search_biomodel 1.0.3 → 2.0.0
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- data/.document +0 -0
- data/.idea/.name +1 -0
- data/.idea/.rakeTasks +7 -0
- data/.idea/dictionaries/root.xml +7 -0
- data/.idea/encodings.xml +5 -0
- data/.idea/misc.xml +8 -0
- data/.idea/modules.xml +9 -0
- data/.idea/search_biomodel.iml +44 -0
- data/.idea/vcs.xml +7 -0
- data/.idea/workspace.xml +443 -0
- data/Gemfile +0 -0
- data/Gemfile.lock +0 -0
- data/LICENSE.txt +26 -17
- data/README.rdoc +47 -18
- data/Rakefile +0 -0
- data/VERSION +1 -1
- data/lib/search_biomodel.rb +114 -43
- data/search_biomodel-1.1.1.gem +0 -0
- data/search_biomodel-1.1.2.gem +0 -0
- data/search_biomodel.gemspec +13 -2
- data/test/helper.rb +1 -1
- data/test/test_search_biomodel.rb +84 -47
- metadata +25 -14
data/.document
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ADDED
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search_biomodel
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data/.idea/.rakeTasks
ADDED
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You are allowed to:
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1. Remove rake task
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2. Add existing rake tasks
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To add existing rake tasks automatically delete this file and reload the project.
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--><RakeGroup description="" fullCmd="" taksId="rake"><RakeTask description="Build gem into pkg/" fullCmd="build" taksId="build" /><RakeTask description="Remove rcov products for rcov" fullCmd="clobber_rcov" taksId="clobber_rcov" /><RakeTask description="Remove rdoc products" fullCmd="clobber_rdoc" taksId="clobber_rdoc" /><RakeTask description="Start IRB with all runtime dependencies loaded" fullCmd="console[script]" taksId="console[script]" /><RakeGroup description="" fullCmd="" taksId="gemcutter"><RakeTask description="Release gem to Gemcutter" fullCmd="gemcutter:release" taksId="release" /></RakeGroup><RakeTask description="Generate and validate gemspec" fullCmd="gemspec" taksId="gemspec" /><RakeGroup description="" fullCmd="" taksId="gemspec"><RakeTask description="Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)" fullCmd="gemspec:debug" taksId="debug" /><RakeTask description="Regenreate the gemspec on the filesystem" fullCmd="gemspec:generate" taksId="generate" /><RakeTask description="Regenerate and validate gemspec, and then commits and pushes to git" fullCmd="gemspec:release" taksId="release" /><RakeTask description="Validates the gemspec on the filesystem" fullCmd="gemspec:validate" taksId="validate" /></RakeGroup><RakeGroup description="" fullCmd="" taksId="git"><RakeTask description="Tag and push release to git" fullCmd="git:release" taksId="release" /></RakeGroup><RakeTask description="Build and install gem using `gem install`" fullCmd="install" taksId="install" /><RakeTask description="Analyze code coverage with tests" fullCmd="rcov" taksId="rcov" /><RakeTask description="Build the rdoc HTML Files" fullCmd="rdoc" taksId="rdoc" /><RakeTask description="Release gem" fullCmd="release" taksId="release" /><RakeTask description="Force a rebuild of the RDOC files" fullCmd="rerdoc" taksId="rerdoc" /><RakeTask description="Run tests" fullCmd="test" taksId="test" /><RakeTask description="Displays the current version" fullCmd="version" taksId="version" /><RakeGroup description="" fullCmd="" taksId="version"><RakeGroup description="" fullCmd="" taksId="bump"><RakeTask description="Bump the major version by 1" fullCmd="version:bump:major" taksId="major" /><RakeTask description="Bump the a minor version by 1" fullCmd="version:bump:minor" taksId="minor" /><RakeTask description="Bump the patch version by 1" fullCmd="version:bump:patch" taksId="patch" /></RakeGroup><RakeTask description="Writes out an explicit version" fullCmd="version:write" taksId="write" /></RakeGroup><RakeTask description="" fullCmd="clobber" taksId="clobber" /><RakeTask description="" fullCmd="console" taksId="console" /><RakeTask description="" fullCmd="default" taksId="default" /><RakeTask description="" fullCmd="gemspec_required" taksId="gemspec_required" /><RakeTask description="" fullCmd="rdoc/index.html" taksId="rdoc/index.html" /><RakeTask description="" fullCmd="version_required" taksId="version_required" /></RakeGroup></Settings>
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<provider selected="true" editor-type-id="text-editor">
|
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|
+
<state line="11" column="32" selection-start="462" selection-end="462" vertical-scroll-proportion="0.2787162">
|
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|
+
<folding />
|
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|
+
</state>
|
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+
</provider>
|
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|
+
</entry>
|
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|
+
<entry file="file://$PROJECT_DIR$/README.rdoc">
|
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|
+
<provider selected="true" editor-type-id="text-editor">
|
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|
+
<state line="16" column="0" selection-start="710" selection-end="710" vertical-scroll-proportion="-0.4189189">
|
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|
+
<folding />
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+
</state>
|
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+
</provider>
|
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</entry>
|
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<entry file="file://$PROJECT_DIR$/test/helper.rb">
|
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|
+
<provider selected="true" editor-type-id="text-editor">
|
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|
+
<state line="7" column="25" selection-start="224" selection-end="224" vertical-scroll-proportion="0.0">
|
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<folding />
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|
+
</state>
|
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|
+
</provider>
|
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|
+
</entry>
|
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|
+
<entry file="file://$PROJECT_DIR$/search_biomodel.gemspec">
|
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|
+
<provider selected="true" editor-type-id="text-editor">
|
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|
+
<state line="59" column="99" selection-start="1896" selection-end="1896" vertical-scroll-proportion="0.0">
|
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|
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<folding />
|
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|
+
</state>
|
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|
+
</provider>
|
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|
+
</entry>
|
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|
+
<entry file="file://$PROJECT_DIR$/test/test_search_biomodel.rb">
|
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|
+
<provider selected="true" editor-type-id="text-editor">
|
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|
+
<state line="28" column="77" selection-start="811" selection-end="811" vertical-scroll-proportion="0.0">
|
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|
+
<folding />
|
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|
+
</state>
|
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|
+
</provider>
|
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|
+
</entry>
|
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|
+
<entry file="file://$PROJECT_DIR$/lib/search_biomodel.rb">
|
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|
+
<provider selected="true" editor-type-id="text-editor">
|
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|
+
<state line="28" column="116" selection-start="768" selection-end="768" vertical-scroll-proportion="0.7094595">
|
437
|
+
<folding />
|
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|
+
</state>
|
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|
+
</provider>
|
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|
+
</entry>
|
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|
+
</component>
|
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|
+
</project>
|
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|
+
|
data/Gemfile
CHANGED
File without changes
|
data/Gemfile.lock
CHANGED
File without changes
|
data/LICENSE.txt
CHANGED
@@ -1,20 +1,29 @@
|
|
1
|
-
Copyright (c) 2011
|
1
|
+
Copyright (c) 2011, The University of Manchester, UK.
|
2
2
|
|
3
|
-
|
4
|
-
a copy of this software and associated documentation files (the
|
5
|
-
"Software"), to deal in the Software without restriction, including
|
6
|
-
without limitation the rights to use, copy, modify, merge, publish,
|
7
|
-
distribute, sublicense, and/or sell copies of the Software, and to
|
8
|
-
permit persons to whom the Software is furnished to do so, subject to
|
9
|
-
the following conditions:
|
3
|
+
All rights reserved.
|
10
4
|
|
11
|
-
|
12
|
-
|
5
|
+
Redistribution and use in source and binary forms, with or without
|
6
|
+
modification, are permitted provided that the following conditions are met:
|
13
7
|
|
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|
-
|
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|
-
|
16
|
-
|
17
|
-
|
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|
-
|
19
|
-
|
20
|
-
|
8
|
+
* Redistributions of source code must retain the above copyright notice,
|
9
|
+
this list of conditions and the following disclaimer.
|
10
|
+
|
11
|
+
* Redistributions in binary form must reproduce the above copyright notice,
|
12
|
+
this list of conditions and the following disclaimer in the documentation
|
13
|
+
and/or other materials provided with the distribution.
|
14
|
+
|
15
|
+
* Neither the names of The University of Manchester nor the names of its
|
16
|
+
contributors may be used to endorse or promote products derived from this
|
17
|
+
software without specific prior written permission.
|
18
|
+
|
19
|
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
20
|
+
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
21
|
+
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
22
|
+
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
|
23
|
+
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
|
24
|
+
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
|
25
|
+
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
|
26
|
+
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
|
27
|
+
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
|
28
|
+
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
29
|
+
POSSIBILITY OF SUCH DAMAGE.
|
data/README.rdoc
CHANGED
@@ -1,45 +1,74 @@
|
|
1
1
|
= search_biomodel
|
2
2
|
|
3
|
-
search biomodel is a small gem ready to be used for running queries through the biomodel web service API.
|
3
|
+
search biomodel is a small ruby gem ready to be used for running queries through the biomodel web service API.
|
4
4
|
|
5
|
-
There are (currently)
|
5
|
+
There are (currently) 5 methods implemented here to communicate with the biomodels website (found at http://www.ebi.ac.uk/biomodels-main/).
|
6
|
+
|
7
|
+
These methods are "search_by_chebiid", "search_by_name", "get_all_models", "search_by_person" and "get_model_name_by_id".
|
6
8
|
|
7
|
-
These methods are "search_by_chebiid", "search_by_name" and "get_all_models". The former two return an array and the latter a hash map of :key and :value
|
8
9
|
|
9
10
|
== Installation
|
10
11
|
|
11
12
|
gem install seach_biomodel
|
12
13
|
|
14
|
+
|
13
15
|
== Usage
|
14
|
-
|
15
|
-
|
16
|
+
The first four methods return an array of model IDs (or an empty array if nothing is found) and the 5th returns the name of the model of an ID you search for. The ChEBIID can take quite some time to run on the biomodel servers side.
|
17
|
+
|
18
|
+
The "get_all_models" method returns a hash map of :key's and :value's which can be retrieved as such:
|
19
|
+
|
20
|
+
|
21
|
+
|
16
22
|
require 'rubygems'
|
17
|
-
require '
|
23
|
+
require 'search_biomodel'
|
18
24
|
|
19
|
-
include SysMODB::SearchBiomodel
|
20
25
|
|
26
|
+
@connection = SysMODB::SearchBiomodel.instance
|
21
27
|
|
22
|
-
puts "\n\n ------------------ List All -----------------------------\n\n"
|
23
28
|
|
24
|
-
|
29
|
+
puts "\n\n ------------------ List All -----------------------------\n"
|
30
|
+
all_models = @connection.get_all_models
|
25
31
|
all_models.each { |item| puts "ID = #{item[:key]} | NAME = #{item[:value]}\n" }
|
32
|
+
puts " ----------------------------------------------------------\n\n\n"
|
26
33
|
|
34
|
+
puts "\n\n ------------------ By Chebiid --------------------------\n"
|
35
|
+
i=0
|
36
|
+
models_by_chebiid = @connection.search_by_ChEBIID("CHEBI:15422")
|
37
|
+
models_by_chebiid.each { |item| puts "#{i+=1} #{item.to_s}\n"}
|
38
|
+
puts " ----------------------------------------------------------\n\n\n"
|
27
39
|
|
28
|
-
puts "\n\n ------------------ By
|
40
|
+
puts "\n\n ------------------ By Name -----------------------------\n"
|
41
|
+
i=0
|
42
|
+
models_by_name = @connection.search_by_name("Kolomeisky2003")
|
43
|
+
models_by_name.each { |item| puts "#{i+=1} #{item.to_s}\n"}
|
44
|
+
puts " ----------------------------------------------------------\n\n\n"
|
29
45
|
|
30
|
-
|
31
|
-
|
46
|
+
|
47
|
+
puts "\n\n ------------------ By Person----------------------------\n"
|
48
|
+
i=0
|
49
|
+
models_by_person = @connection.search_by_person("Jim")
|
50
|
+
models_by_person.each { |item| puts "#{i+=1} #{item.to_s}\n"}
|
51
|
+
puts " ----------------------------------------------------------\n\n\n"
|
52
|
+
|
53
|
+
puts "\n\n ------------------ Model ID by Name---------------------------\n"
|
54
|
+
i=0
|
55
|
+
models_by_person = @connection.get_model_name_by_id("BIOMD0000000190")
|
56
|
+
models_by_person.each { |item| puts "#{i+=1} #{item.to_s}\n"}
|
57
|
+
puts " ----------------------------------------------------------\n\n\n"
|
58
|
+
|
59
|
+
|
60
|
+
== Fun Fact
|
61
|
+
|
62
|
+
You can append the Model ID to the URL http://www.ebi.ac.uk/biomodels-main/ to load the link
|
63
|
+
eg (continuing from above).
|
32
64
|
|
33
65
|
|
34
|
-
puts "\n\n ------------------ By Name -----------------------------\n\n" i=0
|
35
66
|
|
36
|
-
models_by_name = search_by_name("Kolomeisky2003")
|
37
|
-
models_by_name.each { |item| puts "#{i+=1} #{item.to_s}\n"}
|
38
67
|
|
68
|
+
models_by_person.each { |item| puts "http://www.ebi.ac.uk/biomodels-main/#{item.to_s}\n" }
|
39
69
|
|
40
|
-
|
41
|
-
|
42
|
-
|
70
|
+
#=> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000190
|
71
|
+
#=> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000191
|
43
72
|
|
44
73
|
== Contributing to search_biomodel
|
45
74
|
|
data/Rakefile
CHANGED
File without changes
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
|
1
|
+
2.0.0
|
data/lib/search_biomodel.rb
CHANGED
@@ -1,74 +1,145 @@
|
|
1
|
-
|
2
|
-
|
3
|
-
require 'rubygems'
|
4
1
|
require 'savon'
|
5
|
-
|
2
|
+
require 'singleton'
|
6
3
|
|
7
4
|
module SysMODB
|
8
5
|
|
9
6
|
class SearchBiomodelException < Exception
|
10
7
|
end
|
11
8
|
|
12
|
-
|
9
|
+
class SearchBiomodel
|
10
|
+
include Singleton
|
13
11
|
|
14
|
-
def
|
15
|
-
|
16
|
-
|
17
|
-
|
12
|
+
def initialize
|
13
|
+
@connection = Savon.configure do |config|
|
14
|
+
config.log = false
|
15
|
+
HTTPI.log = false
|
16
|
+
config.raise_errors = true
|
17
|
+
Savon::Client.new do
|
18
|
+
wsdl.document = "http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl"
|
19
|
+
wsdl.namespace = "http://biomodels.ebi.ac.uk"
|
20
|
+
end
|
18
21
|
end
|
19
|
-
|
22
|
+
|
20
23
|
end
|
21
|
-
|
22
24
|
|
23
|
-
|
24
|
-
|
25
|
-
|
26
|
-
|
25
|
+
|
26
|
+
def models(search_string)
|
27
|
+
#collect results from sub-methods
|
28
|
+
results = Array.new
|
29
|
+
results << @connection.search_by_name(search_string)
|
30
|
+
results << @connection.search_by_chebiid(search_string)
|
31
|
+
results << @connection.search_by_person(search_string)
|
32
|
+
|
33
|
+
#turn into one big array, remove duplicates and select first X
|
34
|
+
results = results.flatten
|
35
|
+
results = results.uniq
|
36
|
+
results = results.first(3)
|
37
|
+
|
38
|
+
sbml_results = Array.new
|
39
|
+
results.each{ |a| sbml_results << "#{@connection.getModel(a)}" }
|
40
|
+
sbml_results
|
41
|
+
end
|
42
|
+
|
43
|
+
|
44
|
+
|
45
|
+
def getModel(model_id)
|
46
|
+
client = connection
|
47
|
+
response = client.request(:biom, "get_model_by_id") do
|
48
|
+
soap.body = {:id => model_id, :attributes! => {:id => {"xsi:type" => "xsd:string"}}}
|
49
|
+
end
|
50
|
+
|
51
|
+
search_results = response.to_hash[:get_model_by_id_response][:get_model_by_id_return]
|
52
|
+
if search_results.nil?
|
53
|
+
[]
|
54
|
+
else
|
55
|
+
search_results
|
56
|
+
end
|
57
|
+
end
|
58
|
+
|
59
|
+
|
60
|
+
#search_by_chebiid
|
61
|
+
#search_by_name
|
62
|
+
#search_by_person
|
63
|
+
|
64
|
+
def search_by_chebiid(search_string)
|
65
|
+
client = connection
|
66
|
+
response = client.request(:biom, "get_models_id_by_ch_ebi_id") do
|
67
|
+
soap.body = {:ChEBBId => search_string, :attributes! => {:ChEBBId => {"xsi:type" => "xsd:string"}}}
|
68
|
+
end
|
69
|
+
|
70
|
+
search_results = response.to_hash[:get_models_id_by_ch_ebi_id_response][:get_models_id_by_ch_ebi_id_return][:get_models_id_by_ch_ebi_id_return]
|
71
|
+
if search_results.nil?
|
72
|
+
[]
|
73
|
+
else
|
74
|
+
search_results
|
27
75
|
end
|
28
|
-
return response.to_hash[:multi_ref][:item]
|
29
76
|
end
|
30
|
-
|
77
|
+
|
31
78
|
|
32
79
|
def search_by_name (search_string)
|
33
|
-
client =
|
80
|
+
client = connection
|
34
81
|
response = client.request(:biom, "get_models_id_by_name") do
|
35
|
-
soap.body = {
|
82
|
+
soap.body = {:modelName => search_string, :attributes! => {:modelName => {"xsi:type" => "xsd:string"}}}
|
83
|
+
end
|
84
|
+
search_results = response.to_hash[:get_models_id_by_name_response][:get_models_id_by_name_return][:get_models_id_by_name_return]
|
85
|
+
if search_results.nil?
|
86
|
+
[]
|
87
|
+
else
|
88
|
+
search_results
|
36
89
|
end
|
37
|
-
return response.to_hash[:get_models_id_by_name_response][:get_models_id_by_name_return][:get_models_id_by_name_return]
|
38
90
|
end
|
39
91
|
|
40
|
-
|
41
|
-
client =
|
92
|
+
def search_by_person (search_string)
|
93
|
+
client = connection
|
42
94
|
response = client.request(:biom, "get_models_id_by_person") do
|
43
|
-
soap.body = {
|
95
|
+
soap.body = {:personName => search_string, :attributes! => {:personName => {"xsi:type" => "xsd:string"}}}
|
96
|
+
end
|
97
|
+
search_results = response.to_hash[:get_models_id_by_person_response][:get_models_id_by_person_return][:get_models_id_by_person_return]
|
98
|
+
if search_results.nil?
|
99
|
+
[]
|
100
|
+
else
|
101
|
+
search_results
|
44
102
|
end
|
45
|
-
|
46
|
-
end
|
103
|
+
end
|
47
104
|
|
48
|
-
|
49
|
-
|
105
|
+
|
106
|
+
#more used for testing
|
107
|
+
|
108
|
+
def get_model_name_by_id (search_string)
|
109
|
+
client = connection
|
50
110
|
response = client.request(:biom, "get_model_name_by_id") do
|
51
|
-
soap.body = {
|
111
|
+
soap.body = {:id => search_string, :attributes! => {:id => {"xsi:type" => "xsd:string"}}}
|
52
112
|
end
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
113
|
+
search_results = response.to_hash[:get_model_name_by_id_response][:get_model_name_by_id_return]
|
114
|
+
if search_results.nil? || search_results.include?('is an invalid Model ID.')
|
115
|
+
[]
|
116
|
+
else
|
117
|
+
search_results
|
118
|
+
end
|
119
|
+
end
|
57
120
|
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
65
|
-
|
66
|
-
|
67
|
-
|
121
|
+
def get_all_models
|
122
|
+
client = connection
|
123
|
+
response = client.request(:biom, "get_all_models") do
|
124
|
+
soap.body = {:modelName => "?", :attributes! => {:modelName => {"xsi:type" => "xsd:string"}}}
|
125
|
+
end
|
126
|
+
search_results = response.to_hash[:multi_ref][:item]
|
127
|
+
if search_results.nil?
|
128
|
+
[]
|
129
|
+
else
|
130
|
+
search_results
|
68
131
|
end
|
69
|
-
end
|
132
|
+
end
|
133
|
+
|
134
|
+
|
70
135
|
|
71
136
|
|
137
|
+
protected
|
138
|
+
|
139
|
+
def connection
|
140
|
+
@connection
|
141
|
+
end
|
142
|
+
|
72
143
|
end #SearchBiomodel
|
73
144
|
end #SysMODB
|
74
145
|
|
Binary file
|
Binary file
|
data/search_biomodel.gemspec
CHANGED
@@ -5,11 +5,11 @@
|
|
5
5
|
|
6
6
|
Gem::Specification.new do |s|
|
7
7
|
s.name = %q{search_biomodel}
|
8
|
-
s.version = "
|
8
|
+
s.version = "2.0.0"
|
9
9
|
|
10
10
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
11
11
|
s.authors = ["Niall Beard"]
|
12
|
-
s.date = %q{
|
12
|
+
s.date = %q{2012-02-17}
|
13
13
|
s.description = %q{Client package for creating, sending, recieving and consuming SOAP messages from BioModels search engine }
|
14
14
|
s.email = %q{beardn9@cs.man.ac.uk}
|
15
15
|
s.extra_rdoc_files = [
|
@@ -18,6 +18,15 @@ Gem::Specification.new do |s|
|
|
18
18
|
]
|
19
19
|
s.files = [
|
20
20
|
".document",
|
21
|
+
".idea/.name",
|
22
|
+
".idea/.rakeTasks",
|
23
|
+
".idea/dictionaries/root.xml",
|
24
|
+
".idea/encodings.xml",
|
25
|
+
".idea/misc.xml",
|
26
|
+
".idea/modules.xml",
|
27
|
+
".idea/search_biomodel.iml",
|
28
|
+
".idea/vcs.xml",
|
29
|
+
".idea/workspace.xml",
|
21
30
|
"Gemfile",
|
22
31
|
"Gemfile.lock",
|
23
32
|
"LICENSE.txt",
|
@@ -25,6 +34,8 @@ Gem::Specification.new do |s|
|
|
25
34
|
"Rakefile",
|
26
35
|
"VERSION",
|
27
36
|
"lib/search_biomodel.rb",
|
37
|
+
"search_biomodel-1.1.1.gem",
|
38
|
+
"search_biomodel-1.1.2.gem",
|
28
39
|
"search_biomodel.gemspec",
|
29
40
|
"test/helper.rb",
|
30
41
|
"test/test_search_biomodel.rb"
|
data/test/helper.rb
CHANGED
@@ -1,60 +1,97 @@
|
|
1
1
|
require 'test/unit'
|
2
|
-
require '
|
2
|
+
require 'helper'
|
3
|
+
class TestSearchBiomodel < Test::Unit::TestCase
|
3
4
|
|
5
|
+
def setup
|
6
|
+
@instance = SysMODB::SearchBiomodel.instance
|
7
|
+
end
|
4
8
|
|
5
|
-
|
9
|
+
def test_find_all_models
|
10
|
+
puts "\n\n ---------------------find all models---------------------\n\n"
|
11
|
+
response = []
|
12
|
+
i=0
|
13
|
+
response = @instance.get_all_models
|
14
|
+
response.each { |x| puts "Response #{i+=1}: #{x[:key].to_s} " }
|
15
|
+
response.each { |x| assert_not_nil x[:key] }
|
16
|
+
assert_not_nil response
|
17
|
+
end
|
18
|
+
|
19
|
+
|
20
|
+
def test_search_by_chebiid
|
21
|
+
puts "\n\n ---------------------search by chebiid---------------------\n\n"
|
22
|
+
response = []
|
23
|
+
i = 0
|
24
|
+
response = @instance.search_by_chebiid("CHEBI:15422")
|
25
|
+
response.each { |x| puts "Response #{i+=1}: #{x} " }
|
26
|
+
response.each { |x| assert_not_nil x }
|
27
|
+
assert_not_nil response
|
28
|
+
end
|
29
|
+
|
30
|
+
def test_search_by_incorrect_chebiid
|
31
|
+
puts "\n\n ---------------------search by incorrect chebiid---------------------\n\n"
|
32
|
+
response = []
|
33
|
+
i = 0
|
34
|
+
response = @instance.search_by_chebiid("THIS IS NOT A VALID CHEBIID!!!!!<P></P>")
|
35
|
+
response.each { |x| puts "Response #{i+=1}: #{x} " }
|
36
|
+
response.each { |x| assert_not_nil x }
|
37
|
+
assert_not_nil response
|
38
|
+
end
|
39
|
+
|
40
|
+
|
41
|
+
def test_search_by_name
|
42
|
+
puts "\n\n ---------------------model ID by name---------------------\n\n"
|
43
|
+
response = []
|
44
|
+
i = 0
|
45
|
+
response = @instance.search_by_name("Kolomeisky2003") #_MyosinV_Processivity")
|
46
|
+
response.each { |x| puts "Response #{i+=1}: #{x} " }
|
47
|
+
response.each { |x| assert_not_nil x }
|
48
|
+
assert_not_nil response
|
49
|
+
end
|
50
|
+
|
51
|
+
def test_search_by_incorrect_name
|
52
|
+
puts "\n\n ---------------------model ID by incorrect name---------------------\n\n"
|
53
|
+
response = []
|
54
|
+
i = 0
|
55
|
+
response = @instance.search_by_name("THIS IS NOT A VALID NAME!!!!!<P></P>") #_MyosinV_Processivity")
|
56
|
+
response.each { |x| puts "Response #{i+=1}: #{x} " }
|
57
|
+
response.each { |x| assert_not_nil x }
|
58
|
+
assert_not_nil response
|
59
|
+
end
|
6
60
|
|
7
|
-
include SysMODB::SearchBiomodel
|
8
|
-
|
9
|
-
def test_find_all_models
|
10
|
-
puts "\n\n ---------------------find all models---------------------\n\n"
|
11
|
-
response = []
|
12
|
-
i=0
|
13
|
-
response = get_all_models
|
14
|
-
response.each {|x| puts "Response #{i+=1}: #{x[:key].to_s} "}
|
15
|
-
response.each {|x| assert_not_nil x[:key] }
|
16
|
-
assert_not_nil response
|
17
|
-
end
|
18
|
-
|
19
|
-
|
20
|
-
def test_search_by_ChEBIID
|
21
|
-
puts "\n\n ---------------------search by chebiid---------------------\n\n"
|
22
|
-
response = []
|
23
|
-
i = 0
|
24
|
-
response = search_by_ChEBIID("CHEBI:15422")
|
25
|
-
response.each {|x| puts "Response #{i+=1}: #{x} "}
|
26
|
-
response.each {|x| assert_not_nil x }
|
27
|
-
assert_not_nil response
|
28
|
-
end
|
29
|
-
|
30
|
-
def test_search_by_name
|
31
|
-
puts "\n\n ---------------------model ID by name---------------------\n\n"
|
32
|
-
response = []
|
33
|
-
i = 0
|
34
|
-
response = search_by_name("Kolomeisky2003") #_MyosinV_Processivity")
|
35
|
-
response.each {|x| puts "Response #{i+=1}: #{x} "}
|
36
|
-
response.each {|x| assert_not_nil x }
|
37
|
-
assert_not_nil response
|
38
|
-
end
|
39
|
-
|
40
61
|
|
41
62
|
def test_get_model_name_by_id
|
42
|
-
|
43
|
-
|
44
|
-
|
45
|
-
|
63
|
+
puts "\n\n ---------------------model name by ID---------------------\n\n"
|
64
|
+
response = @instance.get_model_name_by_id("BIOMD0000000190")
|
65
|
+
puts response
|
66
|
+
assert_not_nil response
|
67
|
+
end
|
68
|
+
|
69
|
+
def test_get_model_name_by_incorrect_id
|
70
|
+
puts "\n\n ---------------------model name by incorrect ID---------------------\n\n"
|
71
|
+
response = @instance.get_model_name_by_id("THIS IS NOT A VALID ID!!!!!<P></P>")
|
72
|
+
puts response
|
73
|
+
assert_not_nil response
|
46
74
|
end
|
47
75
|
|
48
76
|
|
77
|
+
def test_search_id_by_person
|
78
|
+
puts "\n\n ---------------------model ID by person---------------------\n\n"
|
79
|
+
response = []
|
80
|
+
i=0
|
81
|
+
response = @instance.search_by_person("Jim")
|
82
|
+
response.each { |x| puts "Response #{i+=1}: #{x} " }
|
83
|
+
response.each { |x| assert_not_nil x }
|
84
|
+
assert_not_nil response
|
85
|
+
end
|
49
86
|
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
|
87
|
+
def test_search_by_incorrect_person
|
88
|
+
puts "\n\n ---------------------model ID by incorrect person---------------------\n\n"
|
89
|
+
response = []
|
90
|
+
i=0
|
91
|
+
response = @instance.search_by_person("THIS IS NOT A VALID PERSONS NAME!!!!!<P></P>")
|
92
|
+
response.each { |x| puts "Response #{i+=1}: #{x} " }
|
93
|
+
response.each { |x| assert_not_nil x }
|
94
|
+
assert_not_nil response
|
58
95
|
end
|
59
96
|
|
60
97
|
end
|
metadata
CHANGED
@@ -1,13 +1,13 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: search_biomodel
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
hash:
|
4
|
+
hash: 15
|
5
5
|
prerelease: false
|
6
6
|
segments:
|
7
|
-
-
|
7
|
+
- 2
|
8
8
|
- 0
|
9
|
-
-
|
10
|
-
version:
|
9
|
+
- 0
|
10
|
+
version: 2.0.0
|
11
11
|
platform: ruby
|
12
12
|
authors:
|
13
13
|
- Niall Beard
|
@@ -15,13 +15,13 @@ autorequire:
|
|
15
15
|
bindir: bin
|
16
16
|
cert_chain: []
|
17
17
|
|
18
|
-
date:
|
18
|
+
date: 2012-02-17 00:00:00 +00:00
|
19
19
|
default_executable:
|
20
20
|
dependencies:
|
21
21
|
- !ruby/object:Gem::Dependency
|
22
|
-
prerelease: false
|
23
22
|
name: jeweler
|
24
|
-
|
23
|
+
prerelease: false
|
24
|
+
requirement: &id001 !ruby/object:Gem::Requirement
|
25
25
|
none: false
|
26
26
|
requirements:
|
27
27
|
- - ~>
|
@@ -32,12 +32,12 @@ dependencies:
|
|
32
32
|
- 6
|
33
33
|
- 2
|
34
34
|
version: 1.6.2
|
35
|
-
requirement: *id001
|
36
35
|
type: :development
|
36
|
+
version_requirements: *id001
|
37
37
|
- !ruby/object:Gem::Dependency
|
38
|
-
prerelease: false
|
39
38
|
name: rcov
|
40
|
-
|
39
|
+
prerelease: false
|
40
|
+
requirement: &id002 !ruby/object:Gem::Requirement
|
41
41
|
none: false
|
42
42
|
requirements:
|
43
43
|
- - ">="
|
@@ -46,12 +46,12 @@ dependencies:
|
|
46
46
|
segments:
|
47
47
|
- 0
|
48
48
|
version: "0"
|
49
|
-
requirement: *id002
|
50
49
|
type: :development
|
50
|
+
version_requirements: *id002
|
51
51
|
- !ruby/object:Gem::Dependency
|
52
|
-
prerelease: false
|
53
52
|
name: savon
|
54
|
-
|
53
|
+
prerelease: false
|
54
|
+
requirement: &id003 !ruby/object:Gem::Requirement
|
55
55
|
none: false
|
56
56
|
requirements:
|
57
57
|
- - ~>
|
@@ -62,8 +62,8 @@ dependencies:
|
|
62
62
|
- 9
|
63
63
|
- 2
|
64
64
|
version: 0.9.2
|
65
|
-
requirement: *id003
|
66
65
|
type: :development
|
66
|
+
version_requirements: *id003
|
67
67
|
description: "Client package for creating, sending, recieving and consuming SOAP messages from BioModels search engine "
|
68
68
|
email: beardn9@cs.man.ac.uk
|
69
69
|
executables: []
|
@@ -75,6 +75,15 @@ extra_rdoc_files:
|
|
75
75
|
- README.rdoc
|
76
76
|
files:
|
77
77
|
- .document
|
78
|
+
- .idea/.name
|
79
|
+
- .idea/.rakeTasks
|
80
|
+
- .idea/dictionaries/root.xml
|
81
|
+
- .idea/encodings.xml
|
82
|
+
- .idea/misc.xml
|
83
|
+
- .idea/modules.xml
|
84
|
+
- .idea/search_biomodel.iml
|
85
|
+
- .idea/vcs.xml
|
86
|
+
- .idea/workspace.xml
|
78
87
|
- Gemfile
|
79
88
|
- Gemfile.lock
|
80
89
|
- LICENSE.txt
|
@@ -82,6 +91,8 @@ files:
|
|
82
91
|
- Rakefile
|
83
92
|
- VERSION
|
84
93
|
- lib/search_biomodel.rb
|
94
|
+
- search_biomodel-1.1.1.gem
|
95
|
+
- search_biomodel-1.1.2.gem
|
85
96
|
- search_biomodel.gemspec
|
86
97
|
- test/helper.rb
|
87
98
|
- test/test_search_biomodel.rb
|