# HG changeset patch # User gga # Date 1551094431 18000 # Node ID de7d91ce970b7092d40dffa8842cb214a21f71d9 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 869e5fd8535deca8325777efcd31c70a514b582a diff -r 000000000000 -r de7d91ce970b README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Feb 25 06:33:51 2019 -0500 @@ -0,0 +1,45 @@ +Galaxy-tripal +============= + +Galaxy tools to interface with Tripal using python-tripal + +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 tripal + deactivate + +Environment +----------- + +The following environment variables must be set: + ++--------------------------------+-----------------------------------------------------------+ +| ENV | Use | ++================================+===========================================================+ +| ``$GALAXY_TRIPAL_URL`` | The URL at which Tripal is accessible, internal to Galaxy | +| | and where the tools run. Must be absolute, with FQDN and | +| | protocol. | ++--------------------------------+-----------------------------------------------------------+ +| ``$GALAXY_TRIPAL_USER`` | The admin user which Galaxy should use to talk to Tripal. | +| | | ++--------------------------------+-----------------------------------------------------------+ +| ``$GALAXY_TRIPAL_PASSWORD`` | The password for the admin user. | +| | | +| | | ++--------------------------------+-----------------------------------------------------------+ +| ``$GALAXY_TRIPAL_SHARED_DIR`` | Directory shared between Galaxy and Tripal, used to | +| | exchange data files. | ++--------------------------------+-----------------------------------------------------------+ + + +License +------- + +All python scripts and wrappers are licensed under MIT license. diff -r 000000000000 -r de7d91ce970b expression_get_biomaterials.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/expression_get_biomaterials.xml Mon Feb 25 06:33:51 2019 -0500 @@ -0,0 +1,49 @@ + + + from Tripal + + macros.xml + + + jq + + + $results +]]> + + + + + + + + + + + + + + +List biomaterials in the database + +@HELP@ + + diff -r 000000000000 -r de7d91ce970b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Feb 25 06:33:51 2019 -0500 @@ -0,0 +1,224 @@ + + + + + python-tripal + + + + + + + + + + + + + 3.2 + + + + 10.1093/database/bat075 + + + + + + `_ + + `Tripal REST API module `_: a Tripal module required to use these galaxy tools + ]]> + + \$GALAXY_TRIPAL_SHARED_DIR + + '.auth.yml' && + echo "local:" >> '.auth.yml' && + echo " tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' && + echo " username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' && + echo " password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' && + + TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml' + ]]> + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + ^[0-9]{4}-[0-9]{2}-[0-9]{2}$ + +
+ + + + + + + + + + + + + + + + + + +
+ + + + + + + +
+ + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r de7d91ce970b test-data/blast.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast.xml Mon Feb 25 06:33:51 2019 -0500 @@ -0,0 +1,68 @@ + + + + blastx + blastx 2.2.25 [Feb-01-2011] + ~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs", Nucleic Acids Res. 25:3389-3402. + /scratch/mainlab/data/lib/nr + lcl|1_0 + orange1.1g015632m PAC:18136217 (mRNA) Citrus sinensis + 2075 + + + BLOSUM62 + 1e-06 + 11 + 1 + F + + + + + 1 + lcl|1_0 + orange1.1g015632m PAC:18136217 (mRNA) Citrus sinensis + 2075 + + + 1 + gi|224068663|ref|XP_002302794.1| + predicted protein [Populus trichocarpa] >gi|222844520|gb|EEE82067.1| predicted protein [Populus trichocarpa] + XP_002302794 + 409 + + + 1 + 792.727 + 2046 + 0 + 559 + 1767 + 1 + 409 + 1 + 387 + 394 + 6 + 409 + MASVSVVPASG------NTVGVDRLPEEMNDMKIRDDKEMEATVVDGNGTEAGHIIVTTIGGKNGQPKQTISYMAERVVGHGSFGVVFQAKCLETGEAVAIKKVLQDKRYKNRELQTMRLLDHPNVVSLKHCFFSTTEKDELYLNLVLEYVPETVHRVIKHHYKMSQRMPLIYVKLYFYQICRALAYIHNTIGVCHRDIKPQNLLVNPHTHQLKLCDFGSAKVLVKGEPNISYICSRYYRAPELIFGATEYTAAIDIWSAGCVLAELLLGQPLFPGESGVDQLVEIIKVLGTPTREEIKCMNPNYTEFKFPQIKAHPWHKIFQKRMPPEAVDLVSRLLQYSPNLRSTALEALIHPFFDELRDPNTRLPNGRFLPPLFNFKPHELKGVPVDMLVKLIPEHARKQCAFLGL + MASVSVVPASGLRDTLGNTTGVDKLPEEMNDMKISDDKEMEAAVVDGNGTETGHIIVTTIGGKNGQPKQTISYMAERVVGHGSFGLVFQAKCLETGETVAIKKVLQDKRYKNRELQTMRLLDHPNVVSLKHCFFSTTEKDELYLNLVLEYVPETIHRVIKHYYKMSQRMPLIYVKLYFYQICRALAYIHNSIGVCHRDIKPQNLLVNPHTHQVKLCDFGSAKVLVKGEPNISYICSRYYRAPELIFGATEYTTAIDIWSAGCVLAELLLGQPLFPGESGVDQLVEIIKVLGTPTREEIKCMNPNYTEFKFPQIKAHPWHKIFHKRMPPEAVDLVSRLLQYSPNLRSTALEALIHPFFDELRDPNARLPNGRILPPLFNFKPHELKGVPVEMLVKLIPEHARKQCAFLGL + MASVSVVPASG NT GVD+LPEEMNDMKI DDKEMEA VVDGNGTE GHIIVTTIGGKNGQPKQTISYMAERVVGHGSFG+VFQAKCLETGE VAIKKVLQDKRYKNRELQTMRLLDHPNVVSLKHCFFSTTEKDELYLNLVLEYVPET+HRVIKH+YKMSQRMPLIYVKLYFYQICRALAYIHN+IGVCHRDIKPQNLLVNPHTHQ+KLCDFGSAKVLVKGEPNISYICSRYYRAPELIFGATEYT AIDIWSAGCVLAELLLGQPLFPGESGVDQLVEIIKVLGTPTREEIKCMNPNYTEFKFPQIKAHPWHKIF KRMPPEAVDLVSRLLQYSPNLRSTALEALIHPFFDELRDPN RLPNGR LPPLFNFKPHELKGVPV+MLVKLIPEHARKQCAFLGL + + + + + + + 18996442 + 6510958228 + 0 + 0 + 0.041 + 0.267 + 0.14 + + + + + diff -r 000000000000 -r de7d91ce970b test-data/blast2go.gaf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast2go.gaf Mon Feb 25 06:33:51 2019 -0500 @@ -0,0 +1,6 @@ +!gaf-version: 2.1 + gi|328696447|ref|XP_003240026.1| GO:0016021 + gi|328696447|ref|XP_003240026.1| GO:0006511 + gi|328696447|ref|XP_003240026.1| GO:0030145 + gi|328696447|ref|XP_003240026.1| GO:0004803 + gi|328696447|ref|XP_003240026.1| GO:0004177 diff -r 000000000000 -r de7d91ce970b test-data/citrus_genome.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/citrus_genome.fasta Mon Feb 25 06:33:51 2019 -0500 @@ -0,0 +1,10 @@ +>scaffold00001 length=5927163 +TTTTGTATTCTATGTCCTCTGATCTTTATACTTCTTCATTTTGTCTTTGCAAGAACCGGA +ATTATGGGTACATCACAAATTCTCTAGGTGTGACTTGTGTTGTGGGGCCTTTTTTTtACA +TTTCCATATTGCAAGTATTTTTTTGCTACCATTGGTATATTTGTCTGTTAAAATCAATCT +GCTTTCACTTATGTTCGTGCGTTCTTGTTCCCTCGCCTTGCAATTGCATATCTCAAATTA +TCTTTCTTACTTTGATTTAGATGGCCAAGGTTTTAAGCTAACTTTTTACAATGCCAATTT +TTAAATGGTTTTCTAATGCTGTTCAAAGTTGCAGCCTTTACTTCGTATATTTGTCAGGTT +CTGACGGGTGCGGTCGGCGGCGGGGGCTATAGCATGCGGTCTCGAGAGCCGCAAAGAAAA +ATGGGTGGTTTTCCCGGTTTCGGCCATAACTCGTGATCGGGGCCTCCGATTCTGGTTCCG +TTTCGTCCCACGGGACCAGCCGGGCGGGGGCATCGGATTGCAAAAGTCTTTAAATTTGAA diff -r 000000000000 -r de7d91ce970b test-data/interpro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interpro.xml Mon Feb 25 06:33:51 2019 -0500 @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff -r 000000000000 -r de7d91ce970b test-data/sample.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.gff3 Mon Feb 25 06:33:51 2019 -0500 @@ -0,0 +1,21 @@ +##gff-version 3 +##sequence-region scaffold00001 4058460 4062210 +scaffold00001 phytozome6 supercontig 1 5927163 . . . Name=scaffold00001;ID=scaffold00001 +scaffold00001 phytozome6 gene 4058460 4062210 . + . ID=orange1.1g015632m.g;Name=orange1.1g015632m.g +scaffold00001 phytozome6 mRNA 4058460 4062210 . + . ID=PAC:18136217;Name=orange1.1g015632m;PACid=18136217;Parent=orange1.1g015632m.g +scaffold00001 phytozome6 five_prime_UTR 4058460 4058898 . + . Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 five_prime_UTR 4059019 4059074 . + . Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 five_prime_UTR 4059172 4059234 . + . Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4059235 4059330 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4059422 4059514 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4059600 4059659 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4059790 4060062 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4060285 4060359 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4060480 4060536 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4060625 4060765 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4060857 4060907 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4061250 4061345 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4061417 4061500 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4061617 4061719 . + 0 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 CDS 4061823 4061905 . + 2 Parent=PAC:18136217;PACid=18136217 +scaffold00001 phytozome6 three_prime_UTR 4061906 4062210 . + . Parent=PAC:18136217;PACid=18136217 diff -r 000000000000 -r de7d91ce970b tripal.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tripal.py Mon Feb 25 06:33:51 2019 -0500 @@ -0,0 +1,502 @@ +import collections +import os +import time +from abc import abstractmethod + +import tripal + + +############################################# +# 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 tripal.TripalInstance( + os.environ['GALAXY_TRIPAL_URL'], + os.environ['GALAXY_TRIPAL_USER'], + os.environ['GALAXY_TRIPAL_PASSWORD'] + ) + + +def list_organisms(*args, **kwargs): + + ti = _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(ti, *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(ti, *args, **kwargs) + cache[cacheKey] = data + return data + + +def _list_organisms(ti, *args, **kwargs): + # Fetch the orgs. + orgs_data = [] + for org in ti.organism.get_organisms(): + clean_name = '%s %s' % (org['genus'], org['species']) + if org['infraspecific_name']: + clean_name += ' (%s)' % (org['infraspecific_name']) + orgs_data.append((clean_name, org['organism_id'], False)) + return orgs_data + + +def list_analyses(*args, **kwargs): + + ti = _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(ti, *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(ti, *args, **kwargs) + cache[cacheKey] = data + return data + + +def _list_analyses(ti, *args, **kwargs): + ans_data = [] + for an in ti.analysis.get_analyses(): + ans_data.append((an['name'], an['analysis_id'], False)) + return ans_data + + +def list_blastdbs(*args, **kwargs): + + ti = _get_instance() + + # Key for cached data + cacheKey = 'blastdbs' + # 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_blastdbs(ti, *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_blastdbs(ti, *args, **kwargs) + cache[cacheKey] = data + return data + + +def _list_blastdbs(ti, *args, **kwargs): + dbs_data = [] + for db in ti.db.get_dbs(): + dbs_data.append((db['name'], db['db_id'], False)) + return dbs_data