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Revision 5737

Added by Aaron Marcuse-Kubitza about 12 years ago

inputs/.TNRS/tnrs/: Added Time_submitted column at beginning and populate it in tnrs_db with the time the batch TNRS request was submitted

View differences:

inputs/.TNRS/tnrs/header.csv
1 
Name_number,Name_submitted,Overall_score,Name_matched,Name_matched_rank,Name_score,Name_matched_author,Name_matched_url,Author_matched,Author_score,Family_matched,Family_score,Name_matched_accepted_family,Genus_matched,Genus_score,Specific_epithet_matched,Specific_epithet_score,Infraspecific_rank,Infraspecific_epithet_matched,Infraspecific_epithet_score,Infraspecific_rank_2,Infraspecific_epithet_2_matched,Infraspecific_epithet_2_score,Annotations,Unmatched_terms,Taxonomic_status,Accepted_name,Accepted_name_author,Accepted_name_rank,Accepted_name_url,Accepted_name_species,Accepted_name_family,Selected,Source,Warnings,Accepted_name_lsid
1 
Time_submitted,Name_number,Name_submitted,Overall_score,Name_matched,Name_matched_rank,Name_score,Name_matched_author,Name_matched_url,Author_matched,Author_score,Family_matched,Family_score,Name_matched_accepted_family,Genus_matched,Genus_score,Specific_epithet_matched,Specific_epithet_score,Infraspecific_rank,Infraspecific_epithet_matched,Infraspecific_epithet_score,Infraspecific_rank_2,Infraspecific_epithet_2_matched,Infraspecific_epithet_2_score,Annotations,Unmatched_terms,Taxonomic_status,Accepted_name,Accepted_name_author,Accepted_name_rank,Accepted_name_url,Accepted_name_species,Accepted_name_family,Selected,Source,Warnings,Accepted_name_lsid
inputs/.TNRS/schema.sql
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CREATE TABLE tnrs
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(
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  "Time_submitted" timestamp with time zone,
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  "Name_number" text,
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  "Name_submitted" text NOT NULL,
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  "Overall_score" text,
bin/tnrs_db
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sys.path.append(os.path.dirname(__file__)+"/../lib")
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import csvs


  		




  
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import dates


  		




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import opts


  		




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import profiling


  		




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import sql


  		




  ......




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tnrs_input = sql_gen.Table('tnrs_input_name')


  		




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tnrs_data = sql_gen.Table('tnrs')


  		




  
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time_col_name = 'Time_submitted'


  		




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def main():


  		




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    # Input


  		




  ......




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        # Run TNRS


  		




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        log('Making TNRS request')


  		




  
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        now_str = str(dates.now())


  		




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        tnrs_profiler.start()


  		




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        try:


  		




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            try: stream = tnrs.repeated_tnrs_request(names)


  		




  ......




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        except tnrs.InvalidResponse: pass # skip set in case it caused error


  		




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        else:


  		




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            log('Storing TNRS response data')


  		




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            sql_io.append_csv(db, tnrs_data, *csvs.reader_and_header(stream))


  		




  
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            reader, header = csvs.reader_and_header(stream)


  		




  
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            header.insert(0, time_col_name)


  		




  
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            reader = csvs.ColInsertFilter(reader, lambda row, row_num: now_str)


  		




  
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            sql_io.append_csv(db, tnrs_data, reader, header)


  		




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main()


  		












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