Example #1
0
    def get_pubmed_data(self, max=None, pmids=None):
        if pmids:
            query_pmids = pmids
        else:
            all_pmids = datasources.ochsner.get_all_pmids()
            if not max:
                max = len(all_pmids)
            query_pmids = all_pmids[0:max]

        pubmed_request = """pubmed.pubmed_id, 
                               ochsner.found_geo_data_submission,                               
                               ochsner.found_arrayexpress_data_submission,                               
                               ochsner.found_smd_data_submission,                                                                                             
                               ochsner.found_any_data_submission,                                                                                                                            
                               ochsner.list_data_ids,
                               pubmed.is_humans, 
                               pubmed.is_animals, 
                               pubmed.is_mice,                                
                               pubmed.is_fungi,
                               pubmed.is_bacteria, 
                               pubmed.is_plants, 
                               pubmed.is_viruses,                                
                               pubmed.is_cultured_cells,                                                               
                               pubmed.is_cancer,
                               pubmed.date_published, 
                               pubmed.authors, 
                               pubmed.journal,
                               pubmed.number_times_cited_in_pmc,
                               isi.impact_factor                              
                               """

        data = dataset.collect_data(query_pmids, pubmed_request)
        csv_data = dataset.csv_format(data)

        if False:
            FILENAME = "../../results/aim2b_part2_pubmed.txt"
            writer = open(FILENAME, "w")
            for row in csv_data:
                writer.write("\t".join([str(col) for col in row]))
                writer.write("\r\n")
            writer.close()
        assert_equals(len(csv_data), 1 + len(query_pmids))
        return (csv_data)
Example #2
0
    def get_pubmed_data(self, max=None, pmids=None):
        if pmids:
            query_pmids = pmids
        else:
            all_pmids = datasources.ochsner.get_all_pmids()
            if not max:
                max = len(all_pmids)            
            query_pmids = all_pmids[0:max]

        pubmed_request = """pubmed.pubmed_id, 
                               ochsner.found_geo_data_submission,                               
                               ochsner.found_arrayexpress_data_submission,                               
                               ochsner.found_smd_data_submission,                                                                                             
                               ochsner.found_any_data_submission,                                                                                                                            
                               ochsner.list_data_ids,
                               pubmed.is_humans, 
                               pubmed.is_animals, 
                               pubmed.is_mice,                                
                               pubmed.is_fungi,
                               pubmed.is_bacteria, 
                               pubmed.is_plants, 
                               pubmed.is_viruses,                                
                               pubmed.is_cultured_cells,                                                               
                               pubmed.is_cancer,
                               pubmed.date_published, 
                               pubmed.authors, 
                               pubmed.journal,
                               pubmed.number_times_cited_in_pmc,
                               isi.impact_factor                              
                               """

        data = dataset.collect_data(query_pmids, pubmed_request)
        csv_data = dataset.csv_format(data)

        if False:
            FILENAME = "../../results/aim2b_part2_pubmed.txt"
            writer = open(FILENAME, "w")
            for row in csv_data:
                writer.write("\t".join([str(col) for col in row]))
                writer.write("\r\n")
            writer.close()
        assert_equals(len(csv_data), 1+len(query_pmids))
        return(csv_data)
Example #3
0
    def write_to_file(self, data, filename):
        file = open(filename, "w")
        csv_data = dataset.csv_format(data)
        for row in csv_data:
            joined_row_contents = []
            for col in row:
                if col is None:
                    col = u""
                if col == True:
                    col = u"1"
                if col == False:
                    col = u"0"

                try:
                    file.write(str(col))
                except UnicodeEncodeError:
                    new_string = utils.unicode.clean_up_strange_unicode(col)
                    file.write(new_string)

                file.write(u"\t")

            file.write(u"\r\n")
        file.close()
        return (csv_data)
Example #4
0
    def write_to_file(self, data, filename):
        file = open(filename, "w")
        csv_data = dataset.csv_format(data)
        for row in csv_data:
            joined_row_contents = []
            for col in row:
                if col is None:
                    col = u""
                if col==True:
                    col = u"1"
                if col==False:
                    col = u"0"

                try:
                    file.write(str(col))
                except UnicodeEncodeError:
                    new_string = utils.unicode.clean_up_strange_unicode(col)
                    file.write(new_string)                    

                file.write(u"\t")

            file.write(u"\r\n")        
        file.close()
        return(csv_data)
Example #5
0
 def test_csv_format(self):
     input = test_data_has_geo_data_submission
     response = dataset.csv_format(input)
     assert_equals(response, test_data_csv_format)
Example #6
0
 def test_csv_format(self):
     input = test_data_has_geo_data_submission
     response = dataset.csv_format(input)
     assert_equals(response, test_data_csv_format)