diff options
| -rw-r--r-- | wqflask/maintenance/dataset/load_phenotypes.py | 39 | ||||
| -rw-r--r-- | wqflask/maintenance/dataset/utilities.py | 24 |
2 files changed, 61 insertions, 2 deletions
diff --git a/wqflask/maintenance/dataset/load_phenotypes.py b/wqflask/maintenance/dataset/load_phenotypes.py index e5a85b32..6e7f049b 100644 --- a/wqflask/maintenance/dataset/load_phenotypes.py +++ b/wqflask/maintenance/dataset/load_phenotypes.py @@ -9,8 +9,9 @@ def main(argv): print "config:" for item in config.items('config'): print "\t%s" % (str(item)) - # + # var inbredsetid = config.get('config', 'inbredsetid') + cursor = utilities.get_cursor() print "inbredsetid: %s" % inbredsetid # datafile datafile = open(config.get('config', 'datafile'), 'r') @@ -22,7 +23,41 @@ def main(argv): phenotypemeta = csv.reader(metafile, delimiter='\t', quotechar='"') phenotypemeta_head = phenotypemeta.next() print "phenotypemeta head:\n\t%s" % phenotypemeta_head - # + # load + for metarow in phenotypemeta: + # + datarow_value = phenotypedata.next() + datarow_se = phenotypedata.next() + datarow_n = phenotypedata.next() + # Phenotype + sql = """ + INSERT INTO Phenotype + SET + Phenotype.`Pre_publication_description`=%s, + Phenotype.`Post_publication_description`=%s, + Phenotype.`Original_description`=%s, + Phenotype.`Pre_publication_abbreviation`=%s, + Phenotype.`Post_publication_abbreviation`=%s, + Phenotype.`Lab_code`=%s, + Phenotype.`Submitter`=%s, + Phenotype.`Owner`=%s, + Phenotype.`Authorized_Users`=%s, + Phenotype.`Units`=%s + """ + cursor.execute(sql, ( + metarow[1], + metarow[2], + metarow[3], + metarow[4], + metarow[5], + metarow[6], + metarow[7], + metarow[8], + metarow[9], + metarow[18] + )) + re = cursor.rowcount + print "INSERT INTO Phenotype: %d record" % re if __name__ == "__main__": print "command line arguments:\n\t%s" % sys.argv diff --git a/wqflask/maintenance/dataset/utilities.py b/wqflask/maintenance/dataset/utilities.py index 63a3e84d..e542cb43 100644 --- a/wqflask/maintenance/dataset/utilities.py +++ b/wqflask/maintenance/dataset/utilities.py @@ -41,6 +41,30 @@ def overlap(dic1, dic2): values2.append(value2) return keys, values1, values2 +def to_db_string_null(s): + if s: + s = s.strip() + if len(s) == 0: + return None + elif s == 'x': + return None + else: + return s + else: + return None + +def to_db_string_empty(s): + if s: + s = s.strip() + if len(s) == 0: + return '' + elif s == 'x': + return '' + else: + return s + else: + return '' + def get_config(configfile): config = ConfigParser.ConfigParser() config.read(configfile) |