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Rework search.py to reflect galaxy.model can be imported and not mapped.

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Basically search.py was assuming certain class attributes are available that are not available until after mapping.init has done its thing. This delays evaluation of those class attributes until runtime.
This commit is contained in:
John Chilton
2013-12-05 00:20:54 -06:00
parent 17ea9df5d7
commit 54f8c657b5
1 changed files with 34 additions and 33 deletions
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lib/galaxy/model/search.py
+34 -33
View File
@@ -105,13 +105,15 @@ class ViewQueryBaseClass(object):
self.do_query = True
field = self.FIELDS[left_base]
if field.sqlalchemy_field is not None:
clazz, attribute = field.sqlalchemy_field
sqlalchemy_field_value = getattr(clazz, attribute)
if operator == "=":
#print field.sqlalchemy_field == right, field.sqlalchemy_field, right
self.query = self.query.filter( field.sqlalchemy_field == right )
self.query = self.query.filter( sqlalchemy_field_value == right )
elif operator == "!=":
self.query = self.query.filter( field.sqlalchemy_field != right )
self.query = self.query.filter( sqlalchemy_field_value != right )
elif operator == "like":
self.query = self.query.filter( field.sqlalchemy_field.like(right) )
self.query = self.query.filter( sqlalchemy_field_value.like(right) )
else:
raise GalaxyParseError("Invalid comparison operator: %s" % (operator))
elif field.handler is not None:
@@ -172,11 +174,11 @@ class LibraryDatasetDatasetView(ViewQueryBaseClass):
VIEW_NAME = "library_dataset_dataset"
FIELDS = {
'extended_metadata': ViewField('extended_metadata', handler=library_extended_metadata_filter),
'name': ViewField('name', sqlalchemy_field=LibraryDatasetDatasetAssociation.name),
'name': ViewField('name', sqlalchemy_field=(LibraryDatasetDatasetAssociation, "name")),
'id': ViewField('id', sqlalchemy_field=LibraryDatasetDatasetAssociation.id, id_decode=True),
'deleted': ViewField('deleted', sqlalchemy_field=LibraryDatasetDatasetAssociation.deleted),
'deleted': ViewField('deleted', sqlalchemy_field=(LibraryDatasetDatasetAssociation, "deleted")),
'parent_library_id': ViewField('parent_library_id', id_decode=True, post_filter=ldda_parent_library_filter),
'data_type': ViewField('data_type', sqlalchemy_field=LibraryDatasetDatasetAssociation.extension)
'data_type': ViewField('data_type', sqlalchemy_field=(LibraryDatasetDatasetAssociation, "extension")),
}
def search(self, trans):
@@ -190,9 +192,9 @@ class LibraryDatasetDatasetView(ViewQueryBaseClass):
class LibraryView(ViewQueryBaseClass):
VIEW_NAME = "library"
FIELDS = {
'name': ViewField('name', sqlalchemy_field=Library.name),
'name': ViewField('name', sqlalchemy_field=(Library, "name")),
'id': ViewField('id', sqlalchemy_field=Library.id, id_decode=True),
'deleted': ViewField('deleted', sqlalchemy_field=Library.deleted)
'deleted': ViewField('deleted', sqlalchemy_field=(Library, "deleted")),
}
def search(self, trans):
@@ -222,9 +224,9 @@ def library_path_filter(item, left, operator, right):
class LibraryFolderView(ViewQueryBaseClass):
VIEW_NAME = "library_folder"
FIELDS = {
'name': ViewField('name', sqlalchemy_field=LibraryFolder.name),
'id': ViewField('id', sqlalchemy_field=LibraryFolder.id, id_decode=True),
'parent_id': ViewField('parent_id', sqlalchemy_field=LibraryFolder.parent_id, id_decode=True),
'name': ViewField('name', sqlalchemy_field=(LibraryFolder, "name")),
'id': ViewField('id', sqlalchemy_field=(LibraryFolder, "id"), id_decode=True),
'parent_id': ViewField('parent_id', sqlalchemy_field=(LibraryFolder, "parent_id"), id_decode=True),
'parent_library_id': ViewField('parent_library_id', post_filter=library_folder_parent_library_id_filter, id_decode=True),
'library_path': ViewField('library_path', post_filter=library_path_filter)
}
@@ -248,8 +250,8 @@ class LibraryDatasetView(ViewQueryBaseClass):
VIEW_NAME = "library_dataset"
FIELDS = {
'name': ViewField('name', post_filter=library_dataset_name_filter),
'id': ViewField('id', sqlalchemy_field=LibraryDataset.id, id_decode=True),
'folder_id': ViewField('folder_id', sqlalchemy_field=LibraryDataset.folder_id, id_decode=True)
'id': ViewField('id', sqlalchemy_field=(LibraryDataset, "id"), id_decode=True),
'folder_id': ViewField('folder_id', sqlalchemy_field=(LibraryDataset, "folder_id"), id_decode=True)
}
def search(self, trans):
@@ -262,12 +264,11 @@ class LibraryDatasetView(ViewQueryBaseClass):
class ToolView(ViewQueryBaseClass):
VIEW_NAME = "tool"
FIELDS = {
'tool_id': ViewField('name', sqlalchemy_field=ToolVersion.tool_id),
'id': ViewField('id', sqlalchemy_field=ToolVersion.id)
'tool_id': ViewField('name', sqlalchemy_field=(ToolVersion, "tool_id")),
'id': ViewField('id', sqlalchemy_field=(ToolVersion, "id")),
}
def search(self, trans):
# Likely this will break in subsequent model refactoring. Need to revisit.
self.query = trans.install_model.context.query( ToolVersion )
@@ -294,17 +295,17 @@ def history_dataset_handle_tag(view, left, operator, right):
class HistoryDatasetView(ViewQueryBaseClass):
DOMAIN = "history_dataset"
FIELDS = {
'name': ViewField('name', sqlalchemy_field=HistoryDatasetAssociation.name),
'id': ViewField('id', sqlalchemy_field=HistoryDatasetAssociation.id, id_decode=True),
'history_id': ViewField('history_id', sqlalchemy_field=HistoryDatasetAssociation.history_id, id_decode=True),
'name': ViewField('name', sqlalchemy_field=(HistoryDatasetAssociation, "name")),
'id': ViewField('id', sqlalchemy_field=(HistoryDatasetAssociation, "id"), id_decode=True),
'history_id': ViewField('history_id', sqlalchemy_field=(HistoryDatasetAssociation, "history_id"), id_decode=True),
'tag': ViewField("tag", handler=history_dataset_handle_tag),
'copied_from_ldda_id': ViewField("copied_from_ldda_id",
sqlalchemy_field=HistoryDatasetAssociation.copied_from_library_dataset_dataset_association_id,
sqlalchemy_field=(HistoryDatasetAssociation, "copied_from_library_dataset_dataset_association_id"),
id_decode=True),
'copied_from_hda_id': ViewField("copied_from_hda_id",
sqlalchemy_field=HistoryDatasetAssociation.copied_from_history_dataset_association_id,
sqlalchemy_field=(HistoryDatasetAssociation, "copied_from_history_dataset_association_id"),
id_decode=True),
'deleted': ViewField('deleted', sqlalchemy_field=HistoryDatasetAssociation.deleted)
'deleted': ViewField('deleted', sqlalchemy_field=(HistoryDatasetAssociation, "deleted")),
}
def search(self, trans):
@@ -353,8 +354,8 @@ def history_handle_annotation(view, left, operator, right):
class HistoryView(ViewQueryBaseClass):
DOMAIN = "history"
FIELDS = {
'name': ViewField('name', sqlalchemy_field=History.name),
'id': ViewField('id', sqlalchemy_field=History.id, id_decode=True),
'name': ViewField('name', sqlalchemy_field=(History, "name")),
'id': ViewField('id', sqlalchemy_field=(History, "id"), id_decode=True),
'tag': ViewField("tag", handler=history_handle_tag),
'annotation': ViewField("annotation", handler=history_handle_annotation)
}
@@ -385,8 +386,8 @@ def workflow_tag_handler(view, left, operator, right):
class WorkflowView(ViewQueryBaseClass):
DOMAIN = "workflow"
FIELDS = {
'name': ViewField('name', sqlalchemy_field=StoredWorkflow.name),
'id': ViewField('id', sqlalchemy_field=StoredWorkflow.id, id_decode=True),
'name': ViewField('name', sqlalchemy_field=(StoredWorkflow, "name")),
'id': ViewField('id', sqlalchemy_field=(StoredWorkflow, "id"), id_decode=True),
'tag': ViewField('tag', handler=workflow_tag_handler)
}
@@ -454,8 +455,8 @@ def job_output_hda_filter(view, left, operator, right):
class JobView(ViewQueryBaseClass):
DOMAIN = "job"
FIELDS = {
'tool_name': ViewField('tool_name', sqlalchemy_field=Job.tool_id),
'state': ViewField('state', sqlalchemy_field=Job.state),
'tool_name': ViewField('tool_name', sqlalchemy_field=(Job, "tool_id")),
'state': ViewField('state', sqlalchemy_field=(Job, "state")),
'param': ViewField('param', handler=job_param_filter),
'input_ldda': ViewField('input_ldda', handler=job_input_ldda_filter, id_decode=True),
'input_hda': ViewField('input_hda', handler=job_input_hda_filter, id_decode=True),
@@ -474,8 +475,8 @@ class JobView(ViewQueryBaseClass):
class PageView(ViewQueryBaseClass):
DOMAIN = "page"
FIELDS = {
'id': ViewField('id', sqlalchemy_field=Page.id, id_decode=True),
'title': ViewField('title', sqlalchemy_field=Page.title),
'id': ViewField('id', sqlalchemy_field=(Page, "id"), id_decode=True),
'title': ViewField('title', sqlalchemy_field=(Page, "title")),
}
def search(self, trans):
@@ -490,9 +491,9 @@ class PageView(ViewQueryBaseClass):
class PageRevisionView(ViewQueryBaseClass):
DOMAIN = "page_revision"
FIELDS = {
'id': ViewField('id', sqlalchemy_field=PageRevision.id, id_decode=True),
'title': ViewField('title', sqlalchemy_field=PageRevision.title),
'page_id': ViewField('page_id', sqlalchemy_field=PageRevision.page_id, id_decode=True),
'id': ViewField('id', sqlalchemy_field=(PageRevision, "id"), id_decode=True),
'title': ViewField('title', sqlalchemy_field=(PageRevision, "title")),
'page_id': ViewField('page_id', sqlalchemy_field=(PageRevision, "page_id"), id_decode=True),
}
def search(self, trans):