# HG changeset patch
# User gga
# Date 1529584928 14400
# Node ID b44be6289549570095e08a73ece39ae8da68afe6

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27

diff -r 000000000000 -r b44be6289549 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Jun 21 08:42:08 2018 -0400
@@ -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 b44be6289549 chado.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chado.py	Thu Jun 21 08:42:08 2018 -0400
@@ -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.<?xml version="1.0"?>
+
+        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 b44be6289549 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 21 08:42:08 2018 -0400
@@ -0,0 +1,85 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.1.2">python-chado</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <regex level="fatal" match="Exception:" source="stderr" />
+            <regex level="fatal" match="error" source="stderr" />
+            <exit_code range="1:" />
+        </stdio>
+    </xml>
+
+    <token name="@WRAPPER_VERSION@">2.1.1</token>
+
+    <xml name="citation">
+        <citations>
+        </citations>
+    </xml>
+
+    <token name="@HELP_OVERVIEW@"><![CDATA[
+        **Python-chado Overview**
+
+        Python-cado provides several tools allowing to load data into a remote Chado database.
+    ]]></token>
+
+    <token name="@HELP@"><![CDATA[
+    ]]></token>
+
+    <token name="@AUTH@"><![CDATA[
+        echo "__default: local" > '.auth.yml' &&
+        echo "local:" >> '.auth.yml' &&
+        echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
+        echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
+        echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
+        echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
+        echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
+        echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
+
+        CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
+    ]]></token>
+
+    <xml name="sanitized">
+        <sanitizer>
+            <valid initial="string.printable">
+                <remove value="&apos;"/>
+            </valid>
+            <mapping initial="none">
+                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
+                <add source="(" target="\("/>
+                <add source=")" target="\)"/>
+            </mapping>
+        </sanitizer>
+    </xml>
+
+    <!-- I'm not proud of it, but it is needed for workflows -->
+    <xml name="wait_for">
+        <param name="wait_for"
+               type="data"
+               format="data"
+               optional="true"
+               label="Run this only after the following dataset is ready"
+               help="Use this if you want to delay the job execution until some data is already loaded. The selected dataset will not be used for anything else."/>
+    </xml>
+
+    <xml name="feature_rel">
+        <param name="rel_subject_re"
+               argument="--rel-subject-re"
+               type="text"
+               label="Regular expression to extract the unique name of the parent feature"
+               help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
+            <expand macro="sanitized"/>
+        </param>
+
+        <param name="rel_subject_type"
+               argument="--rel-subject-type"
+               type="text"
+               label="Sequence type of the parent"
+               help="this should be a Sequence Ontology term" />
+    </xml>
+</macros>
diff -r 000000000000 -r b44be6289549 phylogeny_load_tree.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogeny_load_tree.xml	Thu Jun 21 08:42:08 2018 -0400
@@ -0,0 +1,59 @@
+<?xml version="1.0"?>
+<tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.0">
+    <description>for phylogeny module</description>
+	<macros>
+		<import>macros.xml</import>
+	</macros>
+	<expand macro="requirements"/>
+    <code file="chado.py"/>
+	<command detect_errors="aggressive"><![CDATA[
+@AUTH@
+
+chakin phylogeny load_tree
+'$newick'
+'$analysis_id'
+
+#if $name:
+  --name '$name'
+#end if
+#if $xref_db:
+  --xref_db '$xref_db'
+#end if
+#if $xref_accession:
+  --xref_accession '$xref_accession'
+#end if
+#if $match_on_name:
+  $match_on_name
+#end if
+#if $prefix:
+  --prefix '$prefix'
+#end if
+
+| jq -S . > $results
+    ]]></command>
+	<inputs>
+	    <!-- arguments -->
+		<param name="newick" label="Newick" argument="newick" type="data" format="txt" help="Newick file to load (or directory containing multiple newick files to load)" />
+		<param argument="--analysis_id"
+			type="select"
+			dynamic_options="list_analyses()"
+			label="Analysis" />
+
+	    <!-- options -->
+		<param name="name" label="Name" argument="name" type="text" help="The name given to the phylotree entry in the database" />
+		<param name="xref_db" label="Xref db" argument="xref_db" value="null" type="text" help="The name of the db to link dbxrefs for the trees" />
+		<param name="xref_accession" label="Xref Accession" argument="xref_accession" type="text" help="The accession to use for dbxrefs for the trees (assumed same as name unless otherwise specified)" />
+		<param name="match_on_name" label="Match On Name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match polypeptide features using their name instead of their uniquename" />
+		<param name="prefix" label="Prefix" argument="prefix" type="text" help="Comma-separated list of prefix to be removed from identifiers (e.g species prefixes when loading OrthoFinder output)" />
+		<expand macro="wait_for"/>
+
+	</inputs>
+	<outputs>
+		<data format="json" name="results"/>
+	</outputs>
+	<help>
+Load a phylogenetic tree (Newick format) into Chado db
+
+@HELP@
+	</help>
+</tool>