diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/maintenance/dataset/load_phenotypes.py | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/wqflask/maintenance/dataset/load_phenotypes.py b/wqflask/maintenance/dataset/load_phenotypes.py index c47453b7..98c22229 100644 --- a/wqflask/maintenance/dataset/load_phenotypes.py +++ b/wqflask/maintenance/dataset/load_phenotypes.py @@ -59,6 +59,48 @@ def main(argv): rowcount = cursor.rowcount phenotypeid = con.insert_id() print "INSERT INTO Phenotype: %d record: %d" % (rowcount, phenotypeid) + # Publication + publicationid = None # reset + pubmed_id = utilities.to_db_string_null(metarow[0]) + if pubmed_id: + sql = """ + SELECT Publication.`Id` + FROM Publication + WHERE Publication.`PubMed_ID`=%s + """ + cursor.execute(sql, (pubmed_id)) + re = cursor.fetchone() + if re: + publicationid = re[0] + print "get Publication record: %d" % publicationid + if not publicationid: + sql = """ + INSERT INTO Publication + SET + Publication.`PubMed_ID`=%s, + Publication.`Abstract`=%s, + Publication.`Authors`=%s, + Publication.`Title`=%s, + Publication.`Journal`=%s, + Publication.`Volume`=%s, + Publication.`Pages`=%s, + Publication.`Month`=%s, + Publication.`Year`=%s + """ + cursor.execute(sql, ( + utilities.to_db_string_null(metarow[0]), + utilities.to_db_string_null(metarow[12]), + utilities.to_db_string_null(metarow[10]), + utilities.to_db_string_null(metarow[11]), + utilities.to_db_string_null(metarow[13]), + utilities.to_db_string_null(metarow[14]), + utilities.to_db_string_null(metarow[15]), + utilities.to_db_string_null(metarow[16]), + utilities.to_db_string_null(metarow[17]), + )) + rowcount = cursor.rowcount + publicationid = con.insert_id() + print "INSERT INTO Publication: %d record: %d" % (rowcount, publicationid) if __name__ == "__main__": print "command line arguments:\n\t%s" % sys.argv |