+160
-22
lines changedFilter options
+160
-22
lines changed Original file line number Diff line number Diff line change
@@ -143,6 +143,7 @@ def _requirements_to_dependencies_dict(self, requirements, **kwds):
143 143
# Check requirements all at once
144 144
all_unmet = len(requirement_to_dependency) == 0
145 145
if all_unmet and hasattr(resolver, "resolve_all"):
146 +
# TODO: Handle specs.
146 147
dependencies = resolver.resolve_all(resolvable_requirements, **kwds)
147 148
if dependencies:
148 149
assert len(dependencies) == len(resolvable_requirements)
@@ -158,7 +159,17 @@ def _requirements_to_dependencies_dict(self, requirements, **kwds):
158 159
continue
159 160 160 161
if requirement.type in ['package', 'set_environment']:
161 -
dependency = resolver.resolve( requirement.name, requirement.version, requirement.type, **kwds )
162 +
name = requirement.name
163 +
version = requirement.version
164 +
specs = requirement.specs
165 + 166 +
if hasattr(resolver, "find_specification"):
167 +
spec = resolver.find_specification(specs)
168 +
if spec is not None:
169 +
name = spec.short_name
170 +
version = spec.version or version
171 + 172 +
dependency = resolver.resolve( name, version, requirement.type, **kwds )
162 173
if require_exact and not dependency.exact:
163 174
continue
164 175
@@ -10,20 +10,48 @@ class ToolRequirement( object ):
10 10
run (for example, a program, package, or library). Requirements can
11 11
optionally assert a specific version.
12 12
"""
13 -
def __init__( self, name=None, type=None, version=None ):
13 +
def __init__( self, name=None, type=None, version=None, specs=[] ):
14 14
self.name = name
15 15
self.type = type
16 16
self.version = version
17 +
self.specs = specs
17 18 18 19
def to_dict( self ):
19 -
return dict(name=self.name, type=self.type, version=self.version)
20 +
specs = [s.to_dict() for s in self.specs]
21 +
return dict(name=self.name, type=self.type, version=self.version, specs=specs)
20 22 21 23
@staticmethod
22 24
def from_dict( dict ):
23 25
version = dict.get( "version", None )
24 26
name = dict.get("name", None)
25 27
type = dict.get("type", None)
26 -
return ToolRequirement( name=name, type=type, version=version )
28 +
specs = [RequirementSpecification.from_dict(s) for s in dict.get("specs", [])]
29 +
return ToolRequirement( name=name, type=type, version=version, specs=specs )
30 + 31 + 32 +
class RequirementSpecification(object):
33 +
"""Refine a requirement using a URI."""
34 + 35 +
def __init__(self, uri, version=None):
36 +
self.uri = uri
37 +
self.version = version
38 + 39 +
@property
40 +
def specifies_version(self):
41 +
return self.version is not None
42 + 43 +
@property
44 +
def short_name(self):
45 +
return self.uri.split("/")[-1]
46 + 47 +
def to_dict(self):
48 +
return dict(uri=self.uri, version=self.version)
49 + 50 +
@staticmethod
51 +
def from_dict(dict):
52 +
uri = dict.get["uri"]
53 +
version = dict.get("version", None)
54 +
return RequirementSpecification(uri=uri, version=version)
27 55 28 56
def __eq__(self, other):
29 57
return self.name == other.name and self.type == other.type and self.version == other.version
@@ -110,10 +138,29 @@ def parse_requirements_from_xml( xml_root ):
110 138 111 139
requirements = []
112 140
for requirement_elem in requirement_elems:
113 -
name = xml_text( requirement_elem )
141 +
if "name" in requirement_elem.attrib:
142 +
name = requirement_elem.get( "name" )
143 +
spec_elems = requirement_elem.findall("specification")
144 +
specs = map(specification_from_element, spec_elems)
145 +
else:
146 +
name = xml_text( requirement_elem )
147 +
spec_uris_raw = requirement_elem.attrib.get("specification_uris", "")
148 +
specs = []
149 +
for spec_uri in spec_uris_raw.split(","):
150 +
if not spec_uri:
151 +
continue
152 +
version = None
153 +
if "@" in spec_uri:
154 +
uri, version = spec_uri.split("@", 1)
155 +
else:
156 +
uri = spec_uri
157 +
uri = uri.strip()
158 +
if version:
159 +
version = version.strip()
160 +
specs.append(RequirementSpecification(uri, version))
114 161
type = requirement_elem.get( "type", DEFAULT_REQUIREMENT_TYPE )
115 162
version = requirement_elem.get( "version", DEFAULT_REQUIREMENT_VERSION )
116 -
requirement = ToolRequirement( name=name, type=type, version=version )
163 +
requirement = ToolRequirement( name=name, type=type, version=version, specs=specs )
117 164
requirements.append( requirement )
118 165 119 166
container_elems = []
@@ -125,6 +172,12 @@ def parse_requirements_from_xml( xml_root ):
125 172
return requirements, containers
126 173 127 174 175 +
def specification_from_element(specification_elem):
176 +
uri = specification_elem.get("uri", None)
177 +
version = specification_elem.get("version", None)
178 +
return RequirementSpecification(uri, version)
179 + 180 + 128 181
def container_from_element(container_elem):
129 182
identifier = xml_text(container_elem)
130 183
type = container_elem.get("type", DEFAULT_CONTAINER_TYPE)
@@ -67,6 +67,34 @@ def _to_requirement(self, name, version=None):
67 67
return ToolRequirement(name=name, type="package", version=version)
68 68 69 69 70 +
class SpecificationAwareDependencyResolver:
71 +
"""Mix this into a :class:`DependencyResolver` to implement URI specification matching.
72 + 73 +
Allows adapting generic requirements to more specific URIs - to tailor name
74 +
or version to specified resolution system.
75 +
"""
76 +
__metaclass__ = ABCMeta
77 + 78 +
@abstractmethod
79 +
def find_specification(self, specs):
80 +
"""Find closest matching specification for discovered resolver."""
81 + 82 + 83 +
class SpecificationPatternDependencyResolver:
84 +
"""Implement the :class:`SpecificationAwareDependencyResolver` with a regex pattern."""
85 + 86 +
@abstractproperty
87 +
def _specification_pattern(self):
88 +
"""Pattern of URI to match against."""
89 + 90 +
def find_specification(self, specs):
91 +
pattern = self._specification_pattern
92 +
for spec in specs:
93 +
if pattern.match(spec.uri):
94 +
return spec
95 +
return None
96 + 97 + 70 98
class InstallableDependencyResolver:
71 99
""" Mix this into a ``DependencyResolver`` and implement to indicate
72 100
the dependency resolver can attempt to install new dependencies.
@@ -5,6 +5,7 @@
5 5 6 6
import logging
7 7
import os
8 +
import re
8 9 9 10
import galaxy.tools.deps.installable
10 11
@@ -29,6 +30,7 @@
29 30
InstallableDependencyResolver,
30 31
ListableDependencyResolver,
31 32
NullDependency,
33 +
SpecificationPatternDependencyResolver,
32 34
)
33 35 34 36
@@ -39,9 +41,10 @@
39 41
log = logging.getLogger(__name__)
40 42 41 43 42 -
class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, InstallableDependencyResolver):
44 +
class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, InstallableDependencyResolver, SpecificationPatternDependencyResolver):
43 45
dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['conda_prefix', 'versionless', 'ensure_channels', 'auto_install']
44 46
resolver_type = "conda"
47 +
_specification_pattern = re.compile(r"https\:\/\/anaconda.org\/\w+\/\w+")
45 48 46 49
def __init__(self, dependency_manager, **kwds):
47 50
self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
@@ -227,7 +227,7 @@ complete descriptions of the runtime of a tool.
227 227
</xs:sequence>
228 228
</xs:complexType>
229 229 230 -
<xs:complexType name="Requirement">
230 +
<xs:complexType name="Requirement" mixed="true">
231 231
<xs:annotation>
232 232
<xs:documentation xml:lang="en"><![CDATA[
233 233
@@ -276,20 +276,29 @@ resolver.
276 276 277 277
]]></xs:documentation>
278 278
</xs:annotation>
279 -
<xs:simpleContent>
280 -
<xs:extension base="xs:string">
281 -
<xs:attribute name="type" type="RequirementType" use="required">
282 -
<xs:annotation>
283 -
<xs:documentation xml:lang="en"> This value defines the which type of the 3rd party module required by this tool. </xs:documentation>
284 -
</xs:annotation>
285 -
</xs:attribute>
286 -
<xs:attribute name="version" type="xs:string">
287 -
<xs:annotation>
288 -
<xs:documentation xml:lang="en"> For package type requirements this value defines a specific version of the tool dependency. </xs:documentation>
289 -
</xs:annotation>
290 -
</xs:attribute>
291 -
</xs:extension>
292 -
</xs:simpleContent>
279 +
<xs:sequence>
280 +
<xs:element name="specification" minOccurs="0" maxOccurs="unbounded" type="xs:anyType" />
281 +
</xs:sequence>
282 +
<xs:attribute name="type" type="RequirementType" use="required">
283 +
<xs:annotation>
284 +
<xs:documentation xml:lang="en"> This value defines the which type of the 3rd party module required by this tool. </xs:documentation>
285 +
</xs:annotation>
286 +
</xs:attribute>
287 +
<xs:attribute name="version" type="xs:string">
288 +
<xs:annotation>
289 +
<xs:documentation xml:lang="en"> For package type requirements this value defines a specific version of the tool dependency. </xs:documentation>
290 +
</xs:annotation>
291 +
</xs:attribute>
292 +
<xs:attribute name="name" type="xs:string">
293 +
<xs:annotation>
294 +
<xs:documentation xml:lang="en">Name of requirement (if body of ``requirement`` element contains specification URIs).</xs:documentation>
295 +
</xs:annotation>
296 +
</xs:attribute>
297 +
<xs:attribute name="specification_uris" type="xs:string">
298 +
<xs:annotation>
299 +
<xs:documentation xml:lang="en">URIs and versions of requirement specification.</xs:documentation>
300 +
</xs:annotation>
301 +
</xs:attribute>
293 302
</xs:complexType>
294 303
<xs:complexType name="Container">
295 304
<xs:annotation>
@@ -0,0 +1,18 @@
1 +
<tool id="requirement_specification_1" name="requirement_specification_1" version="0.1.0" profile="16.10">
2 +
<command><![CDATA[
3 +
blastn -help > $out_file1 ;
4 +
echo "Moo" >> $out_file1 ;
5 +
]]></command>
6 +
<requirements>
7 +
<requirement type="package" version="2.2.31" name="blast+">
8 +
<specification uri="https://anaconda.org/bioconda/blast" />
9 +
<specification uri="https://packages.debian.org/sid/ncbi-blast+" version="2.2.31-3" />
10 +
</requirement>
11 +
</requirements>
12 +
<inputs>
13 +
<param name="input1" type="data" optional="true" />
14 +
</inputs>
15 +
<outputs>
16 +
<data name="out_file1" format="txt" />
17 +
</outputs>
18 +
</tool>
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
1 +
<tool id="requirement_specification_2" name="requirement_specification_2" version="0.1.0" profile="16.01">
2 +
<command><![CDATA[
3 +
blastn -help > $out_file1 ;
4 +
echo "Moo" >> $out_file1 ;
5 +
]]></command>
6 +
<requirements>
7 +
<!-- Demonstrate backward-compatible-ish specification_uri syntax. -->
8 +
<requirement type="package" version="2.2" specification_uris="https://anaconda.org/bioconda/blast@2.2.31,https://packages.debian.org/jessie/ncbi-blast+@2.2.29-3">blast+</requirement>
9 +
</requirements>
10 +
<inputs>
11 +
<param name="input1" type="data" optional="true" />
12 +
</inputs>
13 +
<outputs>
14 +
<data name="out_file1" format="txt" />
15 +
</outputs>
16 +
</tool>
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