genevalidatorapp 1.5.2 → 1.5.3
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checksums.yaml
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metadata.gz: 9eb1457cc2173c9ef5d4fee437c35f0c3a35ef10
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data.tar.gz: b78826c8f4a6c26d17af027808858e76d9faf44e
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metadata.gz: dbabca96bd30a820f8d99a9e41df220700cbfdf8b9ca50d10e3e351bb8fa6cad98f7b0ecbe501e9f190f45731dd79e9ccee40928c6909de9f64cbc4fbee8aff3
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data.tar.gz: 9e825c7677ec8279bf7d35ee6c04c7fc5ce6f6ab100f47bae9d8e541669aad130a1f38f8aff6ae0ea2ebe532b0561db3a2d750a4e05d23640b46916c836168db
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data/lib/genevalidatorapp.rb
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@@ -108,8 +108,10 @@ module GeneValidatorApp
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# Copy the public folder (in the app root) to the gv_app_dir location - this
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# gv_app_dir is then used by the app to serve all dependencies...
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def init_public_dir
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-
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-
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root_web_files = File.join(GeneValidatorApp.root, 'public/web_files')
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root_gv = File.join(GeneValidatorApp.root, 'public/GeneValidator')
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FileUtils.cp_r(root_web_files, @public_dir)
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FileUtils.cp_r(root_gv, @public_dir)
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end
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def init_binaries
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@@ -38,6 +38,7 @@ module GeneValidatorApp
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@params = params
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validate_params
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obtain_db_path
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@json_url = produce_json_url_link(url)
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@url = produce_result_url_link(url)
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end
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@@ -47,8 +48,8 @@ module GeneValidatorApp
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write_seq_to_file
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run_genevalidator
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copy_json_folder
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-
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{ parsed_json: parse_output_json, json_url: @json_url,
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results_url: @url }
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end
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private
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@@ -212,7 +213,13 @@ module GeneValidatorApp
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# Reuturns the URL of the results page.
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def produce_result_url_link(url)
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url.gsub(/input/, '').gsub(%r{/*$}, '') +
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"/GeneValidator/#{@unique_id}/input_file.fa.html/
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"/GeneValidator/#{@unique_id}/input_file.fa.html/results1.html"
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end
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# Reuturns the URL of the results page.
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def produce_json_url_link(url)
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url.gsub(/input/, '').gsub(%r{/*$}, '') +
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"/GeneValidator/#{@unique_id}/input_file.fa.json"
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end
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def parse_output_json
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@@ -51,8 +51,15 @@ module GeneValidatorApp
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post '/' do
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cross_origin # Required for the API to work...
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RunGeneValidator.init(request.url, params)
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@
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-
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@gv_results = RunGeneValidator.run
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@json_results = @gv_results[:parsed_json]
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if @params[:results_url]
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@gv_results[:results_url]
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elsif @params[:json_url]
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@gv_results[:json_url]
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else
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slim :results, layout: false
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end
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end
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# This error block will only ever be hit if the user gives us a funny
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<!DOCTYPE html><html><head><title>GeneValidator: identify problems with gene predictions</title><meta content="text/html; charset=utf-8" http-equiv="Content-Type"><link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.5/flatly/bootstrap.min.css"><link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css">
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<style type="text/css">html{position:relative;min-height:100%;}body{margin:0 0 100px;background-color:#F5F5F5}footer{bottom:0;width:100%;margin:0 auto;position:absolute;height:100px;overflow:hidden;border-top:2px solid #DBDBDB;padding-top:10px;color:#b4bcc2}
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</style></head>
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<body>
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<div class="container text-center">
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<h1 style="font-size: 78px">GeneValidator</h1>
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<h4 style="margin-bottom:3em">Identify Problems with Protein-Coding Gene Predictions</h4>
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<i class="fa fa-spinner fa-spin" style="font-size: 10em"></i>
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<h2> Calculating...</h2>
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<p class="results_link"> This may take some time. Please leave this page open.</p>
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</div>
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<footer><div class="container center-block"><p class="text-muted text-center">Please cite: "Dragan M<sup>‡</sup>, Moghul MI<sup>‡</sup>, Priyam A, Bustos C & Wurm Y <em>(in prep)</em> GeneValidator: identify problematic gene predictions"<br/> Developed at <a href="https://wurmlab.github.io" target="_blank">Wurm Lab</a>, <a href="http://www.sbcs.qmul.ac.uk" target="_blank">QMUL</a> with funding by <a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank">BBSRC</a> and <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2013" target="_blank">Google Summer of Code 2013</a><br/>This page was created by <a href="https://github.com/wurmlab/genevalidator" target="_blank" >GeneValidator</a> v1.6.5</p></div></footer></body></html>
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metadata
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@@ -1,7 +1,7 @@
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1
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--- !ruby/object:Gem::Specification
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name: genevalidatorapp
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version: !ruby/object:Gem::Version
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version: 1.5.
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version: 1.5.3
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platform: ruby
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authors:
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- Monica Dragan
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@@ -11,7 +11,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2015-
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date: 2015-09-21 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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@@ -218,7 +218,7 @@ files:
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- lib/genevalidatorapp/routes.rb
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- lib/genevalidatorapp/server.rb
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- lib/genevalidatorapp/version.rb
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- public/GeneValidator
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- public/GeneValidator/loading.html
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- public/src/css/bootstrap1.min.css
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- public/src/css/custom.css
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- public/src/css/custom.min.css
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