def appendDatabase(organism):
conn = mysql.connector.connect (host = "127.0.0.1",
user = "******",
password = "******",
db= "bi2_pg5")
cursor = conn.cursor()
cursor_id = conn.cursor()
cursor_com = conn.cursor()
cursor_id.execute("SELECT organism_id FROM organism "
"ORDER BY organism_id DESC "
"LIMIT 1")
(organism_id,) = cursor_id.fetchone()
add_organism = "INSERT INTO organism "\
"(organism_id, name) "\
"VALUES ("+str(organism_id+1)+", '"+organism+"')"
cursor.execute(add_organism)
cursor_com.execute("SELECT compound_id, name FROM compound "
"WHERE organism_id=0;")
compoundList = cursor_com.fetchall()
for i in range(len(compoundList)):
cursor_org = conn.cursor()
cursor_org_id = conn.cursor()
cursor_org_id.execute("SELECT compound_id FROM compound "
"ORDER BY organism_id DESC "
"LIMIT 1")
(compound_id,) = cursor_org_id.fetchone()
add_organism = "INSERT INTO compound "\
"(compound_id, name, organism_id, query) "\
"VALUES ("+str(compound_id+1)+", '"+str(compoundList[i][1])+"', "+str(organism_id+1)+", '"+str(createQuery(organism, str(compoundList[i][1])))+"')"
cursor_org.execute(add_organism)
cursor_org_id.close()
cursor_org.close()
cursor.close()
cursor_id.close()
cursor_com.close()
conn.commit()
conn.close()
return "Succesfully appended: "+organism
def addCompound(compound):
conn = mysql.connector.connect (host = "127.0.0.1",
user = "******",
password = "******",
db= "bi2_pg5")
cursor_org = conn.cursor()
cursor_org.execute("SELECT organism_id, name FROM organism")
organismList = cursor_org.fetchall()
for i in range(len(organismList)):
cursor_compound_id = conn.cursor()
cursor = conn.cursor()
cursor_compound_id.execute("SELECT compound_id FROM compound "
"ORDER BY organism_id DESC "
"LIMIT 1")
(compound_id,) = cursor_compound_id.fetchone()
cursor.execute("INSERT INTO compound "
"(compound_id, name, organism_id, query) "
"VALUES("+str(compound_id+i+1)+", '"+str(compound)+"', "+str(organismList[i][0])+", '"+str(createQuery(str(organismList[i][1]), str(compound)))+"')")
cursor_compound_id.close()
cursor.close()
cursor_org.close()
conn.commit()
conn.close()
return "Succesfully appended: "+compound
cursor_synonyms = conn.cursor()
cursor_synonyms.execute("SELECT name FROM synonyms "
"WHERE organism_id = "+str(organismList[i][0])+"")
synonymList = cursor_synonyms.fetchall()
if synonymList:
synonyms = " OR " + ' OR '.join(elem[0] for elem in synonymList)
cursor_compound_id.execute("SELECT compound_id FROM compound "
"ORDER BY organism_id DESC "
"LIMIT 1")
(compound_id,) = cursor_compound_id.fetchone()
cursor.execute("INSERT INTO compound "
"(compound_id, name, organism_id, query) "
"VALUES("+str(compound_id+i+1)+", '"+str(compound)+"', "+str(organismList[i][0])+", '("+str(createQuery(str(organismList[i][1]+synonyms)+")", str(compound)))+"')")
cursor_compound_id.close()
cursor_synonyms.close()
cursor.close()
cursor_org.close()
conn.commit()
conn.close()
returnString += compound + "\n"
def appendDatabase(organism, synonymList):
synonyms = ""
conn = mysql.connector.connect(host="127.0.0.1",
user="******",
password="******",
db="bi2_pg5")
cursor = conn.cursor()
cursor_id = conn.cursor()
cursor_com = conn.cursor()
cursor_syn_id = conn.cursor()
cursor_id.execute("SELECT organism_id FROM organism "
"ORDER BY organism_id DESC "
"LIMIT 1")
(organism_id, ) = cursor_id.fetchone()
add_organism = "INSERT INTO organism "\
"(organism_id, name) "\
"VALUES ("+str(organism_id+1)+", '"+organism+"')"
cursor.execute(add_organism)
if synonymList:
synonyms += " OR "
cursor_syn_id.execute("SELECT synonym_id FROM synonyms "
"ORDER BY synonym_id DESC "
"LIMIT 1")
(synonym_id, ) = cursor_syn_id.fetchone()
for i in range(len(synonymList)):
if i == len(synonymList) - 1:
synonyms += synonymList[i]
else:
synonyms += synonymList[i] + " OR "
cursor_syn = conn.cursor()
cursor_syn.execute("INSERT INTO synonyms "
"(synonym_id, name, organism_id) "
"VALUES (" + str(synonym_id + 1 + i) + ", '" +
str(synonymList[i]) + "', " +
str(organism_id + 1) + ")")
cursor_syn.close()
cursor_com.execute("SELECT compound_id, name FROM compound "
"WHERE organism_id=0;")
compoundList = cursor_com.fetchall()
for i in range(len(compoundList)):
cursor_org = conn.cursor()
cursor_org_id = conn.cursor()
cursor_org_id.execute("SELECT compound_id FROM compound "
"ORDER BY organism_id DESC "
"LIMIT 1")
(compound_id, ) = cursor_org_id.fetchone()
add_organism = "INSERT INTO compound "\
"(compound_id, name, organism_id, query) "\
"VALUES ("+str(compound_id+1)+", '"+str(compoundList[i][1])+"', "+str(organism_id+1)+", '"+str(createQuery("("+organism+synonyms+")", str(compoundList[i][1])))+"')"
cursor_org.execute(add_organism)
cursor_org_id.close()
cursor_org.close()
cursor.close()
cursor_id.close()
cursor_com.close()
cursor_syn_id.close()
conn.commit()
conn.close()
return "Succesfully appended: " + organism
