finished create_pmid_filter

.gitignore

@@ -0,0 +1 @@
+.idea/

pmid_filter.py

@@ -0,0 +1,45 @@
+from util.db_util import *
+
+
+class DerivedGraphSemMed:
+    def __init__(self):
+        self.handles = PmidKnowledgeHandles()
+
+    def create_pmid_filter(self, pubmed, semmed, tbl):
+        pubmed_source_str = f'pubmed.{pubmed}'
+        semmed_source_str = f'semmed.{semmed}'
+        derived_tbl_str = f'derived.{tbl}'
+        pmid = 'pmid'
+        create_str = '''(PMID VARCHAR(12), PUBTYPE VARCHAR(12), PREDICATION_ID UNSIGNED INT NOT NULL, SENTENCE_ID UNSIGNED INT NOT NULL,
+        PREDICATE VARCHAR(50), SUBJECT_CUI VARCHAR(255), SUBJECT_NAME VARCHAR(999), SUBJECT_SEMTYPE VARCHAR(50), 
+        SUBJECT_NOVELTY TINYINT UNSIGNED, OBJECT_CUI VARCHAR(255), OBJECT_NAME VARCHAR(999), OBJECT_SEMTYPE VARCHAR(50), 
+        OBJECT_NOVELTY TINYINT UNSIGNED'''
+        exec_str = f'''CREATE TABLE 
+                            {derived_tbl_str}{create_str} 
+                        FROM 
+                            {pubmed_source_str}
+                        INNER JOIN
+                            {semmed_source_str}
+                        ON
+                            {pubmed_source_str}.{pmid} = {semmed_source_str}.{pmid}'''
+        self.handles.pubmed.cursor.execute(exec_str)
+        self.handles.pubmed.connection.commit()
+
+
+if __name__ == '__main__':
+    usr = 'greenes2018'
+    pw = getpass()
+    pubmed_db = 'pubmed'
+    pubmed_host = 'db01.healthcreek.org'
+    semmed_db = 'semmed'
+    semmed_host = 'db01.healthcreek.org'
+    der_db = 'derived'
+    der_host = 'db01.healthcreek.org'
+
+    dg_sem = DerivedGraphSemMed()
+    dg_sem.handles.pubmed = DatabaseHandle(usr, pw, pubmed_db, pubmed_host)
+    dg_sem.handles.semmed = DatabaseHandle(usr, pw, semmed_db, semmed_host)
+    dg_sem.handles.derived = DatabaseHandle(usr, pw, der_db, der_host)
+
+    dg_sem.create_pmid_filter('pmid_filter', 'PREDICATION', 'PMID_FILTER')
+

util/db_util.py

@@ -1,5 +1,7 @@
 import MySQLdb as sql
 import MySQLdb.connections as conns
+from getpass import getpass
+from dataclasses import dataclass
 
 from neo4j import GraphDatabase
 
@@ -20,6 +22,13 @@ def __init__(self, user, password, db, host):
         self.db = db
 
 
+@dataclass
+class PmidKnowledgeHandles:
+    pubmed: DatabaseHandle
+    semmed: DatabaseHandle
+    derived: DatabaseHandle
+
+
 class NeoHandle:
     driver = None
     session = None