genevalidatorapp 1.5.2 → 1.5.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml
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@@ -1,7 +1,7 @@
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metadata.gz: 9eb1457cc2173c9ef5d4fee437c35f0c3a35ef10
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data.tar.gz: b78826c8f4a6c26d17af027808858e76d9faf44e
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metadata.gz:
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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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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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{ 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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@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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@@ -0,0 +1,12 @@
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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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--- !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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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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File without changes
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