mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Fix E127 errors introduced by previous commit
using: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 . ```
This commit is contained in:
Nicola Soranzo
committed by
Nicola Soranzo
Nicola Soranzo
parent
21b44bf348
commit
a353b2e88f
@@ -37,9 +37,9 @@ def main(options):
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revision_data['owner'] = options.owner
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revision_url = '%s%s' % (options.local_url.rstrip('/'), '/api/tool_shed_repositories/get_latest_installable_revision')
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latest_installable_revision = submit(options.api,
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revision_url,
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revision_data,
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return_formatted=False)
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revision_url,
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revision_data,
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return_formatted=False)
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data['changeset_revision'] = latest_installable_revision
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if options.tool_panel_section_id:
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data['tool_panel_section_id'] = options.tool_panel_section_id
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@@ -88,8 +88,8 @@ def main():
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ini_file = args[0]
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if not (options.purge_folders ^ options.delete_userless_histories ^
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options.purge_libraries ^ options.purge_histories ^
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options.purge_datasets ^ options.delete_datasets):
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options.purge_libraries ^ options.purge_histories ^
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options.purge_datasets ^ options.delete_datasets):
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parser.print_help()
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sys.exit(0)
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@@ -144,12 +144,12 @@ def delete_userless_histories(app, cutoff_time, info_only=False, force_retry=Fal
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if force_retry:
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histories = app.sa_session.query(app.model.History) \
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.filter(and_(app.model.History.table.c.user_id == null(),
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app.model.History.table.c.update_time < cutoff_time))
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app.model.History.table.c.update_time < cutoff_time))
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else:
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histories = app.sa_session.query(app.model.History) \
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.filter(and_(app.model.History.table.c.user_id == null(),
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app.model.History.table.c.deleted == false(),
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app.model.History.table.c.update_time < cutoff_time))
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app.model.History.table.c.deleted == false(),
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app.model.History.table.c.update_time < cutoff_time))
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for history in histories:
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if not info_only:
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print("Deleting history id ", history.id)
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@@ -174,13 +174,13 @@ def purge_histories(app, cutoff_time, remove_from_disk, info_only=False, force_r
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if force_retry:
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histories = app.sa_session.query(app.model.History) \
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.filter(and_(app.model.History.table.c.deleted == true(),
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app.model.History.table.c.update_time < cutoff_time)) \
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app.model.History.table.c.update_time < cutoff_time)) \
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.options(eagerload('datasets'))
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else:
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histories = app.sa_session.query(app.model.History) \
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.filter(and_(app.model.History.table.c.deleted == true(),
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app.model.History.table.c.purged == false(),
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app.model.History.table.c.update_time < cutoff_time)) \
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app.model.History.table.c.purged == false(),
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app.model.History.table.c.update_time < cutoff_time)) \
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.options(eagerload('datasets'))
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for history in histories:
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print("### Processing history id %d (%s)" % (history.id, unicodify(history.name)))
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@@ -216,12 +216,12 @@ def purge_libraries(app, cutoff_time, remove_from_disk, info_only=False, force_r
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if force_retry:
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libraries = app.sa_session.query(app.model.Library) \
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.filter(and_(app.model.Library.table.c.deleted == true(),
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app.model.Library.table.c.update_time < cutoff_time))
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app.model.Library.table.c.update_time < cutoff_time))
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else:
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libraries = app.sa_session.query(app.model.Library) \
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.filter(and_(app.model.Library.table.c.deleted == true(),
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app.model.Library.table.c.purged == false(),
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app.model.Library.table.c.update_time < cutoff_time))
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app.model.Library.table.c.purged == false(),
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app.model.Library.table.c.update_time < cutoff_time))
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for library in libraries:
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_purge_folder(library.root_folder, app, remove_from_disk, info_only=info_only)
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if not info_only:
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@@ -247,12 +247,12 @@ def purge_folders(app, cutoff_time, remove_from_disk, info_only=False, force_ret
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if force_retry:
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folders = app.sa_session.query(app.model.LibraryFolder) \
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.filter(and_(app.model.LibraryFolder.table.c.deleted == true(),
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app.model.LibraryFolder.table.c.update_time < cutoff_time))
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app.model.LibraryFolder.table.c.update_time < cutoff_time))
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else:
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folders = app.sa_session.query(app.model.LibraryFolder) \
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.filter(and_(app.model.LibraryFolder.table.c.deleted == true(),
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app.model.LibraryFolder.table.c.purged == false(),
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app.model.LibraryFolder.table.c.update_time < cutoff_time))
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app.model.LibraryFolder.table.c.purged == false(),
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app.model.LibraryFolder.table.c.update_time < cutoff_time))
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for folder in folders:
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_purge_folder(folder, app, remove_from_disk, info_only=info_only)
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folder_count += 1
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@@ -267,29 +267,29 @@ def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_r
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start = time.time()
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if force_retry:
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history_dataset_ids_query = sa.select((app.model.Dataset.table.c.id,
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app.model.Dataset.table.c.state),
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whereclause=app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
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from_obj=[sa.outerjoin(app.model.Dataset.table,
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app.model.HistoryDatasetAssociation.table)])
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app.model.Dataset.table.c.state),
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whereclause=app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
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from_obj=[sa.outerjoin(app.model.Dataset.table,
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app.model.HistoryDatasetAssociation.table)])
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library_dataset_ids_query = sa.select((app.model.LibraryDataset.table.c.id,
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app.model.LibraryDataset.table.c.deleted),
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whereclause=app.model.LibraryDataset.table.c.update_time < cutoff_time,
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from_obj=[app.model.LibraryDataset.table])
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app.model.LibraryDataset.table.c.deleted),
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whereclause=app.model.LibraryDataset.table.c.update_time < cutoff_time,
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from_obj=[app.model.LibraryDataset.table])
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else:
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# We really only need the id column here, but sqlalchemy barfs when trying to select only 1 column
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history_dataset_ids_query = sa.select((app.model.Dataset.table.c.id,
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app.model.Dataset.table.c.state),
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whereclause=and_(app.model.Dataset.table.c.deleted == false(),
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app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
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app.model.HistoryDatasetAssociation.table.c.deleted == true()),
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from_obj=[sa.outerjoin(app.model.Dataset.table,
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app.model.HistoryDatasetAssociation.table)])
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app.model.Dataset.table.c.state),
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whereclause=and_(app.model.Dataset.table.c.deleted == false(),
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app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
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app.model.HistoryDatasetAssociation.table.c.deleted == true()),
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from_obj=[sa.outerjoin(app.model.Dataset.table,
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app.model.HistoryDatasetAssociation.table)])
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library_dataset_ids_query = sa.select((app.model.LibraryDataset.table.c.id,
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app.model.LibraryDataset.table.c.deleted),
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whereclause=and_(app.model.LibraryDataset.table.c.deleted == true(),
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app.model.LibraryDataset.table.c.purged == false(),
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app.model.LibraryDataset.table.c.update_time < cutoff_time),
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from_obj=[app.model.LibraryDataset.table])
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app.model.LibraryDataset.table.c.deleted),
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whereclause=and_(app.model.LibraryDataset.table.c.deleted == true(),
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app.model.LibraryDataset.table.c.purged == false(),
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app.model.LibraryDataset.table.c.update_time < cutoff_time),
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from_obj=[app.model.LibraryDataset.table])
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deleted_dataset_count = 0
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deleted_instance_count = 0
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skip = []
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@@ -357,14 +357,14 @@ def purge_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_re
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if force_retry:
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datasets = app.sa_session.query(app.model.Dataset) \
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.filter(and_(app.model.Dataset.table.c.deleted == true(),
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app.model.Dataset.table.c.purgable == true(),
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app.model.Dataset.table.c.update_time < cutoff_time))
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app.model.Dataset.table.c.purgable == true(),
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app.model.Dataset.table.c.update_time < cutoff_time))
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else:
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datasets = app.sa_session.query(app.model.Dataset) \
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.filter(and_(app.model.Dataset.table.c.deleted == true(),
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app.model.Dataset.table.c.purgable == true(),
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app.model.Dataset.table.c.purged == false(),
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app.model.Dataset.table.c.update_time < cutoff_time))
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app.model.Dataset.table.c.purgable == true(),
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app.model.Dataset.table.c.purged == false(),
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app.model.Dataset.table.c.update_time < cutoff_time))
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for dataset in datasets:
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file_size = dataset.file_size
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_purge_dataset(app, dataset, remove_from_disk, info_only=info_only)
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@@ -100,9 +100,9 @@ def get_sa_session(ini_file):
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if not db_con:
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db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % ini_config.database
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model = galaxy.model.mapping.init(ini_config.file_path,
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db_con,
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engine_options={},
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create_tables=False)
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db_con,
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engine_options={},
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create_tables=False)
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return model.context.current, ini_config
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@@ -44,10 +44,10 @@ def build_index(sa_session, whoosh_index_dir):
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lddas_indexed = 0
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for id, name, info, dbkey, message in get_lddas(sa_session):
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writer.add_document(id=id,
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name=to_unicode(name),
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info=to_unicode(info),
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dbkey=to_unicode(dbkey),
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message=to_unicode(message))
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name=to_unicode(name),
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info=to_unicode(info),
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dbkey=to_unicode(dbkey),
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message=to_unicode(message))
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lddas_indexed += 1
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writer.commit()
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print("Number of active library datasets indexed: ", lddas_indexed)
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@@ -16,7 +16,7 @@ import sys
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import drmaa
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DRMAA_jobTemplate_attributes = ['args', 'remoteCommand', 'outputPath', 'errorPath', 'nativeSpecification',
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'workingDirectory', 'jobName', 'email', 'project']
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'workingDirectory', 'jobName', 'email', 'project']
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def load_job_template_from_file(jt, filename):
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@@ -89,7 +89,7 @@ def main():
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newelements.append("<tags/>\n ")
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contents = (contents[0:addelementsatposition] + newelements +
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contents[addelementsatposition:])
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contents[addelementsatposition:])
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# add .new for testing/safety purposes :P
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newtoolconffile = open(toolconffile, 'w')
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+2
-2
@@ -33,8 +33,8 @@ except:
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options.config = os.path.abspath(options.config)
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config = ConfigParser(dict(file_path='database/files',
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id_secret='USING THE DEFAULT IS NOT SECURE!',
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database_connection='sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE'))
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id_secret='USING THE DEFAULT IS NOT SECURE!',
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database_connection='sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE'))
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config.read(options.config)
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helper = security.SecurityHelper(id_secret=config.get('app:main', 'id_secret'))
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@@ -39,107 +39,107 @@ VARIANTS = 'chrM,chr21,full,canon,female,male,haps,nohaps'
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VARIANT_EXCLUSIONS = ':full'
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DBKEY_DESCRIPTION_MAP = {'AaegL1': 'Mosquito (Aedes aegypti): AaegL1',
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'AgamP3': 'Mosquito (Anopheles gambiae): AgamP3',
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'anoCar1': 'Lizard (Anolis carolinensis): anoCar1',
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'anoGam1': 'Mosquito (Anopheles gambiae): anoGam1',
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'apiMel1': 'Honeybee (Apis mellifera): apiMel1',
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'apiMel2': 'Honeybee (Apis mellifera): apiMel2',
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'apiMel3': 'Honeybee (Apis mellifera): apiMel3',
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'Arabidopsis_thaliana_TAIR9': '',
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'borEut13': 'Boreoeutherian: borEut13',
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'bosTau2': 'Cow (Bos taurus): bosTau2',
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'bosTau3': 'Cow (Bos taurus): bosTau3',
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'bosTau4': 'Cow (Bos taurus): bosTau4',
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'bosTauMd3': 'Cow (Bos taurus): bosTauMd3',
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'calJac1': 'Marmoset (Callithrix jacchus): calJac1',
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'canFam1': 'Dog (Canis lupus familiaris): canFam1',
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'canFam2': 'Dog (Canis lupus familiaris): canFam2',
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'cavPor3': 'Guinea Pig (Cavia porcellus): cavPor3',
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'ce2': 'Caenorhabditis elegans: ce2',
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'ce4': 'Caenorhabditis elegans: ce4',
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'ce5': 'Caenorhabditis elegans: ce5',
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'ce6': 'Caenorhabditis elegans: ce6',
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'CpipJ1': 'Mosquito (Culex quinquefasciatus): CpipJ1',
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'danRer2': 'Zebrafish (Danio rerio): danRer2',
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'danRer3': 'Zebrafish (Danio rerio): danRer3',
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'danRer4': 'Zebrafish (Danio rerio): danRer4',
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'danRer5': 'Zebrafish (Danio rerio): danRer5',
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'danRer6': 'Zebrafish (Danio rerio): danRer6',
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'dm1': 'Fruit Fly (Drosophila melanogaster): dm1',
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'dm2': 'Fruit Fly (Drosophila melanogaster): dm2',
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'dm3': 'Fruit Fly (Drosophila melanogaster): dm3',
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'dm4': 'Fruit Fly (Drosophila melanogaster): dm',
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'dp3': 'Fruit Fly (Drosophila pseudoobscura): dp3',
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'dp4': 'Fruit Fly (Drosophila pseudoobscura): dp4',
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'droAna1': 'Fruit Fly (Drosophila ananassae): droAna1',
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'droAna2': 'Fruit Fly (Drosophila ananassae): droAna2',
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'droAna3': 'Fruit Fly (Drosophila ananassae): droAna3',
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'droEre1': 'Fruit Fly (Drosophila erecta): droEre1',
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'droEre2': 'Fruit Fly (Drosophila erecta): droEre2',
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'droGri1': 'Fruit Fly (Drosophila grimshawi): droGri1',
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'droGri2': 'Fruit Fly (Drosophila grimshawi): droGri2',
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'droMoj1': 'Fruit Fly (Drosophila mojavensis): droMoj1',
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'droMoj2': 'Fruit Fly (Drosophila mojavensis): droMoj2',
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'droMoj3': 'Fruit Fly (Drosophila mojavensis): droMoj3',
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'droPer1': 'Fruit Fly (Drosophila persimilis): droPer1',
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'droSec1': 'Fruit Fly (Drosophila sechellia): droSec1',
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'droSim1': 'Fruit Fly (Drosophila simulans): droSim1',
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'droVir1': 'Fruit Fly (Drosophila virilis): droVir1',
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'droVir2': 'Fruit Fly (Drosophila virilis): droVir2',
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'droVir3': 'Fruit Fly (Drosophila virilis): droVir3',
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'droYak1': 'Fruit Fly (Drosophila yakuba): droYak1',
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'droYak2': 'Fruit Fly (Drosophila yakuba): droYak2',
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'echTel1': 'Tenrec (Echinops telfairi): echTel1',
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'equCab1': 'Horse (Equus caballus): equCab1',
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'equCab2': 'Horse (Equus caballus): equCab2',
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'eriEur1': 'Hedgehog (Erinaceus europaeus): eriEur1',
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'felCat3': 'Cat (Felis catus): felCat3',
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'fr1': 'Fugu (Takifugu rubripes): fr1',
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'fr2': 'Fugu (Takifugu rubripes): fr2',
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'galGal2': 'Chicken (Gallus gallus): galGal2',
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'galGal3': 'Chicken (Gallus gallus): galGal3',
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'gasAcu1': 'Stickleback (Gasterosteus aculeatus): gasAcu1',
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'hg16': 'Human (Homo sapiens): hg16',
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'hg17': 'Human (Homo sapiens): hg17',
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'hg18': 'Human (Homo sapiens): hg18',
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'hg19': 'Human (Homo sapiens): hg19',
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'IscaW1': 'Deer Tick (Ixodes scapularis): IscaW1',
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'lMaj5': 'Leishmania major: lMaj5',
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'mm5': 'Mouse (Mus musculus): mm5',
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'mm6': 'Mouse (Mus musculus): mm6',
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'mm7': 'Mouse (Mus musculus): mm7',
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'mm8': 'Mouse (Mus musculus): mm8',
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'mm9': 'Mouse (Mus musculus): mm9',
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'monDom4': 'Opossum (Monodelphis domestica): monDom4',
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'monDom5': 'Opossum (Monodelphis domestica): monDom5',
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'ornAna1': 'Platypus (Ornithorhynchus anatinus): ornAna1',
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'oryCun1': 'Rabbit (Oryctolagus cuniculus): oryCun1',
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'oryLat1': 'Medaka (Oryzias latipes): oryLat1',
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'oryLat2': 'Medaka (Oryzias latipes): oryLat2',
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'oryza_sativa_japonica_nipponbare_IRGSP4.0': 'Rice (Oryza sativa L. ssp. japonica var. Nipponbare): IRGSP4.0',
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'otoGar1': 'Bushbaby (Otolemur garnetti): otoGar1',
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'panTro1': 'Chimpanzee (Pan troglodytes): panTro1',
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'panTro2': 'Chimpanzee (Pan troglodytes): panTro2',
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'petMar1': 'Lamprey (Petromyzon marinus): petMar1',
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'phiX': 'phiX174 (AF176034)',
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'PhumU1': 'Head Louse (Pediculus humanus): PhumU1',
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'ponAbe2': 'Orangutan (Pongo pygmaeus abelii): ponAbe2',
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'pUC18': 'pUC18 (L09136)',
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'rheMac2': 'Rhesus Macaque (Macaca mulatta): rheMac2',
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'rn3': 'Rat (Rattus norvegicus): rn3',
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'rn4': 'Rat (Rattus norvegicus): rn4',
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'sacCer1': 'Yeast (Saccharomyces cerevisiae): sacCer1',
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'sacCer2': 'Yeast (Saccharomyces cerevisiae): sacCer2',
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'sorAra1': 'Common Shrew (Sorex araneus): sorAra1',
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'Sscrofa9.58': 'Pig (Sus scrofa): Sscrofa9.58',
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'strPur2': 'Purple Sea Urchin (Strongylocentrotus purpuratus): strPur2',
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'susScr2': 'Pig (Sus scrofa): susScr2',
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'taeGut1': 'Zebra Finch (Taeniopygia guttata): taeGut1',
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'tetNig1': 'Tetraodon (Tetraodon nigroviridis): tetNig1',
|
||||
'tetNig2': 'Tetraodon (Tetraodon nigroviridis): tetNig2',
|
||||
'tupBel1': 'Tree Shrew (Tupaia belangeri): tupBel1',
|
||||
'venter1': 'Human (J. Craig Venter): venter1',
|
||||
'xenTro2': 'Frog (Xenopus tropicalis): xenTro2'}
|
||||
'AgamP3': 'Mosquito (Anopheles gambiae): AgamP3',
|
||||
'anoCar1': 'Lizard (Anolis carolinensis): anoCar1',
|
||||
'anoGam1': 'Mosquito (Anopheles gambiae): anoGam1',
|
||||
'apiMel1': 'Honeybee (Apis mellifera): apiMel1',
|
||||
'apiMel2': 'Honeybee (Apis mellifera): apiMel2',
|
||||
'apiMel3': 'Honeybee (Apis mellifera): apiMel3',
|
||||
'Arabidopsis_thaliana_TAIR9': '',
|
||||
'borEut13': 'Boreoeutherian: borEut13',
|
||||
'bosTau2': 'Cow (Bos taurus): bosTau2',
|
||||
'bosTau3': 'Cow (Bos taurus): bosTau3',
|
||||
'bosTau4': 'Cow (Bos taurus): bosTau4',
|
||||
'bosTauMd3': 'Cow (Bos taurus): bosTauMd3',
|
||||
'calJac1': 'Marmoset (Callithrix jacchus): calJac1',
|
||||
'canFam1': 'Dog (Canis lupus familiaris): canFam1',
|
||||
'canFam2': 'Dog (Canis lupus familiaris): canFam2',
|
||||
'cavPor3': 'Guinea Pig (Cavia porcellus): cavPor3',
|
||||
'ce2': 'Caenorhabditis elegans: ce2',
|
||||
'ce4': 'Caenorhabditis elegans: ce4',
|
||||
'ce5': 'Caenorhabditis elegans: ce5',
|
||||
'ce6': 'Caenorhabditis elegans: ce6',
|
||||
'CpipJ1': 'Mosquito (Culex quinquefasciatus): CpipJ1',
|
||||
'danRer2': 'Zebrafish (Danio rerio): danRer2',
|
||||
'danRer3': 'Zebrafish (Danio rerio): danRer3',
|
||||
'danRer4': 'Zebrafish (Danio rerio): danRer4',
|
||||
'danRer5': 'Zebrafish (Danio rerio): danRer5',
|
||||
'danRer6': 'Zebrafish (Danio rerio): danRer6',
|
||||
'dm1': 'Fruit Fly (Drosophila melanogaster): dm1',
|
||||
'dm2': 'Fruit Fly (Drosophila melanogaster): dm2',
|
||||
'dm3': 'Fruit Fly (Drosophila melanogaster): dm3',
|
||||
'dm4': 'Fruit Fly (Drosophila melanogaster): dm',
|
||||
'dp3': 'Fruit Fly (Drosophila pseudoobscura): dp3',
|
||||
'dp4': 'Fruit Fly (Drosophila pseudoobscura): dp4',
|
||||
'droAna1': 'Fruit Fly (Drosophila ananassae): droAna1',
|
||||
'droAna2': 'Fruit Fly (Drosophila ananassae): droAna2',
|
||||
'droAna3': 'Fruit Fly (Drosophila ananassae): droAna3',
|
||||
'droEre1': 'Fruit Fly (Drosophila erecta): droEre1',
|
||||
'droEre2': 'Fruit Fly (Drosophila erecta): droEre2',
|
||||
'droGri1': 'Fruit Fly (Drosophila grimshawi): droGri1',
|
||||
'droGri2': 'Fruit Fly (Drosophila grimshawi): droGri2',
|
||||
'droMoj1': 'Fruit Fly (Drosophila mojavensis): droMoj1',
|
||||
'droMoj2': 'Fruit Fly (Drosophila mojavensis): droMoj2',
|
||||
'droMoj3': 'Fruit Fly (Drosophila mojavensis): droMoj3',
|
||||
'droPer1': 'Fruit Fly (Drosophila persimilis): droPer1',
|
||||
'droSec1': 'Fruit Fly (Drosophila sechellia): droSec1',
|
||||
'droSim1': 'Fruit Fly (Drosophila simulans): droSim1',
|
||||
'droVir1': 'Fruit Fly (Drosophila virilis): droVir1',
|
||||
'droVir2': 'Fruit Fly (Drosophila virilis): droVir2',
|
||||
'droVir3': 'Fruit Fly (Drosophila virilis): droVir3',
|
||||
'droYak1': 'Fruit Fly (Drosophila yakuba): droYak1',
|
||||
'droYak2': 'Fruit Fly (Drosophila yakuba): droYak2',
|
||||
'echTel1': 'Tenrec (Echinops telfairi): echTel1',
|
||||
'equCab1': 'Horse (Equus caballus): equCab1',
|
||||
'equCab2': 'Horse (Equus caballus): equCab2',
|
||||
'eriEur1': 'Hedgehog (Erinaceus europaeus): eriEur1',
|
||||
'felCat3': 'Cat (Felis catus): felCat3',
|
||||
'fr1': 'Fugu (Takifugu rubripes): fr1',
|
||||
'fr2': 'Fugu (Takifugu rubripes): fr2',
|
||||
'galGal2': 'Chicken (Gallus gallus): galGal2',
|
||||
'galGal3': 'Chicken (Gallus gallus): galGal3',
|
||||
'gasAcu1': 'Stickleback (Gasterosteus aculeatus): gasAcu1',
|
||||
'hg16': 'Human (Homo sapiens): hg16',
|
||||
'hg17': 'Human (Homo sapiens): hg17',
|
||||
'hg18': 'Human (Homo sapiens): hg18',
|
||||
'hg19': 'Human (Homo sapiens): hg19',
|
||||
'IscaW1': 'Deer Tick (Ixodes scapularis): IscaW1',
|
||||
'lMaj5': 'Leishmania major: lMaj5',
|
||||
'mm5': 'Mouse (Mus musculus): mm5',
|
||||
'mm6': 'Mouse (Mus musculus): mm6',
|
||||
'mm7': 'Mouse (Mus musculus): mm7',
|
||||
'mm8': 'Mouse (Mus musculus): mm8',
|
||||
'mm9': 'Mouse (Mus musculus): mm9',
|
||||
'monDom4': 'Opossum (Monodelphis domestica): monDom4',
|
||||
'monDom5': 'Opossum (Monodelphis domestica): monDom5',
|
||||
'ornAna1': 'Platypus (Ornithorhynchus anatinus): ornAna1',
|
||||
'oryCun1': 'Rabbit (Oryctolagus cuniculus): oryCun1',
|
||||
'oryLat1': 'Medaka (Oryzias latipes): oryLat1',
|
||||
'oryLat2': 'Medaka (Oryzias latipes): oryLat2',
|
||||
'oryza_sativa_japonica_nipponbare_IRGSP4.0': 'Rice (Oryza sativa L. ssp. japonica var. Nipponbare): IRGSP4.0',
|
||||
'otoGar1': 'Bushbaby (Otolemur garnetti): otoGar1',
|
||||
'panTro1': 'Chimpanzee (Pan troglodytes): panTro1',
|
||||
'panTro2': 'Chimpanzee (Pan troglodytes): panTro2',
|
||||
'petMar1': 'Lamprey (Petromyzon marinus): petMar1',
|
||||
'phiX': 'phiX174 (AF176034)',
|
||||
'PhumU1': 'Head Louse (Pediculus humanus): PhumU1',
|
||||
'ponAbe2': 'Orangutan (Pongo pygmaeus abelii): ponAbe2',
|
||||
'pUC18': 'pUC18 (L09136)',
|
||||
'rheMac2': 'Rhesus Macaque (Macaca mulatta): rheMac2',
|
||||
'rn3': 'Rat (Rattus norvegicus): rn3',
|
||||
'rn4': 'Rat (Rattus norvegicus): rn4',
|
||||
'sacCer1': 'Yeast (Saccharomyces cerevisiae): sacCer1',
|
||||
'sacCer2': 'Yeast (Saccharomyces cerevisiae): sacCer2',
|
||||
'sorAra1': 'Common Shrew (Sorex araneus): sorAra1',
|
||||
'Sscrofa9.58': 'Pig (Sus scrofa): Sscrofa9.58',
|
||||
'strPur2': 'Purple Sea Urchin (Strongylocentrotus purpuratus): strPur2',
|
||||
'susScr2': 'Pig (Sus scrofa): susScr2',
|
||||
'taeGut1': 'Zebra Finch (Taeniopygia guttata): taeGut1',
|
||||
'tetNig1': 'Tetraodon (Tetraodon nigroviridis): tetNig1',
|
||||
'tetNig2': 'Tetraodon (Tetraodon nigroviridis): tetNig2',
|
||||
'tupBel1': 'Tree Shrew (Tupaia belangeri): tupBel1',
|
||||
'venter1': 'Human (J. Craig Venter): venter1',
|
||||
'xenTro2': 'Frog (Xenopus tropicalis): xenTro2'}
|
||||
|
||||
VARIANT_MAP = {'canon': 'Canonical',
|
||||
'full': 'Full',
|
||||
|
||||
@@ -404,10 +404,10 @@ class Tag(PageElement):
|
||||
"""Represents a found HTML tag with its attributes and contents."""
|
||||
|
||||
XML_ENTITIES_TO_CHARS = {'apos': "'",
|
||||
"quot": '"',
|
||||
"amp": "&",
|
||||
"lt": "<",
|
||||
"gt": ">"
|
||||
"quot": '"',
|
||||
"amp": "&",
|
||||
"lt": "<",
|
||||
"gt": ">"
|
||||
}
|
||||
# An RE for finding ampersands that aren't the start of of a
|
||||
# numeric entity.
|
||||
@@ -1341,11 +1341,11 @@ class BeautifulSoup(BeautifulStoneSoup):
|
||||
|
||||
# Lists can contain other lists, but there are restrictions.
|
||||
NESTABLE_LIST_TAGS = {'ol': [],
|
||||
'ul': [],
|
||||
'li': ['ul', 'ol'],
|
||||
'dl': [],
|
||||
'dd': ['dl'],
|
||||
'dt': ['dl']}
|
||||
'ul': [],
|
||||
'li': ['ul', 'ol'],
|
||||
'dl': [],
|
||||
'dd': ['dl'],
|
||||
'dt': ['dl']}
|
||||
|
||||
# Tables can contain other tables, but there are restrictions.
|
||||
NESTABLE_TABLE_TAGS = {'table': [],
|
||||
@@ -1564,7 +1564,7 @@ class UnicodeDammit:
|
||||
# values that aren't in Python's aliases and can't be determined
|
||||
# by the heuristics in find_codec.
|
||||
CHARSET_ALIASES = {"macintosh": "mac-roman",
|
||||
"x-sjis": "shift-jis"}
|
||||
"x-sjis": "shift-jis"}
|
||||
|
||||
def __init__(self, markup, overrideEncodings=[],
|
||||
smartQuotesTo='xml'):
|
||||
@@ -1767,37 +1767,37 @@ class UnicodeDammit:
|
||||
return s.translate(c.EBCDIC_TO_ASCII_MAP)
|
||||
|
||||
MS_CHARS = {'\x80': ('euro', '20AC'),
|
||||
'\x81': ' ',
|
||||
'\x82': ('sbquo', '201A'),
|
||||
'\x83': ('fnof', '192'),
|
||||
'\x84': ('bdquo', '201E'),
|
||||
'\x85': ('hellip', '2026'),
|
||||
'\x86': ('dagger', '2020'),
|
||||
'\x87': ('Dagger', '2021'),
|
||||
'\x88': ('circ', '2C6'),
|
||||
'\x89': ('permil', '2030'),
|
||||
'\x8A': ('Scaron', '160'),
|
||||
'\x8B': ('lsaquo', '2039'),
|
||||
'\x8C': ('OElig', '152'),
|
||||
'\x8D': '?',
|
||||
'\x8E': ('#x17D', '17D'),
|
||||
'\x8F': '?',
|
||||
'\x90': '?',
|
||||
'\x91': ('lsquo', '2018'),
|
||||
'\x92': ('rsquo', '2019'),
|
||||
'\x93': ('ldquo', '201C'),
|
||||
'\x94': ('rdquo', '201D'),
|
||||
'\x95': ('bull', '2022'),
|
||||
'\x96': ('ndash', '2013'),
|
||||
'\x97': ('mdash', '2014'),
|
||||
'\x98': ('tilde', '2DC'),
|
||||
'\x99': ('trade', '2122'),
|
||||
'\x9a': ('scaron', '161'),
|
||||
'\x9b': ('rsaquo', '203A'),
|
||||
'\x9c': ('oelig', '153'),
|
||||
'\x9d': '?',
|
||||
'\x9e': ('#x17E', '17E'),
|
||||
'\x9f': ('Yuml', '178')}
|
||||
'\x81': ' ',
|
||||
'\x82': ('sbquo', '201A'),
|
||||
'\x83': ('fnof', '192'),
|
||||
'\x84': ('bdquo', '201E'),
|
||||
'\x85': ('hellip', '2026'),
|
||||
'\x86': ('dagger', '2020'),
|
||||
'\x87': ('Dagger', '2021'),
|
||||
'\x88': ('circ', '2C6'),
|
||||
'\x89': ('permil', '2030'),
|
||||
'\x8A': ('Scaron', '160'),
|
||||
'\x8B': ('lsaquo', '2039'),
|
||||
'\x8C': ('OElig', '152'),
|
||||
'\x8D': '?',
|
||||
'\x8E': ('#x17D', '17D'),
|
||||
'\x8F': '?',
|
||||
'\x90': '?',
|
||||
'\x91': ('lsquo', '2018'),
|
||||
'\x92': ('rsquo', '2019'),
|
||||
'\x93': ('ldquo', '201C'),
|
||||
'\x94': ('rdquo', '201D'),
|
||||
'\x95': ('bull', '2022'),
|
||||
'\x96': ('ndash', '2013'),
|
||||
'\x97': ('mdash', '2014'),
|
||||
'\x98': ('tilde', '2DC'),
|
||||
'\x99': ('trade', '2122'),
|
||||
'\x9a': ('scaron', '161'),
|
||||
'\x9b': ('rsaquo', '203A'),
|
||||
'\x9c': ('oelig', '153'),
|
||||
'\x9d': '?',
|
||||
'\x9e': ('#x17E', '17E'),
|
||||
'\x9f': ('Yuml', '178')}
|
||||
|
||||
#######################################################################
|
||||
|
||||
|
||||
@@ -43,14 +43,14 @@ def main():
|
||||
jobs = {}
|
||||
try:
|
||||
for job in app.model.Job.filter(sa.and_(app.model.Job.table.c.create_time.between('2008-05-23', '2008-11-29'),
|
||||
app.model.Job.table.c.state == 'ok',
|
||||
sa.or_(sa.and_(sa.or_(app.model.Job.table.c.tool_id == 'gops_intersect_1',
|
||||
app.model.Job.table.c.tool_id == 'gops_subtract_1',
|
||||
app.model.Job.table.c.tool_id == 'gops_coverage_1'),
|
||||
sa.not_(app.model.Job.table.c.command_line.like('%-2 1,2,3%'))),
|
||||
sa.and_(sa.or_(app.model.Job.table.c.tool_id == 'gops_complement_1',
|
||||
app.model.Job.table.c.tool_id == 'gops_merge_1'),
|
||||
sa.not_(app.model.Job.table.c.command_line.like('%-1 1,2,3%')))))).all():
|
||||
app.model.Job.table.c.state == 'ok',
|
||||
sa.or_(sa.and_(sa.or_(app.model.Job.table.c.tool_id == 'gops_intersect_1',
|
||||
app.model.Job.table.c.tool_id == 'gops_subtract_1',
|
||||
app.model.Job.table.c.tool_id == 'gops_coverage_1'),
|
||||
sa.not_(app.model.Job.table.c.command_line.like('%-2 1,2,3%'))),
|
||||
sa.and_(sa.or_(app.model.Job.table.c.tool_id == 'gops_complement_1',
|
||||
app.model.Job.table.c.tool_id == 'gops_merge_1'),
|
||||
sa.not_(app.model.Job.table.c.command_line.like('%-1 1,2,3%')))))).all():
|
||||
print "# processing job id %s" % str(job.id)
|
||||
for jtoda in job.output_datasets:
|
||||
print "# --> processing JobToOutputDatasetAssociation id %s" % str(jtoda.id)
|
||||
|
||||
@@ -42,9 +42,9 @@ def main():
|
||||
jobs = {}
|
||||
try:
|
||||
for job in app.model.Job.filter(sa.and_(app.model.Job.table.c.create_time < '2008-12-16',
|
||||
app.model.Job.table.c.state == 'ok',
|
||||
app.model.Job.table.c.tool_id == 'gops_join_1',
|
||||
sa.not_(app.model.Job.table.c.command_line.like('%-m 1 %')))).all():
|
||||
app.model.Job.table.c.state == 'ok',
|
||||
app.model.Job.table.c.tool_id == 'gops_join_1',
|
||||
sa.not_(app.model.Job.table.c.command_line.like('%-m 1 %')))).all():
|
||||
print "# processing job id %s" % str(job.id)
|
||||
for jtoda in job.output_datasets:
|
||||
print "# --> processing JobToOutputDatasetAssociation id %s" % str(jtoda.id)
|
||||
|
||||
@@ -21,7 +21,7 @@ def init():
|
||||
options.config = os.path.abspath(options.config)
|
||||
|
||||
config_parser = ConfigParser(dict(here=os.getcwd(),
|
||||
database_connection='sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE'))
|
||||
database_connection='sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE'))
|
||||
config_parser.read(options.config)
|
||||
|
||||
config_dict = {}
|
||||
|
||||
@@ -30,7 +30,7 @@ def init():
|
||||
options.email = None
|
||||
|
||||
config_parser = ConfigParser(dict(here=os.getcwd(),
|
||||
database_connection='sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE'))
|
||||
database_connection='sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE'))
|
||||
config_parser.read(options.config)
|
||||
|
||||
config_dict = {}
|
||||
|
||||
@@ -26,10 +26,10 @@ class HTTPRedirectWithDataHandler(urllib2.HTTPRedirectHandler):
|
||||
if str(code) in self.redirect_codes and request_method in self.valid_methods:
|
||||
new_url = new_url.replace(' ', '%20')
|
||||
request = urllib2.Request(new_url,
|
||||
data=request.data,
|
||||
headers=request.headers,
|
||||
origin_req_host=request.get_origin_req_host(),
|
||||
unverifiable=True)
|
||||
data=request.data,
|
||||
headers=request.headers,
|
||||
origin_req_host=request.get_origin_req_host(),
|
||||
unverifiable=True)
|
||||
if self.method in self.valid_methods:
|
||||
if request.get_method() != self.method:
|
||||
request.get_method = lambda: self.method
|
||||
|
||||
@@ -36,7 +36,7 @@ def main(options):
|
||||
description = category_dict.get('description', None)
|
||||
if name is not None and description is not None:
|
||||
data = dict(name=name,
|
||||
description=description)
|
||||
description=description)
|
||||
url = '%s/api/categories' % to_tool_shed
|
||||
try:
|
||||
response = submit(url, data, api_key)
|
||||
|
||||
@@ -38,8 +38,8 @@ def main(options):
|
||||
email = '%s@test.org' % username
|
||||
password = 'testuser'
|
||||
data = dict(email=email,
|
||||
password=password,
|
||||
username=username)
|
||||
password=password,
|
||||
username=username)
|
||||
url = '%s/api/users' % to_tool_shed
|
||||
try:
|
||||
response = submit(url, data, api_key)
|
||||
|
||||
@@ -24,21 +24,21 @@ CHUNK_SIZE = 2 ** 20 # 1Mb
|
||||
|
||||
|
||||
def generate_repository_archive_filename(tool_shed_url, name, owner, changeset_revision, file_type,
|
||||
export_repository_dependencies, use_tmp_archive_dir=False):
|
||||
export_repository_dependencies, use_tmp_archive_dir=False):
|
||||
tool_shed = remove_protocol_from_tool_shed_url(tool_shed_url)
|
||||
file_type_str = basic_util.get_file_type_str(changeset_revision, file_type)
|
||||
if export_repository_dependencies:
|
||||
repositories_archive_filename = '%s_%s_%s_%s_%s' % (CAPSULE_WITH_DEPENDENCIES_FILENAME,
|
||||
tool_shed,
|
||||
name,
|
||||
owner,
|
||||
file_type_str)
|
||||
tool_shed,
|
||||
name,
|
||||
owner,
|
||||
file_type_str)
|
||||
else:
|
||||
repositories_archive_filename = '%s_%s_%s_%s_%s' % (CAPSULE_FILENAME,
|
||||
tool_shed,
|
||||
name,
|
||||
owner,
|
||||
file_type_str)
|
||||
tool_shed,
|
||||
name,
|
||||
owner,
|
||||
file_type_str)
|
||||
if use_tmp_archive_dir:
|
||||
tmp_archive_dir = tempfile.mkdtemp(prefix="tmp-toolshed-arcdir")
|
||||
repositories_archive_filename = os.path.join(tmp_archive_dir, repositories_archive_filename)
|
||||
@@ -89,12 +89,12 @@ def main(options):
|
||||
export_repository_dependencies = string_as_bool(options.export_repository_dependencies)
|
||||
repositories_archive_filename = \
|
||||
generate_repository_archive_filename(base_tool_shed_url,
|
||||
options.name,
|
||||
options.owner,
|
||||
options.changeset_revision,
|
||||
file_type,
|
||||
export_repository_dependencies=export_repository_dependencies,
|
||||
use_tmp_archive_dir=False)
|
||||
options.name,
|
||||
options.owner,
|
||||
options.changeset_revision,
|
||||
file_type,
|
||||
export_repository_dependencies=export_repository_dependencies,
|
||||
use_tmp_archive_dir=False)
|
||||
download_url = export_dict['download_url']
|
||||
download_dir = os.path.abspath(options.download_dir)
|
||||
file_path = os.path.join(download_dir, repositories_archive_filename)
|
||||
|
||||
@@ -44,13 +44,13 @@ def main(options):
|
||||
tools_functionally_correct = str(options.tools_functionally_correct)
|
||||
parts = ['repository_revisions']
|
||||
params = dict(do_not_test=do_not_test,
|
||||
downloadable=downloadable,
|
||||
includes_tools=includes_tools,
|
||||
malicious=malicious,
|
||||
missing_test_components=missing_test_components,
|
||||
skip_tool_test=skip_tool_test,
|
||||
test_install_error=test_install_error,
|
||||
tools_functionally_correct=tools_functionally_correct)
|
||||
downloadable=downloadable,
|
||||
includes_tools=includes_tools,
|
||||
malicious=malicious,
|
||||
missing_test_components=missing_test_components,
|
||||
skip_tool_test=skip_tool_test,
|
||||
test_install_error=test_install_error,
|
||||
tools_functionally_correct=tools_functionally_correct)
|
||||
api_url = get_api_url(base=base_tool_shed_url, parts=parts, params=params)
|
||||
baseline_repository_dicts, error_message = json_from_url(api_url)
|
||||
if baseline_repository_dicts is None or error_message:
|
||||
@@ -84,7 +84,7 @@ if __name__ == '__main__':
|
||||
parser = argparse.ArgumentParser(description='Get a filtered list of repository dictionaries.')
|
||||
parser.add_argument("-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL")
|
||||
parser.add_argument("-l", "--latest_revision_only", dest="latest_revision_only", default=True,
|
||||
help="Restrict results to latest downloadable revision only")
|
||||
help="Restrict results to latest downloadable revision only")
|
||||
parser.add_argument("-n", "--do_not_test", help="do_not_test", default=False)
|
||||
parser.add_argument("-d", "--downloadable", help="downloadable", default=True)
|
||||
parser.add_argument("-i", "--includes_tools", help="includes_tools", default=True)
|
||||
|
||||
@@ -70,7 +70,7 @@ def main(options):
|
||||
sys.exit(1)
|
||||
else:
|
||||
data = dict(encoded_ids_to_skip=encoded_ids_to_skip,
|
||||
my_writable=my_writable)
|
||||
my_writable=my_writable)
|
||||
url = '%s/api/repositories/reset_metadata_on_repositories' % base_tool_shed_url
|
||||
try:
|
||||
submit(url, data, options.api)
|
||||
|
||||
@@ -35,9 +35,9 @@ class BootstrapApplication(object):
|
||||
print 'Using database connection: ', self.config.database_connection
|
||||
# Setup the database engine and ORM
|
||||
self.model = mapping.init(self.config.file_path,
|
||||
self.config.database_connection,
|
||||
engine_options={},
|
||||
create_tables=False)
|
||||
self.config.database_connection,
|
||||
engine_options={},
|
||||
create_tables=False)
|
||||
self.security = security.SecurityHelper(id_secret=self.config.id_secret)
|
||||
self.hgweb_config_manager = self.model.hgweb_config_manager
|
||||
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
|
||||
|
||||
@@ -97,13 +97,13 @@ def build_index(sa_session, whoosh_index_dir, path_to_repositories):
|
||||
for tool in repo.get('tools_list'):
|
||||
# print tool
|
||||
tool_index_writer.add_document(id=to_unicode(tool.get('id')),
|
||||
name=to_unicode(tool.get('name')),
|
||||
version=to_unicode(tool.get('version')),
|
||||
description=to_unicode(tool.get('description')),
|
||||
help=to_unicode(tool.get('help')),
|
||||
repo_owner_username=to_unicode(repo.get('repo_owner_username')),
|
||||
repo_name=to_unicode(repo.get('name')),
|
||||
repo_id=repo.get('id'))
|
||||
name=to_unicode(tool.get('name')),
|
||||
version=to_unicode(tool.get('version')),
|
||||
description=to_unicode(tool.get('description')),
|
||||
help=to_unicode(tool.get('help')),
|
||||
repo_owner_username=to_unicode(repo.get('repo_owner_username')),
|
||||
repo_name=to_unicode(repo.get('name')),
|
||||
repo_id=repo.get('id'))
|
||||
tools_indexed += 1
|
||||
print tools_indexed, 'tools (', tool.get('id'), ')'
|
||||
|
||||
@@ -164,17 +164,17 @@ def get_repos(sa_session, path_to_repositories):
|
||||
tools_list.extend(tools_in_dir)
|
||||
|
||||
results.append(dict(id=repo_id,
|
||||
name=name,
|
||||
description=description,
|
||||
long_description=long_description,
|
||||
homepage_url=homepage_url,
|
||||
remote_repository_url=remote_repository_url,
|
||||
repo_owner_username=repo_owner_username,
|
||||
times_downloaded=times_downloaded,
|
||||
approved=approved,
|
||||
last_updated=last_updated,
|
||||
full_last_updated=full_last_updated,
|
||||
tools_list=tools_list))
|
||||
name=name,
|
||||
description=description,
|
||||
long_description=long_description,
|
||||
homepage_url=homepage_url,
|
||||
remote_repository_url=remote_repository_url,
|
||||
repo_owner_username=repo_owner_username,
|
||||
times_downloaded=times_downloaded,
|
||||
approved=approved,
|
||||
last_updated=last_updated,
|
||||
full_last_updated=full_last_updated,
|
||||
tools_list=tools_list))
|
||||
return results
|
||||
|
||||
|
||||
@@ -191,8 +191,8 @@ def load_one_dir(path):
|
||||
if root.find('description') is not None:
|
||||
tool.update(dict(description=root.find('description').text))
|
||||
tool.update(dict(id=root.attrib.get('id'),
|
||||
name=root.attrib.get('name'),
|
||||
version=root.attrib.get('version')))
|
||||
name=root.attrib.get('name'),
|
||||
version=root.attrib.get('version')))
|
||||
tools_in_dir.append(tool)
|
||||
return tools_in_dir
|
||||
|
||||
|
||||
+10
-10
@@ -55,16 +55,16 @@ if __name__ == '__main__':
|
||||
description += 'the --delete command line argument is provided.'
|
||||
parser = argparse.ArgumentParser(description=description)
|
||||
parser.add_argument('--delete',
|
||||
dest='delete',
|
||||
required=False,
|
||||
action='store_true',
|
||||
default=False,
|
||||
help='Whether to delete empty folders or list them on exit.')
|
||||
dest='delete',
|
||||
required=False,
|
||||
action='store_true',
|
||||
default=False,
|
||||
help='Whether to delete empty folders or list them on exit.')
|
||||
parser.add_argument('--basepath',
|
||||
dest='basepath',
|
||||
required=True,
|
||||
action='store',
|
||||
metavar='name',
|
||||
help='The base path where tool dependencies are installed.')
|
||||
dest='basepath',
|
||||
required=True,
|
||||
action='store',
|
||||
metavar='name',
|
||||
help='The base path where tool dependencies are installed.')
|
||||
args = parser.parse_args()
|
||||
sys.exit(main(args))
|
||||
|
||||
@@ -116,38 +116,38 @@ if __name__ == '__main__':
|
||||
description += 'the --delete command line argument is provided with a true value.'
|
||||
parser = argparse.ArgumentParser(description=description)
|
||||
parser.add_argument('--delete',
|
||||
dest='delete',
|
||||
required=True,
|
||||
action='store',
|
||||
default=False,
|
||||
type=asbool,
|
||||
help='Whether to delete empty folders or list them on exit.')
|
||||
dest='delete',
|
||||
required=True,
|
||||
action='store',
|
||||
default=False,
|
||||
type=asbool,
|
||||
help='Whether to delete empty folders or list them on exit.')
|
||||
parser.add_argument('--bucket',
|
||||
dest='bucket',
|
||||
required=True,
|
||||
action='store',
|
||||
metavar='name',
|
||||
help='The S3 bucket where tool dependencies are installed.')
|
||||
dest='bucket',
|
||||
required=True,
|
||||
action='store',
|
||||
metavar='name',
|
||||
help='The S3 bucket where tool dependencies are installed.')
|
||||
parser.add_argument('--id',
|
||||
dest='id',
|
||||
required=False,
|
||||
action='store',
|
||||
default=None,
|
||||
metavar='ACCESS_KEY',
|
||||
help='The identifier for an amazon account that has read access to the bucket.')
|
||||
dest='id',
|
||||
required=False,
|
||||
action='store',
|
||||
default=None,
|
||||
metavar='ACCESS_KEY',
|
||||
help='The identifier for an amazon account that has read access to the bucket.')
|
||||
parser.add_argument('--secret',
|
||||
dest='secret',
|
||||
required=False,
|
||||
action='store',
|
||||
default=None,
|
||||
metavar='SECRET_KEY',
|
||||
help='The secret key for an amazon account that has upload/delete access to the bucket.')
|
||||
dest='secret',
|
||||
required=False,
|
||||
action='store',
|
||||
default=None,
|
||||
metavar='SECRET_KEY',
|
||||
help='The secret key for an amazon account that has upload/delete access to the bucket.')
|
||||
parser.add_argument('--s3passwd',
|
||||
dest='s3passwd',
|
||||
required=False,
|
||||
action='store',
|
||||
default=None,
|
||||
metavar='path/file',
|
||||
help='The path to a file containing Amazon access credentials, in the format KEY:SECRET.')
|
||||
dest='s3passwd',
|
||||
required=False,
|
||||
action='store',
|
||||
default=None,
|
||||
metavar='path/file',
|
||||
help='The path to a file containing Amazon access credentials, in the format KEY:SECRET.')
|
||||
args = parser.parse_args()
|
||||
sys.exit(main(args))
|
||||
|
||||
@@ -23,10 +23,10 @@ if __name__ == '__main__':
|
||||
description = 'Clean out the configured tool dependency path, creating it if it does not exist.'
|
||||
parser = argparse.ArgumentParser(description=description)
|
||||
parser.add_argument('--tool_dependency_dir',
|
||||
dest='tool_dependency_dir',
|
||||
required=True,
|
||||
action='store',
|
||||
metavar='name',
|
||||
help='The base path where tool dependencies will be installed.')
|
||||
dest='tool_dependency_dir',
|
||||
required=True,
|
||||
action='store',
|
||||
metavar='name',
|
||||
help='The base path where tool dependencies will be installed.')
|
||||
args = parser.parse_args()
|
||||
sys.exit(main(args))
|
||||
|
||||
@@ -105,18 +105,18 @@ def deprecate_repositories(app, cutoff_time, days=14, info_only=False, verbose=F
|
||||
# Get a unique list of repository ids from the repository_metadata table. Any repository ID found in this table is not
|
||||
# empty, and will not be checked.
|
||||
metadata_records = sa.select([distinct(app.model.RepositoryMetadata.table.c.repository_id)],
|
||||
from_obj=app.model.RepositoryMetadata.table) \
|
||||
.execute()
|
||||
from_obj=app.model.RepositoryMetadata.table) \
|
||||
.execute()
|
||||
for metadata_record in metadata_records:
|
||||
repository_ids_to_not_check.append(metadata_record.repository_id)
|
||||
# Get the repositories that are A) not present in the above list, and b) older than the specified time.
|
||||
# This will yield a list of repositories that have been created more than n days ago, but never populated.
|
||||
repository_query = sa.select([app.model.Repository.table.c.id],
|
||||
whereclause=and_(app.model.Repository.table.c.create_time < cutoff_time,
|
||||
app.model.Repository.table.c.deprecated == false(),
|
||||
app.model.Repository.table.c.deleted == false(),
|
||||
not_(app.model.Repository.table.c.id.in_(repository_ids_to_not_check))),
|
||||
from_obj=[app.model.Repository.table])
|
||||
whereclause=and_(app.model.Repository.table.c.create_time < cutoff_time,
|
||||
app.model.Repository.table.c.deprecated == false(),
|
||||
app.model.Repository.table.c.deleted == false(),
|
||||
not_(app.model.Repository.table.c.id.in_(repository_ids_to_not_check))),
|
||||
from_obj=[app.model.Repository.table])
|
||||
query_result = repository_query.execute()
|
||||
repositories = []
|
||||
repositories_by_owner = {}
|
||||
|
||||
@@ -52,9 +52,9 @@ def directory_hash_id(id):
|
||||
def get_versions(app, item):
|
||||
"""Get all versions of item whose state is a valid state"""
|
||||
valid_states = [app.model.Tool.states.NEW,
|
||||
app.model.Tool.states.WAITING,
|
||||
app.model.Tool.states.APPROVED,
|
||||
app.model.Tool.states.ARCHIVED]
|
||||
app.model.Tool.states.WAITING,
|
||||
app.model.Tool.states.APPROVED,
|
||||
app.model.Tool.states.ARCHIVED]
|
||||
versions = [item]
|
||||
this_item = item
|
||||
while item.newer_version:
|
||||
@@ -85,8 +85,8 @@ def create_repository_from_tool(app, sa_session, tool):
|
||||
repo_name = tool.tool_id.lower().replace(' ', '_')
|
||||
print "Creating repository '%s' in database" % (repo_name)
|
||||
repository = app.model.Repository(name=repo_name,
|
||||
description=tool.description,
|
||||
user_id=tool.user_id)
|
||||
description=tool.description,
|
||||
user_id=tool.user_id)
|
||||
# Flush to get the id
|
||||
sa_session.add(repository)
|
||||
sa_session.flush()
|
||||
@@ -116,8 +116,8 @@ def create_repository_from_tool(app, sa_session, tool):
|
||||
print "Associating ratings for tool '%s' with repository '%s'" % (tool.name, repository.name)
|
||||
for tra in tool.ratings:
|
||||
rra = app.model.RepositoryRatingAssociation(user=tra.user,
|
||||
rating=tra.rating,
|
||||
comment=tra.comment)
|
||||
rating=tra.rating,
|
||||
comment=tra.comment)
|
||||
rra.repository = repository
|
||||
sa_session.add(rra)
|
||||
sa_session.flush()
|
||||
|
||||
@@ -54,17 +54,17 @@ if __name__ == '__main__':
|
||||
description += '--delete command line argument is provided.'
|
||||
parser = argparse.ArgumentParser(description=description)
|
||||
parser.add_argument('--basepath',
|
||||
dest='basepath',
|
||||
required=True,
|
||||
action='store',
|
||||
metavar='name',
|
||||
help='The base path where tool dependencies are installed.')
|
||||
dest='basepath',
|
||||
required=True,
|
||||
action='store',
|
||||
metavar='name',
|
||||
help='The base path where tool dependencies are installed.')
|
||||
parser.add_argument('--dburi',
|
||||
dest='dburi',
|
||||
required=True,
|
||||
action='store',
|
||||
metavar='dburi',
|
||||
help='The database URI to connect to.')
|
||||
dest='dburi',
|
||||
required=True,
|
||||
action='store',
|
||||
metavar='dburi',
|
||||
help='The database URI to connect to.')
|
||||
args = parser.parse_args()
|
||||
database_connection = args.dburi
|
||||
config_dict = dict(database_connection=database_connection, tool_dependency_dir=args.basepath)
|
||||
|
||||
+9
-9
@@ -52,7 +52,7 @@ class ArgHandler(object):
|
||||
def __init__(self):
|
||||
self.parser = optparse.OptionParser()
|
||||
self.parser.add_option('-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)',
|
||||
default=os.path.abspath(os.path.join(galaxy_root, 'config/galaxy.ini')))
|
||||
default=os.path.abspath(os.path.join(galaxy_root, 'config/galaxy.ini')))
|
||||
self.parser.add_option('-d', '--debug', action='store_true', dest='debug', help="Debug (don't detach)")
|
||||
self.parser.add_option('-s', '--slow', action='store_true', dest='slow', help="Transfer slowly (for debugging)")
|
||||
self.opts = None
|
||||
@@ -83,9 +83,9 @@ class GalaxyApp(object):
|
||||
"""
|
||||
def __init__(self, config_file):
|
||||
self.config = ConfigParser.ConfigParser(dict(database_file='database/universe.sqlite',
|
||||
file_path='database/files',
|
||||
transfer_worker_port_range='12275-12675',
|
||||
transfer_worker_log=None))
|
||||
file_path='database/files',
|
||||
transfer_worker_port_range='12275-12675',
|
||||
transfer_worker_log=None))
|
||||
self.config.read(config_file)
|
||||
self.model = bunch.Bunch()
|
||||
self.connect_database()
|
||||
@@ -275,12 +275,12 @@ def scp_transfer(transfer_job):
|
||||
try:
|
||||
# TODO: add the ability to determine progress of the copy here like we do in the http_transfer above.
|
||||
cmd = "scp %s@%s:'%s' '%s'" % (user_name,
|
||||
host,
|
||||
file_path.replace(' ', '\ '),
|
||||
fn)
|
||||
host,
|
||||
file_path.replace(' ', '\ '),
|
||||
fn)
|
||||
pexpect.run(cmd, events={'.ssword:*': password + '\r\n',
|
||||
pexpect.TIMEOUT: print_ticks},
|
||||
timeout=10)
|
||||
pexpect.TIMEOUT: print_ticks},
|
||||
timeout=10)
|
||||
return dict(state=transfer_job.states.DONE, path=fn)
|
||||
except Exception as e:
|
||||
return dict(state=transfer_job.states.ERROR, info='Error during file transfer: %s' % str(e))
|
||||
|
||||
Reference in New Issue
Block a user