# HG changeset patch
# User gga
# Date 1541423134 18000
# Node ID 3af5ba30d0cd6076ac824e5e822c4ede94ffc0f0
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
diff -r 000000000000 -r 3af5ba30d0cd README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Mon Nov 05 08:05:34 2018 -0500
@@ -0,0 +1,43 @@
+Galaxy-chado
+=============
+
+Galaxy tools to interface with Tripal using python-chado
+
+Dependencies
+------------
+
+You will need to install some python modules in the Galaxy virtualenv for these
+tools to be fully functional:
+
+.. code:: bash
+
+ . /path/to/galaxy/.venv/bin/activate
+ pip install future chado
+ deactivate
+
+Environment
+-----------
+
+The following environment variables must be set:
+
++--------------------------------+-----------------------------------------------------------+
+| ENV | Use |
++================================+===========================================================+
+| ``$GALAXY_CHADO_DBHOST`` | Host of the Chado database |
++--------------------------------+-----------------------------------------------------------+
+| ``$GALAXY_CHADO_DBNAME`` | Name of the Chado database |
++--------------------------------+-----------------------------------------------------------+
+| ``$GALAXY_CHADO_DBUSER`` | Username to connect to the database |
++--------------------------------+-----------------------------------------------------------+
+| ``$GALAXY_CHADO_DBPASS`` | Password to connect to the database |
++--------------------------------+-----------------------------------------------------------+
+| ``$GALAXY_CHADO_DBSCHEMA`` | Database schema. |
++--------------------------------+-----------------------------------------------------------+
+| ``$GALAXY_CHADO_DBPORT`` | Port of the Chado database |
++--------------------------------+-----------------------------------------------------------+
+
+
+License
+-------
+
+All python scripts and wrappers are licensed under MIT license.
diff -r 000000000000 -r 3af5ba30d0cd chado.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chado.py Mon Nov 05 08:05:34 2018 -0500
@@ -0,0 +1,470 @@
+import collections
+import os
+import time
+from abc import abstractmethod
+
+import chado
+
+
+#############################################
+# BEGIN IMPORT OF CACHING LIBRARY #
+#############################################
+# This code is licensed under the MIT #
+# License and is a copy of code publicly #
+# available in rev. #
+# e27332bc82f4e327aedaec17c9b656ae719322ed #
+# of https://github.com/tkem/cachetools/ #
+#############################################
+class DefaultMapping(collections.MutableMapping):
+
+ __slots__ = ()
+
+ @abstractmethod
+ def __contains__(self, key): # pragma: nocover
+ return False
+
+ @abstractmethod
+ def __getitem__(self, key): # pragma: nocover
+ if hasattr(self.__class__, '__missing__'):
+ return self.__class__.__missing__(self, key)
+ else:
+ raise KeyError(key)
+
+ def get(self, key, default=None):
+ if key in self:
+ return self[key]
+ else:
+ return default
+
+ __marker = object()
+
+ def pop(self, key, default=__marker):
+ if key in self:
+ value = self[key]
+ del self[key]
+ elif default is self.__marker:
+ raise KeyError(key)
+ else:
+ value = default
+ return value
+
+ def setdefault(self, key, default=None):
+ if key in self:
+ value = self[key]
+ else:
+ self[key] = value = default
+ return value
+
+
+DefaultMapping.register(dict)
+
+
+class _DefaultSize(object):
+ def __getitem__(self, _):
+ return 1
+
+ def __setitem__(self, _, value):
+ assert value == 1
+
+ def pop(self, _):
+ return 1
+
+
+class Cache(DefaultMapping):
+ """Mutable mapping to serve as a simple cache or cache base class."""
+
+ __size = _DefaultSize()
+
+ def __init__(self, maxsize, missing=None, getsizeof=None):
+ if missing:
+ self.__missing = missing
+ if getsizeof:
+ self.__getsizeof = getsizeof
+ self.__size = dict()
+ self.__data = dict()
+ self.__currsize = 0
+ self.__maxsize = maxsize
+
+ def __repr__(self):
+ return '%s(%r, maxsize=%r, currsize=%r)' % (
+ self.__class__.__name__,
+ list(self.__data.items()),
+ self.__maxsize,
+ self.__currsize,
+ )
+
+ def __getitem__(self, key):
+ try:
+ return self.__data[key]
+ except KeyError:
+ return self.__missing__(key)
+
+ def __setitem__(self, key, value):
+ maxsize = self.__maxsize
+ size = self.getsizeof(value)
+ if size > maxsize:
+ raise ValueError('value too large')
+ if key not in self.__data or self.__size[key] < size:
+ while self.__currsize + size > maxsize:
+ self.popitem()
+ if key in self.__data:
+ diffsize = size - self.__size[key]
+ else:
+ diffsize = size
+ self.__data[key] = value
+ self.__size[key] = size
+ self.__currsize += diffsize
+
+ def __delitem__(self, key):
+ size = self.__size.pop(key)
+ del self.__data[key]
+ self.__currsize -= size
+
+ def __contains__(self, key):
+ return key in self.__data
+
+ def __missing__(self, key):
+ value = self.__missing(key)
+ try:
+ self.__setitem__(key, value)
+ except ValueError:
+ pass # value too large
+ return value
+
+ def __iter__(self):
+ return iter(self.__data)
+
+ def __len__(self):
+ return len(self.__data)
+
+ @staticmethod
+ def __getsizeof(value):
+ return 1
+
+ @staticmethod
+ def __missing(key):
+ raise KeyError(key)
+
+ @property
+ def maxsize(self):
+ """The maximum size of the cache."""
+ return self.__maxsize
+
+ @property
+ def currsize(self):
+ """The current size of the cache."""
+ return self.__currsize
+
+ def getsizeof(self, value):
+ """Return the size of a cache element's value."""
+ return self.__getsizeof(value)
+
+
+class _Link(object):
+
+ __slots__ = ('key', 'expire', 'next', 'prev')
+
+ def __init__(self, key=None, expire=None):
+ self.key = key
+ self.expire = expire
+
+ def __reduce__(self):
+ return _Link, (self.key, self.expire)
+
+ def unlink(self):
+ next = self.next
+ prev = self.prev
+ prev.next = next
+ next.prev = prev
+
+
+class _Timer(object):
+
+ def __init__(self, timer):
+ self.__timer = timer
+ self.__nesting = 0
+
+ def __call__(self):
+ if self.__nesting == 0:
+ return self.__timer()
+ else:
+ return self.__time
+
+ def __enter__(self):
+ if self.__nesting == 0:
+ self.__time = time = self.__timer()
+ else:
+ time = self.__time
+ self.__nesting += 1
+ return time
+
+ def __exit__(self, *exc):
+ self.__nesting -= 1
+
+ def __reduce__(self):
+ return _Timer, (self.__timer,)
+
+ def __getattr__(self, name):
+ return getattr(self.__timer, name)
+
+
+class TTLCache(Cache):
+ """LRU Cache implementation with per-item time-to-live (TTL) value."""
+
+ def __init__(self, maxsize, ttl, timer=time.time, missing=None,
+ getsizeof=None):
+ Cache.__init__(self, maxsize, missing, getsizeof)
+ self.__root = root = _Link()
+ root.prev = root.next = root
+ self.__links = collections.OrderedDict()
+ self.__timer = _Timer(timer)
+ self.__ttl = ttl
+
+ def __contains__(self, key):
+ try:
+ link = self.__links[key] # no reordering
+ except KeyError:
+ return False
+ else:
+ return not (link.expire < self.__timer())
+
+ def __getitem__(self, key, cache_getitem=Cache.__getitem__):
+ try:
+ link = self.__getlink(key)
+ except KeyError:
+ expired = False
+ else:
+ expired = link.expire < self.__timer()
+ if expired:
+ return self.__missing__(key)
+ else:
+ return cache_getitem(self, key)
+
+ def __setitem__(self, key, value, cache_setitem=Cache.__setitem__):
+ with self.__timer as time:
+ self.expire(time)
+ cache_setitem(self, key, value)
+ try:
+ link = self.__getlink(key)
+ except KeyError:
+ self.__links[key] = link = _Link(key)
+ else:
+ link.unlink()
+ link.expire = time + self.__ttl
+ link.next = root = self.__root
+ link.prev = prev = root.prev
+ prev.next = root.prev = link
+
+ def __delitem__(self, key, cache_delitem=Cache.__delitem__):
+ cache_delitem(self, key)
+ link = self.__links.pop(key)
+ link.unlink()
+ if link.expire < self.__timer():
+ raise KeyError(key)
+
+ def __iter__(self):
+ root = self.__root
+ curr = root.next
+ while curr is not root:
+ # "freeze" time for iterator access
+ with self.__timer as time:
+ if not (curr.expire < time):
+ yield curr.key
+ curr = curr.next
+
+ def __len__(self):
+ root = self.__root
+ curr = root.next
+ time = self.__timer()
+ count = len(self.__links)
+ while curr is not root and curr.expire < time:
+ count -= 1
+ curr = curr.next
+ return count
+
+ def __setstate__(self, state):
+ self.__dict__.update(state)
+ root = self.__root
+ root.prev = root.next = root
+ for link in sorted(self.__links.values(), key=lambda obj: obj.expire):
+ link.next = root
+ link.prev = prev = root.prev
+ prev.next = root.prev = link
+ self.expire(self.__timer())
+
+ def __repr__(self, cache_repr=Cache.__repr__):
+ with self.__timer as time:
+ self.expire(time)
+ return cache_repr(self)
+
+ @property
+ def currsize(self):
+ with self.__timer as time:
+ self.expire(time)
+ return super(TTLCache, self).currsize
+
+ @property
+ def timer(self):
+ """The timer function used by the cache."""
+ return self.__timer
+
+ @property
+ def ttl(self):
+ """The time-to-live value of the cache's items."""
+ return self.__ttl
+
+ def expire(self, time=None):
+ """Remove expired items from the cache."""
+ if time is None:
+ time = self.__timer()
+ root = self.__root
+ curr = root.next
+ links = self.__links
+ cache_delitem = Cache.__delitem__
+ while curr is not root and curr.expire < time:
+ cache_delitem(self, curr.key)
+ del links[curr.key]
+ next = curr.next
+ curr.unlink()
+ curr = next
+
+ def clear(self):
+ with self.__timer as time:
+ self.expire(time)
+ Cache.clear(self)
+
+ def get(self, *args, **kwargs):
+ with self.__timer:
+ return Cache.get(self, *args, **kwargs)
+
+ def pop(self, *args, **kwargs):
+ with self.__timer:
+ return Cache.pop(self, *args, **kwargs)
+
+ def setdefault(self, *args, **kwargs):
+ with self.__timer:
+ return Cache.setdefault(self, *args, **kwargs)
+
+ def popitem(self):
+ """Remove and return the `(key, value)` pair least recently used that
+ has not already expired.
+
+ """
+ with self.__timer as time:
+ self.expire(time)
+ try:
+ key = next(iter(self.__links))
+ except StopIteration:
+ raise KeyError('%s is empty' % self.__class__.__name__)
+ else:
+ return (key, self.pop(key))
+
+ if hasattr(collections.OrderedDict, 'move_to_end'):
+ def __getlink(self, key):
+ value = self.__links[key]
+ self.__links.move_to_end(key)
+ return value
+ else:
+ def __getlink(self, key):
+ value = self.__links.pop(key)
+ self.__links[key] = value
+ return value
+
+
+#############################################
+# END IMPORT OF CACHING LIBRARY #
+#############################################
+
+cache = TTLCache(
+ 100, # Up to 100 items
+ 1 * 60 # 5 minute cache life
+)
+
+
+def _get_instance():
+ return chado.ChadoInstance(
+ os.environ['GALAXY_CHADO_DBHOST'],
+ os.environ['GALAXY_CHADO_DBNAME'],
+ os.environ['GALAXY_CHADO_DBUSER'],
+ os.environ['GALAXY_CHADO_DBPASS'],
+ os.environ['GALAXY_CHADO_DBSCHEMA'],
+ os.environ['GALAXY_CHADO_DBPORT'],
+ no_reflect=True
+ )
+
+
+def list_organisms(*args, **kwargs):
+
+ ci = _get_instance()
+
+ # Key for cached data
+ cacheKey = 'orgs'
+ # We don't want to trust "if key in cache" because between asking and fetch
+ # it might through key error.
+ if cacheKey not in cache:
+ # However if it ISN'T there, we know we're safe to fetch + put in
+ # there.
+ data = _list_organisms(ci, *args, **kwargs)
+ cache[cacheKey] = data
+ return data
+ try:
+ # The cache key may or may not be in the cache at this point, it
+ # /likely/ is. However we take no chances that it wasn't evicted between
+ # when we checked above and now, so we reference the object from the
+ # cache in preparation to return.
+ data = cache[cacheKey]
+ return data
+ except KeyError:
+ # If access fails due to eviction, we will fail over and can ensure that
+ # data is inserted.
+ data = _list_organisms(ci, *args, **kwargs)
+ cache[cacheKey] = data
+ return data
+
+
+def _list_organisms(ci, *args, **kwargs):
+ # Fetch the orgs.
+ orgs_data = []
+ for org in ci.organism.get_organisms():
+ clean_name = '%s %s' % (org['genus'], org['species'])
+ if 'infraspecific_name' in org and org['infraspecific_name']:
+ clean_name += ' (%s)' % (org['infraspecific_name'])
+ orgs_data.append((clean_name, str(org['organism_id']), False))
+ return orgs_data
+
+
+def list_analyses(*args, **kwargs):
+
+ ci = _get_instance()
+
+ # Key for cached data
+ cacheKey = 'analyses'
+ # We don't want to trust "if key in cache" because between asking and fetch
+ # it might through key error.
+ if cacheKey not in cache:
+ # However if it ISN'T there, we know we're safe to fetch + put in
+ # there.
+
+ data = _list_analyses(ci, *args, **kwargs)
+ cache[cacheKey] = data
+ return data
+ try:
+ # The cache key may or may not be in the cache at this point, it
+ # /likely/ is. However we take no chances that it wasn't evicted between
+ # when we checked above and now, so we reference the object from the
+ # cache in preparation to return.
+ data = cache[cacheKey]
+ return data
+ except KeyError:
+ # If access fails due to eviction, we will fail over and can ensure that
+ # data is inserted.
+ data = _list_analyses(ci, *args, **kwargs)
+ cache[cacheKey] = data
+ return data
+
+
+def _list_analyses(ci, *args, **kwargs):
+ ans_data = []
+ for an in ci.analysis.get_analyses():
+ ans_data.append((an['name'], str(an['analysis_id']), False))
+ return ans_data
diff -r 000000000000 -r 3af5ba30d0cd expression_delete_biomaterials.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/expression_delete_biomaterials.xml Mon Nov 05 08:05:34 2018 -0500
@@ -0,0 +1,45 @@
+
+
+
+
+ macros.xml
+
+
+