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Module: ClassyFireAPI
— Documentation by YARD 0.8.7.6
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< span class = "title" > ClassyFireAPI< / span >
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Class List
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Method List
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File List
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< div id = "content" > < h1 > Module: ClassyFireAPI
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< dl class = "box" >
< dt class = "r1 last" > Defined in:< / dt >
< dd class = "r1 last" > lib/classyfire_api.rb< / dd >
< / dl >
< div class = "clear" > < / div >
< h2 > Constant Summary< / h2 >
< dl class = "constants" >
< dt id = "URL-constant" class = "" > URL =
< / dt >
< dd > < pre class = "code" > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > http://classyfire.wishartlab.com< / span > < span class = 'tstring_end' > ' < / span > < / span > < / pre > < / dd >
< / dl >
< h2 >
Class Method Summary
< small > (< a href = "#" class = "summary_toggle" > collapse< / a > )< / small >
< / h2 >
< ul class = "summary" >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#get_entity_classification-class_method" title = "get_entity_classification (class method)" > + (Text) < strong > get_entity_classification< / strong > (inchikey, format = " json" ) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
< p > Retrieves the classification results for a given entity.< / p >
< / div > < / span >
< / li >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#get_query-class_method" title = "get_query (class method)" > + (Text) < strong > get_query< / strong > (query_id, format = " json" ) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
< p > Retrieves the classification results for a given query.< / p >
< / div > < / span >
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< / li >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#get_sequence_classification-class_method" title = "get_sequence_classification (class method)" > + (Text) < strong > get_sequence_classification< / strong > (fingerprint, format = " json" ) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
< p > Retrieves the classification results for a given sequence.< / p >
< / div > < / span >
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< / li >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#query_status-class_method" title = "query_status (class method)" > + (String) < strong > query_status< / strong > (query_id) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
< p > Retrieves the status of a query.< / p >
< / div > < / span >
< / li >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#retrieve_classification-class_method" title = "retrieve_classification (class method)" > + (String) < strong > retrieve_classification< / strong > (input, output) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
< p > Reads a tab separated file, and use the structure representation to
retrieve the strutcure' s classification from ClassyFire.< / p >
< / div > < / span >
< / li >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#retrieve_entities_json-class_method" title = "retrieve_entities_json (class method)" > + (String) < strong > retrieve_entities_json< / strong > (input, output) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
< p > Reads a tab separated file, and use the structure representation to
retrieve the strutcure' s classification from ClassyFire in a JSON
format.< / p >
< / div > < / span >
< / li >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#retrieve_entities_sdf-class_method" title = "retrieve_entities_sdf (class method)" > + (String) < strong > retrieve_entities_sdf< / strong > (input, output) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
< p > Reads a tab separated file, and use the structure representation to
retrieve the strutcure' s classification from ClassyFire in a SDF
format.< / p >
< / div > < / span >
< / li >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#submit_queries_from_directory-class_method" title = "submit_queries_from_directory (class method)" > + (Object) < strong > submit_queries_from_directory< / strong > (folder, slice_length, type = " STRUCTURE" ) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
< p > Takes each file in a folder, and submit the contained structures in bluks
of a given size.< / p >
< / div > < / span >
< / li >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#submit_query-class_method" title = "submit_query (class method)" > + (Hash) < strong > submit_query< / strong > (label, input, type = ' STRUCTURE' ) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
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< p > Submits a ClassyFire query in a JSON format.< / p >
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< / div > < / span >
< / li >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#submit_query_input_in_chunks-class_method" title = "submit_query_input_in_chunks (class method)" > + (Object) < strong > submit_query_input_in_chunks< / strong > (input_file, slice_length, start, type = ' STRUCTURE' ) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
< p > Takes a tab-separated file and submit the contained structures in bulks of
a given size.< / p >
< / div > < / span >
< / li >
< li class = "public " >
< span class = "summary_signature" >
< a href = "#submit_random_subset_of_query_input_in_chunks-class_method" title = "submit_random_subset_of_query_input_in_chunks (class method)" > + (Object) < strong > submit_random_subset_of_query_input_in_chunks< / strong > (tab_separated_input_file, size, type = ' STRUCTURE' ) < / a >
< / span >
< span class = "summary_desc" > < div class = 'inline' >
< p > Takes a tab-separated file and submit randomly selected structures in bulks
of a given size.< / p >
< / div > < / span >
< / li >
< / ul >
< div id = "class_method_details" class = "method_details_list" >
< h2 > Class Method Details< / h2 >
< div class = "method_details first" >
< h3 class = "signature first" id = "get_entity_classification-class_method" >
+ (< tt > Text< / tt > ) < strong > get_entity_classification< / strong > (inchikey, format = " json" )
< / h3 > < div class = "docstring" >
< div class = "discussion" >
< p > Retrieves the classification results for a given entity.< / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > inchikey< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
—
< div class = 'inline' >
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< p > the InChIKey of the entity.< / p >
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< / div >
< / li >
< li >
< span class = 'name' > format< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
< em class = "default" > (defaults to: < tt > " json" < / tt > )< / em >
—
< div class = 'inline' >
< p > the format of the query, ' text' (either JSON, CSV, or SDF)< / p >
< / div >
< / li >
< / ul >
< p class = "tag_title" > Returns:< / p >
< ul class = "return" >
< li >
< span class = 'type' > (< tt > Text< / tt > )< / span >
—
< div class = 'inline' >
< p > A text file displaying the classification results for the entity in the
specified format.< / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
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< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 62< / span >
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< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get_entity_classification' > get_entity_classification< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_inchikey' > inchikey< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > json< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_inchikey_id' > inchikey_id< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_inchikey' > inchikey< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_to_s' > to_s< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_gsub' > gsub< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > InChIKey=< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'comma' > ,< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > begin< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > ==< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > json< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'const' > RestClient< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get' > get< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > URL< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > /entities/< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_inchikey_id' > inchikey_id< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > .< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :accept< / span > < span class = 'op' > => < / span > < span class = 'symbol' > :json< / span >
< span class = 'kw' > elsif< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > ==< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > sdf< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'const' > RestClient< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get' > get< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > URL< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > /entities/< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_inchikey_id' > inchikey_id< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > .< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :accept< / span > < span class = 'op' > => < / span > < span class = 'symbol' > :sdf< / span >
< span class = 'kw' > elsif< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > ==< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > csv< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'const' > RestClient< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get' > get< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > URL< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > /entities/< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_inchikey_id' > inchikey_id< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > .< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :accept< / span > < span class = 'op' > => < / span > < span class = 'symbol' > :csv< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > ResourceNotFound< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > InternalServerError< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > GatewayTimeout< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > RequestTimeout< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
< / div >
< div class = "method_details " >
< h3 class = "signature " id = "get_query-class_method" >
+ (< tt > Text< / tt > ) < strong > get_query< / strong > (query_id, format = " json" )
< / h3 > < div class = "docstring" >
< div class = "discussion" >
< p > Retrieves the classification results for a given query.< / p >
< p > the query' s entities in the specified format.< / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > query_id< / span >
< span class = 'type' > (< tt > Integer< / tt > )< / span >
—
< div class = 'inline' >
< p > the ID of the query.< / p >
< / div >
< / li >
< li >
< span class = 'name' > format< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
< em class = "default" > (defaults to: < tt > " json" < / tt > )< / em >
—
< div class = 'inline' >
< p > the format of the query (either JSON, CSV, or SDF)< / p >
< / div >
< / li >
< / ul >
< p class = "tag_title" > Returns:< / p >
< ul class = "return" >
< li >
< span class = 'type' > (< tt > Text< / tt > )< / span >
—
< div class = 'inline' >
< p > A text file displaying the classification results for< / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
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< / td >
< td >
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< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 37< / span >
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< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get_query' > get_query< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_query_id' > query_id< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > json< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > begin< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > ==< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > json< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'const' > RestClient< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get' > get< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > URL< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > /queries/< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_query_id' > query_id< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > .json< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :accept< / span > < span class = 'op' > => < / span > < span class = 'symbol' > :json< / span >
< span class = 'kw' > elsif< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > ==< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > sdf< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'const' > RestClient< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get' > get< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > URL< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > /queries/< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_query_id' > query_id< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > .sdf< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :accept< / span > < span class = 'op' > => < / span > < span class = 'symbol' > :sdf< / span >
< span class = 'kw' > elsif< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > ==< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > csv< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'const' > RestClient< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get' > get< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > URL< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > /queries/< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_query_id' > query_id< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > .csv< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :accept< / span > < span class = 'op' > => < / span > < span class = 'symbol' > :csv< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > ResourceNotFound< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > InternalServerError< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > GatewayTimeout< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > RequestTimeout< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
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< / div >
< div class = "method_details " >
< h3 class = "signature " id = "get_sequence_classification-class_method" >
+ (< tt > Text< / tt > ) < strong > get_sequence_classification< / strong > (fingerprint, format = " json" )
< / h3 > < div class = "docstring" >
< div class = "discussion" >
< p > Retrieves the classification results for a given sequence.< / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > the< / span >
< span class = 'type' > < / span >
—
< div class = 'inline' >
< p > fingerprint [String] the fingerprint (generated from the sequence using
Digest::MD5).< / p >
< / div >
< / li >
< li >
< span class = 'name' > format< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
< em class = "default" > (defaults to: < tt > " json" < / tt > )< / em >
—
< div class = 'inline' >
< p > the format of the query (Only JSON)< / p >
< / div >
< / li >
< / ul >
< p class = "tag_title" > Returns:< / p >
< ul class = "return" >
< li >
< span class = 'type' > (< tt > Text< / tt > )< / span >
—
< div class = 'inline' >
< p > A text file displaying the classification results for the entity in the
specified format.< / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
88
89
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95
96
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98
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100
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102< / pre >
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< / td >
< td >
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< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 88< / span >
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< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get_sequence_classification' > get_sequence_classification< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_fingerprint' > fingerprint< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > json< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > begin< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > ==< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > json< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'const' > RestClient< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get' > get< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > URL< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > /entities/< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_fingerprint' > fingerprint< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > .< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :accept< / span > < span class = 'op' > => < / span > < span class = 'symbol' > :json< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > ResourceNotFound< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > InternalServerError< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > GatewayTimeout< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > RequestTimeout< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
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< / div >
< div class = "method_details " >
< h3 class = "signature " id = "query_status-class_method" >
+ (< tt > String< / tt > ) < strong > query_status< / strong > (query_id)
< / h3 > < div class = "docstring" >
< div class = "discussion" >
< p > Retrieves the status of a query< / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > query_id< / span >
< span class = 'type' > (< tt > Integer< / tt > )< / span >
—
< div class = 'inline' >
< p > the ID of the query< / p >
< / div >
< / li >
< / ul >
< p class = "tag_title" > Returns:< / p >
< ul class = "return" >
< li >
< span class = 'type' > (< tt > String< / tt > )< / span >
—
< div class = 'inline' >
< p > the query status, ' Done' or ' In progress' , ' string' < / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
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136< / pre >
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< / td >
< td >
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< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 129< / span >
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< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_query_status' > query_status< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_query_id' > query_id< / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > begin< / span >
< span class = 'const' > RestClient< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get' > get< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > URL< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > /queries/< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_query_id' > query_id< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > /status.json< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :accept< / span > < span class = 'op' > => < / span > < span class = 'symbol' > :json< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > Exception< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'gvar' > $stderr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_message' > message< / span >
< span class = 'kw' > nil< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
< / div >
< div class = "method_details " >
< h3 class = "signature " id = "retrieve_classification-class_method" >
+ (< tt > String< / tt > ) < strong > retrieve_classification< / strong > (input, output)
< / h3 > < div class = "docstring" >
< div class = "discussion" >
< p > Reads a tab separated file, and use the structure representation to
retrieve the strutcure' s classification from ClassyFire.< / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > input< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
—
< div class = 'inline' >
< p > path to the input file.< / p >
< / div >
< / li >
< / ul >
< p class = "tag_title" > Returns:< / p >
< ul class = "return" >
< li >
< span class = 'type' > (< tt > String< / tt > )< / span >
—
< div class = 'inline' >
< p > path to the output file.< / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
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373< / pre >
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< / td >
< td >
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< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 311< / span >
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< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_retrieve_classification' > retrieve_classification< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_output' > output< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_expand_path' > expand_path< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_f_input' > f_input< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_open' > open< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'comma' > ,< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > r< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_h' > h< / span > < span class = 'op' > =< / span > < span class = 'const' > Hash< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_new' > new< / span >
< span class = 'id identifier rubyid_directory' > directory< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > /< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'op' > ...< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_join' > join< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > /< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_f_output' > f_output< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_new' > new< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_output' > output< / span > < span class = 'comma' > ,< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > w< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > =< / span > < span class = 'const' > String< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_new' > new< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > {< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > " id" : 1,< / span > < span class = 'tstring_end' > ' < / span > < / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > " label" :" < / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'op' > +< / span > < span class = 'id identifier rubyid_output' > output< / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > " ,< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > " classification_status" :" Done" ,< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > " entities" :[< / span > < span class = 'tstring_end' > ' < / span > < / span >
< span class = 'id identifier rubyid_f_input' > f_input< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_each_line' > each_line< / span > < span class = 'kw' > do< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'op' > |< / span >
< span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_strip' > strip< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \t< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'op' > ==< / span > < span class = 'int' > 1< / span >
< span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'rbracket' > ]< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span >
< span class = 'kw' > elsif< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'op' > ==< / span > < span class = 'int' > 2< / span >
< span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'rbracket' > ]< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_strip' > strip< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_uniq' > uniq< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'op' > > < / span > < span class = 'int' > 0< / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > =< / span > < span class = 'int' > 1< / span >
< span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_uniq' > uniq< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'op' > ..< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_each' > each< / span > < span class = 'kw' > do< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'op' > |< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_i' > i< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > :: < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > begin< / span >
< span class = 'id identifier rubyid_qs' > qs< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_submit_query' > submit_query< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'rbracket' > ]< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_qs_decoded' > qs_decoded< / span > < span class = 'op' > =< / span > < span class = 'const' > JSON< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_parse' > parse< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_qs' > qs< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'op' > =< / span > < span class = 'const' > JSON< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_parse' > parse< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_get_query' > get_query< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_qs_decoded' > qs_decoded< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > id< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rbracket' > ]< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > json< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > entities< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rbracket' > ]< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_to_json' > to_json< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > ,< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > +=< / span > < span class = 'int' > 1< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > Exception< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_message' > message< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_key' > key< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'lbracket' > [< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > :: < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > begin< / span >
< span class = 'id identifier rubyid_qs' > qs< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_submit_query' > submit_query< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'rbracket' > ]< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_sleep' > sleep< / span > < span class = 'lparen' > (< / span > < span class = 'float' > 0.2< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_qs_decoded' > qs_decoded< / span > < span class = 'op' > =< / span > < span class = 'const' > JSON< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_parse' > parse< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_qs' > qs< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'op' > =< / span > < span class = 'const' > JSON< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_parse' > parse< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_get_query' > get_query< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_qs_decoded' > qs_decoded< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > id< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rbracket' > ]< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > json< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'rparen' > )< / span >
< span class = 'comment' > # puts qr[" entities" ]
< / span > < span class = 'comment' > # sleep(0.2)
< / span > < span class = 'comment' > # f_output.print qr[" entities" ][0]," \n"
< / span > < span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > entities< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rbracket' > ]< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_to_json' > to_json< / span >
< span class = 'comment' > # res += " ,"
< / span > < span class = 'kw' > rescue< / span > < span class = 'const' > Exception< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_message' > message< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > ]}< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_f_output' > f_output< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_print' > print< / span > < span class = 'id identifier rubyid_res' > res< / span >
< span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
< / div >
< div class = "method_details " >
< h3 class = "signature " id = "retrieve_entities_json-class_method" >
+ (< tt > String< / tt > ) < strong > retrieve_entities_json< / strong > (input, output)
< / h3 > < div class = "docstring" >
< div class = "discussion" >
< p > Reads a tab separated file, and use the structure representation to
retrieve the strutcure' s classification from ClassyFire in a JSON
format.< / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > input< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
—
< div class = 'inline' >
< p > path to the input file< / p >
< / div >
< / li >
< / ul >
< p class = "tag_title" > Returns:< / p >
< ul class = "return" >
< li >
< span class = 'type' > (< tt > String< / tt > )< / span >
—
< div class = 'inline' >
< p > path to the output file< / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
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433< / pre >
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< / td >
< td >
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< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 380< / span >
2016-03-10 02:26:59 +00:00
< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_retrieve_entities_json' > retrieve_entities_json< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_output' > output< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_expand_path' > expand_path< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_f_input' > f_input< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_open' > open< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'comma' > ,< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > r< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_h' > h< / span > < span class = 'op' > =< / span > < span class = 'const' > Hash< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_new' > new< / span >
< span class = 'id identifier rubyid_directory' > directory< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > /< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'op' > ...< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_join' > join< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > /< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_f_output' > f_output< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_new' > new< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_output' > output< / span > < span class = 'comma' > ,< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > w< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_puts' > puts< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > =< / span > < span class = 'const' > String< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_new' > new< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > {< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > " id" : 1,< / span > < span class = 'tstring_end' > ' < / span > < / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > " label" :" < / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'op' > +< / span > < span class = 'id identifier rubyid_output' > output< / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > " ,< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > " classification_status" :" Done" ,< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > " entities" :[< / span > < span class = 'tstring_end' > ' < / span > < / span >
< span class = 'id identifier rubyid_f_input' > f_input< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_each_line' > each_line< / span > < span class = 'kw' > do< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'op' > |< / span >
< span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_strip' > strip< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \t< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'rbracket' > ]< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_uniq' > uniq< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'op' > > < / span > < span class = 'int' > 0< / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > =< / span > < span class = 'int' > 1< / span >
< span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_uniq' > uniq< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'op' > ...< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_each' > each< / span > < span class = 'kw' > do< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'op' > |< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_i' > i< / span >
< span class = 'comment' > # puts " #{key} :: #{h[key]}"
< / span > < span class = 'kw' > begin< / span >
< span class = 'id identifier rubyid_inchikey' > inchikey< / span > < span class = 'op' > =< / span > < span class = 'backtick' > %x(< / span > < span class = 'tstring_content' > /Applications/ChemAxon/JChem/bin/molconvert inchikey -s " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > " < / span > < span class = 'tstring_end' > )< / span > < / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_strip' > strip< / span >
< span class = 'comment' > # puts inchikey
< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'op' > =< / span > < span class = 'const' > JSON< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_parse' > parse< / span > < span class = 'lparen' > (< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get_entity_classification' > get_entity_classification< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_inchikey' > inchikey< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > json< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > identifier< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rbracket' > ]< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_key' > key< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_to_json' > to_json< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > ,< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > :: RETURN NIL< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'kw' > if< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_nil?' > nil?< / span > < span class = 'op' > ||< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > direct_parent< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rbracket' > ]< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > name< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_nil?' > nil?< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > Exception< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_message' > message< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > +=< / span > < span class = 'int' > 1< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_key' > key< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'lbracket' > [< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span >
< span class = 'comment' > # puts " #{key} :: #{h[key]}"
< / span > < span class = 'kw' > begin< / span >
< span class = 'id identifier rubyid_inchikey' > inchikey< / span > < span class = 'op' > =< / span > < span class = 'backtick' > %x(< / span > < span class = 'tstring_content' > /Applications/ChemAxon/JChem/bin/molconvert inchikey -s " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > " < / span > < span class = 'tstring_end' > )< / span > < / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_strip' > strip< / span >
< span class = 'comment' > # puts inchikey
< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'op' > =< / span > < span class = 'const' > JSON< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_parse' > parse< / span > < span class = 'lparen' > (< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get_entity_classification' > get_entity_classification< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_inchikey' > inchikey< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > json< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > identifier< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rbracket' > ]< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_key' > key< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_to_json' > to_json< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > :: RETURN NIL< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'kw' > if< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_nil?' > nil?< / span > < span class = 'op' > ||< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > direct_parent< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rbracket' > ]< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > name< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_nil?' > nil?< / span >
< span class = 'comment' > # res += " ,"
< / span > < span class = 'kw' > rescue< / span > < span class = 'const' > Exception< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_message' > message< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > +=< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > ]}< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_f_output' > f_output< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_print' > print< / span > < span class = 'id identifier rubyid_res' > res< / span >
< span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
< / div >
< div class = "method_details " >
< h3 class = "signature " id = "retrieve_entities_sdf-class_method" >
+ (< tt > String< / tt > ) < strong > retrieve_entities_sdf< / strong > (input, output)
< / h3 > < div class = "docstring" >
< div class = "discussion" >
< p > Reads a tab separated file, and use the structure representation to
retrieve the strutcure' s classification from ClassyFire in a SDF
format.< / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > input< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
—
< div class = 'inline' >
< p > path to the input file< / p >
< / div >
< / li >
< / ul >
< p class = "tag_title" > Returns:< / p >
< ul class = "return" >
< li >
< span class = 'type' > (< tt > String< / tt > )< / span >
—
< div class = 'inline' >
< p > path to the output file< / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
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< / td >
< td >
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< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 442< / span >
2016-03-10 02:26:59 +00:00
< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_retrieve_entities_sdf' > retrieve_entities_sdf< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_output' > output< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_expand_path' > expand_path< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_f_input' > f_input< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_open' > open< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'comma' > ,< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > r< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_h' > h< / span > < span class = 'op' > =< / span > < span class = 'const' > Hash< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_new' > new< / span >
< span class = 'id identifier rubyid_directory' > directory< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > /< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'op' > ...< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_join' > join< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > /< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_f_output' > f_output< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_new' > new< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_output' > output< / span > < span class = 'comma' > ,< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > w< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_res' > res< / span > < span class = 'op' > =< / span > < span class = 'const' > String< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_new' > new< / span >
< span class = 'id identifier rubyid_f_input' > f_input< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_each_line' > each_line< / span > < span class = 'kw' > do< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'op' > |< / span >
< span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_strip' > strip< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \t< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'rbracket' > ]< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_uniq' > uniq< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'op' > > < / span > < span class = 'int' > 0< / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > =< / span > < span class = 'int' > 1< / span >
< span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_uniq' > uniq< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'op' > ...< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_each' > each< / span > < span class = 'kw' > do< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'op' > |< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_i' > i< / span >
< span class = 'comment' > # puts " #{key} :: #{h[key]}"
< / span > < span class = 'kw' > begin< / span >
< span class = 'id identifier rubyid_inchikey' > inchikey< / span > < span class = 'op' > =< / span > < span class = 'backtick' > %x(< / span > < span class = 'tstring_content' > /Applications/ChemAxon/JChem/bin/molconvert inchikey -s " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > " < / span > < span class = 'tstring_end' > )< / span > < / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_strip' > strip< / span >
< span class = 'comment' > # puts inchikey
< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'op' > =< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get_entity_classification' > get_entity_classification< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_inchikey' > inchikey< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > sdf< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_include?' > include?< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > The page you were looking for doesn' t exist< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > The page you were looking for doesn' t exist< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > elsif< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_empty?' > empty?< / span >
< span class = 'kw' > else< / span >
< span class = 'id identifier rubyid_input' > input< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \n< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 1< / span > < span class = 'op' > ..< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_join' > join< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \n< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_input' > input< / span >
< span class = 'id identifier rubyid_f_output' > f_output< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > \n< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_f_output' > f_output< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_input' > input< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > Exception< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_message' > message< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > +=< / span > < span class = 'int' > 1< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_key' > key< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_keys' > keys< / span > < span class = 'lbracket' > [< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span >
< span class = 'comment' > # puts " #{key} :: #{h[key]}"
< / span > < span class = 'kw' > begin< / span >
< span class = 'id identifier rubyid_inchikey' > inchikey< / span > < span class = 'op' > =< / span > < span class = 'backtick' > %x(< / span > < span class = 'tstring_content' > /Applications/ChemAxon/JChem/bin/molconvert inchikey -s " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_h' > h< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > " < / span > < span class = 'tstring_end' > )< / span > < / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_strip' > strip< / span >
< span class = 'comment' > # puts inchikey
< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'op' > =< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_get_entity_classification' > get_entity_classification< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_inchikey' > inchikey< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_format' > format< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > sdf< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_include?' > include?< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > The page you were looking for doesn' t exist< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > The page you were looking for doesn' t exist< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > elsif< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_empty?' > empty?< / span >
< span class = 'kw' > else< / span >
< span class = 'id identifier rubyid_input' > input< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_qr' > qr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \n< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 1< / span > < span class = 'op' > ..< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_join' > join< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \n< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_input' > input< / span >
< span class = 'id identifier rubyid_f_output' > f_output< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_key' > key< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > \n< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_f_output' > f_output< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_input' > input< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > Exception< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_message' > message< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'comment' > # f_output.print res
< / span > < span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
< / div >
< div class = "method_details " >
< h3 class = "signature " id = "submit_queries_from_directory-class_method" >
+ (< tt > Object< / tt > ) < strong > submit_queries_from_directory< / strong > (folder, slice_length, type = " STRUCTURE" )
< / h3 > < div class = "docstring" >
< div class = "discussion" >
< p > Takes each file in a folder, and submit the contained structures in bluks
of a given size.< / p >
< p > For ' STRUCTURE' or ' IUPAC_NAME' query types, each line must
contain either< / p >
< pre class = "code ruby" > < code class = "ruby" > 1) Only a structural represenation: SMILES, InChI for the ' STRUCTURE' query_type or a IUPAC name
for the ' IUPAC NAME' query type.
2) a tab-separated pair of an ID and the corresponding sructure representation: SMILES, InChI for the
' STRUCTURE' query_type or a IUPAC name for the ' IUPAC NAME' query type.< / code > < / pre >
< p > For ' FASTA' query type, just submit the query as a standard FASTA
text. @param: input_file [String] The path to the folder. @param:
slice_length [Integer] The maximum number of entries for each query input
(each file is fragmented into n part of #slice_length entries each),
' integer' < / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > type< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
< em class = "default" > (defaults to: < tt > " STRUCTURE" < / tt > )< / em >
—
< div class = 'inline' >
< p > the query_type ' STRUCTURE' (default) or ' IUPAC_NAME' or
' FASTA' < / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
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238< / pre >
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< / td >
< td >
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< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 229< / span >
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< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_submit_queries_from_directory' > submit_queries_from_directory< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_folder' > folder< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_slice_length' > slice_length< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_type' > type< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > STRUCTURE< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > if< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_directory?' > directory?< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_folder' > folder< / span > < span class = 'rparen' > )< / span >
< span class = 'const' > Dir< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_foreach' > foreach< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_folder' > folder< / span > < span class = 'rparen' > )< / span > < span class = 'kw' > do< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_filename' > filename< / span > < span class = 'op' > |< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > Filename: < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_filename' > filename< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_submit_query_input_in_chunks' > submit_query_input_in_chunks< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_folder' > folder< / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > /< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'op' > +< / span > < span class = 'id identifier rubyid_filename' > filename< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_slice_length' > slice_length< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_type' > type< / span > < span class = 'rparen' > )< / span > < span class = 'kw' > unless< / span > < span class = 'id identifier rubyid_filename' > filename< / span > < span class = 'op' > ==< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > .< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'op' > ||< / span > < span class = 'id identifier rubyid_filename' > filename< / span > < span class = 'op' > ==< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > ..< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'op' > ||< / span > < span class = 'id identifier rubyid_filename' > filename< / span > < span class = 'op' > ==< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > .DS_Store< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > else< / span >
< span class = 'gvar' > $stderr< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_folder' > folder< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > is not a folder.< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
< / div >
< div class = "method_details " >
< h3 class = "signature " id = "submit_query-class_method" >
+ (< tt > Hash< / tt > ) < strong > submit_query< / strong > (label, input, type = ' STRUCTURE' )
< / h3 > < div class = "docstring" >
< div class = "discussion" >
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< p > Submits a ClassyFire query in a JSON format.< / p >
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< p > if there is an error.< / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > label< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
—
< div class = 'inline' >
< p > the label of the query.< / p >
< / div >
< / li >
< li >
< span class = 'name' > input< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
—
< div class = 'inline' >
< p > the input of the query.< / p >
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< / div >
< / li >
< li >
< span class = 'name' > type< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
< em class = "default" > (defaults to: < tt > ' STRUCTURE' < / tt > )< / em >
—
< div class = 'inline' >
< p > the type of the query.< / p >
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< / div >
< / li >
< / ul >
< p class = "tag_title" > Returns:< / p >
< ul class = "return" >
< li >
< span class = 'type' > (< tt > Hash< / tt > )< / span >
—
< div class = 'inline' >
< p > A Ruby Hash with the id (and other attributes) of the Query or nil< / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
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29< / pre >
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< / td >
< td >
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< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 14< / span >
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< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_submit_query' > submit_query< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_label' > label< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_type' > type< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > STRUCTURE< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > begin< / span >
< span class = 'id identifier rubyid_q' > q< / span > < span class = 'op' > =< / span > < span class = 'const' > RestClient< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_post' > post< / span > < span class = 'const' > URL< / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > /queries< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'comma' > ,< / span > < span class = 'lbrace' > {< / span > < span class = 'symbol' > :label< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_label' > label< / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :query_input< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :query_type< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_type' > type< / span > < span class = 'rbrace' > }< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_to_json' > to_json< / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :accept< / span > < span class = 'op' > => < / span > < span class = 'symbol' > :json< / span > < span class = 'comma' > ,< / span > < span class = 'symbol' > :content_type< / span > < span class = 'op' > => < / span > < span class = 'symbol' > :json< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > BadRequest< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > InternalServerError< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > GatewayTimeout< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > RequestTimeout< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > RestClient< / span > < span class = 'op' > ::< / span > < span class = 'const' > UnprocessableEntity< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_response' > response< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_q' > q< / span >
< span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
< / div >
< div class = "method_details " >
< h3 class = "signature " id = "submit_query_input_in_chunks-class_method" >
+ (< tt > Object< / tt > ) < strong > submit_query_input_in_chunks< / strong > (input_file, slice_length, start, type = ' STRUCTURE' )
< / h3 > < div class = "docstring" >
< div class = "discussion" >
< p > Takes a tab-separated file and submit the contained structures in bulks of
a given size< / p >
< p > For ' STRUCTURE' or ' IUPAC_NAME' query types, each line must
contain either< / p >
< pre class = "code ruby" > < code class = "ruby" > 1) Only a structural represenation: SMILES, InChI for the ' STRUCTURE' query_type or a IUPAC name
for the ' IUPAC NAME' query type.
2) a tab-separated pair of an ID and the corresponding sructure representation: SMILES, InChI for the
' STRUCTURE' query_type or a IUPAC name for the ' IUPAC NAME' query type.< / code > < / pre >
< p > For ' FASTA' query type, just submit the query as a standard FASTA
text. @param: slice_length [Integer] The maximum number of entries for each
query input (the whole file is fragmented into n part of #slice_length
entries each). @param: start [Integer] The starting index. Submit
framgments from the index ' start' .< / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > input_file< / span >
< span class = 'type' > (< tt > Text< / tt > )< / span >
—
< div class = 'inline' >
< p > The path to the input file.< / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
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< / td >
< td >
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< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 151< / span >
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< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_submit_query_input_in_chunks' > submit_query_input_in_chunks< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_input_file' > input_file< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_slice_length' > slice_length< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_start' > start< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_type' > type< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > STRUCTURE< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'ivar' > @start_time< / span > < span class = 'op' > =< / span > < span class = 'const' > Time< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_now' > now< / span >
< span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_expand_path' > expand_path< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_input_file' > input_file< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_f' > f< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_open' > open< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'comma' > ,< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > r< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_input' > input< / span > < span class = 'op' > =< / span > < span class = 'lbracket' > [< / span > < span class = 'rbracket' > ]< / span >
< span class = 'id identifier rubyid_lines' > lines< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_readlines' > readlines< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_lines' > lines< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_uniq' > uniq< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_each' > each< / span > < span class = 'kw' > do< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'op' > |< / span >
< span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_strip' > strip< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \t< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'op' > ==< / span > < span class = 'int' > 1< / span >
< span class = 'id identifier rubyid_input' > input< / span > < span class = 'op' > < < < / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > elsif< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'op' > > =< / span > < span class = 'int' > 2< / span >
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< span class = 'id identifier rubyid_input' > input< / span > < span class = 'op' > < < < / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > \t< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
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< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_query_ids' > query_ids< / span > < span class = 'op' > =< / span > < span class = 'lbracket' > [< / span > < span class = 'rbracket' > ]< / span >
< span class = 'id identifier rubyid_subdivised_groups' > subdivised_groups< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_uniq' > uniq< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_each_slice' > each_slice< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_slice_length' > slice_length< / span > < span class = 'rparen' > )< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_to_a' > to_a< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > nr of subdivised_groups: < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_subdivised_groups' > subdivised_groups< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_subdivised_groups' > subdivised_groups< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span >
< span class = 'id identifier rubyid_sleeping_time' > sleeping_time< / span > < span class = 'op' > =< / span > < span class = 'int' > 120< / span >
< span class = 'id identifier rubyid_initial_nr_of_jobs' > initial_nr_of_jobs< / span > < span class = 'op' > =< / span > < span class = 'int' > 60< / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_start' > start< / span >
< span class = 'kw' > while< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > < < / span > < span class = 'id identifier rubyid_initial_nr_of_jobs' > initial_nr_of_jobs< / span >
< span class = 'id identifier rubyid_title' > title< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_basename' > basename< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'rparen' > )< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > .< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > _yannick< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > _part_< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
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< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > < =< / span > < span class = 'id identifier rubyid_subdivised_groups' > subdivised_groups< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span >
< span class = 'kw' > begin< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > submitting < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_title' > title< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_q' > q< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_submit_query' > submit_query< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_title' > title< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_subdivised_groups' > subdivised_groups< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_join' > join< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \n< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_type' > type< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_query_ids' > query_ids< / span > < span class = 'op' > < < < / span > < span class = 'const' > JSON< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_parse' > parse< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_q' > q< / span > < span class = 'rparen' > )< / span > < span class = 'lbracket' > [< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > id< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rbracket' > ]< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > Exception< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_message' > message< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_backtrace' > backtrace< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_inspect' > inspect< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > +< / span > < span class = 'int' > 1< / span >
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< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > Going to sleep at < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > Time< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_now' > now< / span > < span class = 'op' > -< / span > < span class = 'ivar' > @start_time< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > for < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_sleeping_time' > sleeping_time< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > s.< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_sleep' > sleep< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_sleeping_time' > sleeping_time< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > Waking up at < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > Time< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_now' > now< / span > < span class = 'op' > -< / span > < span class = 'ivar' > @start_time< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > while< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > < < / span > < span class = 'id identifier rubyid_subdivised_groups' > subdivised_groups< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span >
< span class = 'id identifier rubyid_k' > k< / span > < span class = 'op' > =< / span > < span class = 'int' > 0< / span >
< span class = 'kw' > for< / span > < span class = 'id identifier rubyid_k' > k< / span > < span class = 'kw' > in< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > ..< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > +< / span > < span class = 'int' > 80< / span > < span class = 'rparen' > )< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_title' > title< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_basename' > basename< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'rparen' > )< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > .< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > _yannick< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > _part_< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_k' > k< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > +< / span > < span class = 'int' > 1< / span >
< span class = 'kw' > begin< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > submitting < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_title' > title< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_q' > q< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_submit_query' > submit_query< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_title' > title< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_subdivised_groups' > subdivised_groups< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_k' > k< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_join' > join< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \n< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_type' > type< / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > Exception< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_message' > message< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_backtrace' > backtrace< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_inspect' > inspect< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_k' > k< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > Going to sleep at < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > Time< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_now' > now< / span > < span class = 'op' > -< / span > < span class = 'ivar' > @start_time< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > for < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_sleeping_time' > sleeping_time< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > s.< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_sleep' > sleep< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_sleeping_time' > sleeping_time< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > Waking up at < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > Time< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_now' > now< / span > < span class = 'op' > -< / span > < span class = 'ivar' > @start_time< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
< / div >
< div class = "method_details " >
< h3 class = "signature " id = "submit_random_subset_of_query_input_in_chunks-class_method" >
+ (< tt > Object< / tt > ) < strong > submit_random_subset_of_query_input_in_chunks< / strong > (tab_separated_input_file, size, type = ' STRUCTURE' )
< / h3 > < div class = "docstring" >
< div class = "discussion" >
< p > Takes a tab-separated file and submit randomly selected structures in bulks
of a given size.< / p >
< p > For ' STRUCTURE' or ' IUPAC_NAME' query types, each line must
contain either< / p >
< pre class = "code ruby" > < code class = "ruby" > 1) Only a structural represenation: SMILES, InChI for the ' STRUCTURE' query_type or a IUPAC name
for the ' IUPAC NAME' query type.
2) a tab-separated pair of an ID and the corresponding sructure representation: SMILES, InChI for the
' STRUCTURE' query_type or a IUPAC name for the ' IUPAC NAME' query type.< / code > < / pre >
< p > For ' FASTA' query type, just submit the query as a standard FASTA
text. is fragmented into n part of #slice_length entries each).< / p >
< / div >
< / div >
< div class = "tags" >
< p class = "tag_title" > Parameters:< / p >
< ul class = "param" >
< li >
< span class = 'name' > tab_separated_input_file< / span >
< span class = 'type' > (< tt > Text< / tt > )< / span >
—
< div class = 'inline' >
< p > The path to the input file.< / p >
< / div >
< / li >
< li >
< span class = 'name' > size< / span >
< span class = 'type' > (< tt > Integer< / tt > )< / span >
—
< div class = 'inline' >
< p > The maximum number of entries for each query input (the whole file< / p >
< / div >
< / li >
< li >
< span class = 'name' > type< / span >
< span class = 'type' > (< tt > String< / tt > )< / span >
< em class = "default" > (defaults to: < tt > ' STRUCTURE' < / tt > )< / em >
—
< div class = 'inline' >
< p > The query_type, ' STRUCTURE' (default) or ' IUPAC_NAME' or
' FASTA' .< / p >
< / div >
< / li >
< / ul >
< / div > < table class = "source_code" >
< tr >
< td >
< pre class = "lines" >
254
255
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302
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304< / pre >
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< / td >
< td >
2016-03-10 22:54:39 +00:00
< pre class = "code" > < span class = "info file" > # File 'lib/classyfire_api.rb', line 254< / span >
2016-03-10 02:26:59 +00:00
< span class = 'kw' > def< / span > < span class = 'const' > ClassyFireAPI< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_submit_random_subset_of_query_input_in_chunks' > submit_random_subset_of_query_input_in_chunks< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_tab_separated_input_file' > tab_separated_input_file< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_size' > size< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_type' > type< / span > < span class = 'op' > =< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > STRUCTURE< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'ivar' > @start_time< / span > < span class = 'op' > =< / span > < span class = 'const' > Time< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_now' > now< / span >
< span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_expand_path' > expand_path< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_tab_separated_input_file' > tab_separated_input_file< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_f' > f< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_open' > open< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'comma' > ,< / span > < span class = 'tstring' > < span class = 'tstring_beg' > ' < / span > < span class = 'tstring_content' > r< / span > < span class = 'tstring_end' > ' < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_input' > input< / span > < span class = 'op' > =< / span > < span class = 'lbracket' > [< / span > < span class = 'rbracket' > ]< / span >
< span class = 'id identifier rubyid_f' > f< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_each_line' > each_line< / span > < span class = 'kw' > do< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'op' > |< / span >
< span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_line' > line< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_strip' > strip< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \t< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > if< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'op' > ==< / span > < span class = 'int' > 1< / span >
< span class = 'id identifier rubyid_input' > input< / span > < span class = 'op' > < < < / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > elsif< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'op' > ==< / span > < span class = 'int' > 2< / span >
< span class = 'id identifier rubyid_input' > input< / span > < span class = 'op' > < < < / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > \t< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_sline' > sline< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 1< / span > < span class = 'rbracket' > ]< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_query_ids' > query_ids< / span > < span class = 'op' > =< / span > < span class = 'lbracket' > [< / span > < span class = 'rbracket' > ]< / span >
< span class = 'id identifier rubyid_indexes' > indexes< / span > < span class = 'op' > =< / span > < span class = 'lbracket' > [< / span > < span class = 'rbracket' > ]< / span >
< span class = 'id identifier rubyid_r' > r< / span > < span class = 'op' > =< / span > < span class = 'int' > 1< / span >
< span class = 'kw' > while< / span > < span class = 'id identifier rubyid_r' > r< / span > < span class = 'op' > < =< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_size' > size< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_s' > s< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_rand' > rand< / span > < span class = 'lparen' > (< / span > < span class = 'int' > 0< / span > < span class = 'op' > ..< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span > < span class = 'op' > -< / span > < span class = 'int' > 1< / span > < span class = 'rparen' > )< / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > unless< / span > < span class = 'id identifier rubyid_indexes' > indexes< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_include?' > include?< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_s' > s< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_indexes' > indexes< / span > < span class = 'op' > < < < / span > < span class = 'id identifier rubyid_s' > s< / span >
< span class = 'id identifier rubyid_r' > r< / span > < span class = 'op' > +=< / span > < span class = 'int' > 1< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_random_subset' > random_subset< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_indexes' > indexes< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_map' > map< / span > < span class = 'lbrace' > {< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_x' > x< / span > < span class = 'op' > |< / span > < span class = 'id identifier rubyid_input' > input< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_x' > x< / span > < span class = 'rbracket' > ]< / span > < span class = 'rbrace' > }< / span >
< span class = 'id identifier rubyid_subdivised_groups' > subdivised_groups< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_random_subset' > random_subset< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_each_slice' > each_slice< / span > < span class = 'lparen' > (< / span > < span class = 'int' > 100< / span > < span class = 'rparen' > )< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_to_a' > to_a< / span >
< span class = 'id identifier rubyid_sleeping_time' > sleeping_time< / span > < span class = 'op' > =< / span > < span class = 'int' > 120< / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > =< / span > < span class = 'int' > 0< / span >
< span class = 'kw' > while< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > < < / span > < span class = 'id identifier rubyid_subdivised_groups' > subdivised_groups< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_length' > length< / span >
< span class = 'id identifier rubyid_k' > k< / span > < span class = 'op' > =< / span > < span class = 'int' > 0< / span >
< span class = 'kw' > for< / span > < span class = 'id identifier rubyid_k' > k< / span > < span class = 'kw' > in< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > ..< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > +< / span > < span class = 'int' > 5< / span > < span class = 'rparen' > )< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_title' > title< / span > < span class = 'op' > =< / span > < span class = 'const' > File< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_basename' > basename< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_absolute_path' > absolute_path< / span > < span class = 'rparen' > )< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_split' > split< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > .< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'lbracket' > [< / span > < span class = 'int' > 0< / span > < span class = 'rbracket' > ]< / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > _yannick< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'op' > +< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > _part_< / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_k' > k< / span > < span class = 'op' > +< / span > < span class = 'int' > 1< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > +< / span > < span class = 'int' > 1< / span >
< span class = 'kw' > begin< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > submitting < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_title' > title< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_q' > q< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_submit_query' > submit_query< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_title' > title< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_subdivised_groups' > subdivised_groups< / span > < span class = 'lbracket' > [< / span > < span class = 'id identifier rubyid_k' > k< / span > < span class = 'rbracket' > ]< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_join' > join< / span > < span class = 'lparen' > (< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > \n< / span > < span class = 'tstring_end' > " < / span > < / span > < span class = 'rparen' > )< / span > < span class = 'comma' > ,< / span > < span class = 'id identifier rubyid_type' > type< / span > < span class = 'rparen' > )< / span >
< span class = 'kw' > rescue< / span > < span class = 'const' > Exception< / span > < span class = 'op' > => < / span > < span class = 'id identifier rubyid_e' > e< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_message' > message< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'id identifier rubyid_e' > e< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_backtrace' > backtrace< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_inspect' > inspect< / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span >
< span class = 'id identifier rubyid_i' > i< / span > < span class = 'op' > =< / span > < span class = 'id identifier rubyid_k' > k< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > Going to sleep at < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > Time< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_now' > now< / span > < span class = 'op' > -< / span > < span class = 'ivar' > @start_time< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > for < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'id identifier rubyid_sleeping_time' > sleeping_time< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_content' > s.< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'id identifier rubyid_sleep' > sleep< / span > < span class = 'lparen' > (< / span > < span class = 'id identifier rubyid_sleeping_time' > sleeping_time< / span > < span class = 'rparen' > )< / span >
< span class = 'id identifier rubyid_puts' > puts< / span > < span class = 'tstring' > < span class = 'tstring_beg' > " < / span > < span class = 'tstring_content' > Waking up at < / span > < span class = 'embexpr_beg' > #{< / span > < span class = 'const' > Time< / span > < span class = 'period' > .< / span > < span class = 'id identifier rubyid_now' > now< / span > < span class = 'op' > -< / span > < span class = 'ivar' > @start_time< / span > < span class = 'embexpr_end' > }< / span > < span class = 'tstring_end' > " < / span > < / span >
< span class = 'kw' > end< / span >
< span class = 'kw' > end< / span > < / pre >
< / td >
< / tr >
< / table >
< / div >
< / div >
< / div >
< div id = "footer" >
2016-03-10 22:54:39 +00:00
Generated on Thu Mar 10 15:54:06 2016 by
2016-03-10 02:26:59 +00:00
< a href = "http://yardoc.org" title = "Yay! A Ruby Documentation Tool" target = "_parent" > yard< / a >
0.8.7.6 (ruby-2.3.0).
< / div >
< / body >
< / html >
