies_to_quota)
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if target_user:
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@@ -3110,7 +3110,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
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self.version = self.version + 1 if self.version else 1
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session.add(past_hda)
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def copy(self, parent_id=None, copy_tags=None, force_flush=True, copy_hid=True, new_name=None):
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def copy(self, parent_id=None, copy_tags=None, flush=True, copy_hid=True, new_name=None):
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"""
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Create a copy of this HDA.
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"""
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@@ -3147,7 +3147,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
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object_session(self).flush([self])
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hda.set_peek()
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if force_flush:
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if flush:
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object_session(self).flush()
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return hda
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@@ -4120,7 +4120,7 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
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error_message = "Dataset collection has no %s with key %s." % (get_by_attribute, key)
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raise KeyError(error_message)
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def copy(self, destination=None, element_destination=None):
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def copy(self, destination=None, element_destination=None, flush=True):
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new_collection = DatasetCollection(
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collection_type=self.collection_type,
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element_count=self.element_count
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@@ -4130,6 +4130,7 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
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new_collection,
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destination=destination,
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element_destination=element_destination,
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flush=flush
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)
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object_session(self).add(new_collection)
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object_session(self).flush()
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@@ -4537,16 +4538,17 @@ class DatasetCollectionElement(Dictifiable, RepresentById):
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else:
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return [element_object]
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def copy_to_collection(self, collection, destination=None, element_destination=None):
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def copy_to_collection(self, collection, destination=None, element_destination=None, flush=True):
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element_object = self.element_object
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if element_destination:
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if self.is_collection:
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element_object = element_object.copy(
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destination=destination,
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element_destination=element_destination
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element_destination=element_destination,
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flush=flush
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)
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else:
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new_element_object = element_object.copy()
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new_element_object = element_object.copy(flush=flush)
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if destination is not None and element_object.hidden_beneath_collection_instance:
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new_element_object.hidden_beneath_collection_instance = destination
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# Ideally we would not need to give the following
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@@ -2902,7 +2902,7 @@ class MergeCollectionTool(DatabaseOperationTool):
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new_elements = OrderedDict()
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for key, value in new_element_structure.items():
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if getattr(value, "history_content_type", None) == "dataset":
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copied_value = value.copy(force_flush=False)
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copied_value = value.copy(flush=False)
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else:
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copied_value = value.copy()
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new_elements[key] = copied_value
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@@ -2920,7 +2920,7 @@ class FilterDatasetsTool(DatabaseOperationTool):
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for dce in elements_to_copy:
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element_identifier = dce.element_identifier
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if getattr(dce.element_object, "history_content_type", None) == "dataset":
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copied_value = dce.element_object.copy(force_flush=False)
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copied_value = dce.element_object.copy(flush=False)
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else:
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copied_value = dce.element_object.copy()
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new_elements[element_identifier] = copied_value
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@@ -2995,7 +2995,7 @@ class FlattenTool(DatabaseOperationTool):
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if dce.is_collection:
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add_elements(dce_object, prefix=identifier)
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else:
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copied_dataset = dce_object.copy(force_flush=False)
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copied_dataset = dce_object.copy(flush=False)
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new_elements[identifier] = copied_dataset
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copied_datasets.append(copied_dataset)
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@@ -3041,7 +3041,7 @@ class SortTool(DatabaseOperationTool):
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for dce in sorted_elements:
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dce_object = dce.element_object
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copied_dataset = dce_object.copy(force_flush=False)
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copied_dataset = dce_object.copy(flush=False)
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new_elements[dce.element_identifier] = copied_dataset
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self._add_datasets_to_history(history, itervalues(new_elements))
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@@ -3065,7 +3065,7 @@ class RelabelFromFileTool(DatabaseOperationTool):
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if new_label in new_elements:
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raise Exception("New identifier [%s] appears twice in resulting collection, these values must be unique." % new_label)
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if getattr(dce_object, "history_content_type", None) == "dataset":
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copied_value = dce_object.copy(force_flush=False)
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copied_value = dce_object.copy(flush=False)
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else:
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copied_value = dce_object.copy()
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new_elements[new_label] = copied_value
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@@ -3111,7 +3111,7 @@ class ApplyRulesTool(DatabaseOperationTool):
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copied_datasets = []
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def copy_dataset(dataset):
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copied_dataset = dataset.copy(force_flush=False)
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copied_dataset = dataset.copy(flush=False)
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copied_datasets.append(copied_dataset)
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return copied_dataset
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@@ -3137,7 +3137,7 @@ class TagFromFileTool(DatabaseOperationTool):
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def add_copied_value_to_new_elements(new_tags_dict, dce):
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if getattr(dce.element_object, "history_content_type", None) == "dataset":
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copied_value = dce.element_object.copy(force_flush=False)
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copied_value = dce.element_object.copy(flush=False)
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# copy should never be visible, since part of a collection
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copied_value.visble = False
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new_datasets.append(copied_value)
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@@ -3208,7 +3208,7 @@ class FilterFromFileTool(DatabaseOperationTool):
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passes_filter = in_filter_file if how_filter == "remove_if_absent" else not in_filter_file
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if getattr(dce_object, "history_content_type", None) == "dataset":
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copied_value = dce_object.copy(force_flush=False)
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copied_value = dce_object.copy(flush=False)
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else:
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copied_value = dce_object.copy()
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@@ -7,7 +7,7 @@
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<action module="galaxy.tools.actions.model_operations"
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class="ModelOperationToolAction"/>
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<inputs>
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<param type="data_collection" collection_type="list" name="input" label="Input Collection" />
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<param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
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<conditional name="sort_type">
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<param type="select" name="sort_type" label="Sort collection identifiers" help="All element identifiers must be present once.">
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<option value="alpha">alphabetically</option>
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@@ -22,7 +22,7 @@
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</conditional>
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</inputs>
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<outputs>
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<collection name="output" format_source="input" type="list" label="${on_string} (sorted)" >
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<collection name="output" format_source="input" type_source="input" label="${on_string} (sorted)" >
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</collection>
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</outputs>
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<tests>
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@@ -91,6 +91,51 @@
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</element>
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</output_collection>
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</test>
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<test>
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<param name="input">
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<collection type="list:paired">
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<element name="def456">
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<collection type="paired">
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<element name="forward" value="simple_line.txt" />
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<element name="reverse" value="simple_line_alternative.txt" />
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</collection>
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</element>
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<element name="abc789">
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<collection type="paired">
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<element name="forward" value="simple_line.txt" />
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<element name="reverse" value="simple_line_alternative.txt" />
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</collection>
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</element>
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</collection>
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</param>
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<param name="sort_type" value="alpha" />
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<output_collection name="output" type="list:paired">
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<element name="abc789">
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<element name="forward">
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<assert_contents>
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<has_text_matching expression="^This is a line of text.\n$" />
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</assert_contents>
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</element>
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<element name="reverse">
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<assert_contents>
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<has_text_matching expression="^This is a different line of text.\n$" />
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</assert_contents>
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</element>
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</element>
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<element name="def456">
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<element name="forward">
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<assert_contents>
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<has_text_matching expression="^This is a line of text.\n$" />
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</assert_contents>
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</element>
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<element name="reverse">
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<assert_contents>
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<has_text_matching expression="^This is a different line of text.\n$" />
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</assert_contents>
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</element>
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</element>
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</output_collection>
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</test>
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</tests>
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<help><![CDATA[
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