galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00

Files

T

mvdbeek 366701cfb2 Strip unicode control characters from tags

Leaving them in can trip up postgresql:
```
Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 396, in create
    return self.__create_dataset_collection(trans, history, payload, **kwd)
  File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 525, in __create_dataset_collection
    **create_params
  File "lib/galaxy/managers/collections.py", line 108, in create
    copy_elements=copy_elements,
  File "lib/galaxy/managers/collections.py", line 181, in create_dataset_collection
    copy_elements=copy_elements)
  File "lib/galaxy/managers/collections.py", line 217, in _element_identifiers_to_elements
    copy_elements=copy_elements)
  File "lib/galaxy/managers/collections.py", line 389, in __load_elements
    copy_elements=copy_elements)
  File "lib/galaxy/managers/collections.py", line 434, in __load_element
    self.tag_manager.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)
  File "lib/galaxy/managers/tags.py", line 182, in apply_item_tags
    self.apply_item_tag(user, item, name, value)
  File "lib/galaxy/managers/tags.py", line 154, in apply_item_tag
    tag = self._get_or_create_tag(lc_name)
  File "lib/galaxy/managers/tags.py", line 233, in _get_or_create_tag
    tag = self.get_tag_by_name(scrubbed_tag_str)
  File "lib/galaxy/managers/tags.py", line 205, in get_tag_by_name
    return self.sa_session.query(galaxy.model.Tag).filter_by(name=tag_name.lower()).first()
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2789, in first
    ret = list(self[0:1])
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2581, in __getitem__
    return list(res)
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__
    return self._execute_and_instances(context)
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances
    result = conn.execute(querycontext.statement, self._params)
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute
    return meth(self, multiparams, params)
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement
    compiled_sql, distilled_params
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context
    context)
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1416, in _handle_dbapi_exception
    util.reraise(*exc_info)
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context
    context)
  File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute
    cursor.execute(statement, parameters)
ValueError: A string literal cannot contain NUL (0x00) characters.
```

2018-08-26 22:29:23 +02:00

__init__.py

Testing: move managers, web/base, datatypes/dataproviders, and visualization 'unit'(?) tests to using common mock objects and loading system; cleanup

2015-04-16 10:25:34 -04:00

base.py

Fix import order everywhere

2017-11-14 19:42:39 +00:00

test_CollectionManager.py

Revert "Adapt unit tests to copying HDAs when creating collections"

2018-08-26 22:13:50 +02:00

test_DatasetManager.py

Remove unused dataset deserializer stuff.