Skip to content

Commit 1e8c2c2

Browse files
author
Richard Boyce
committed
finished full update for prescription drugs - SPLs 09262015
1 parent 4597c0c commit 1e8c2c2

File tree

8 files changed

+23994
-9728
lines changed

8 files changed

+23994
-9728
lines changed

‎linkedSPLs/LinkedSPLs-activeMoiety/README

Lines changed: 3 additions & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -7,17 +7,11 @@ This folder will hold a graph that maps the active moiety components of an SPL t
77
Inputs are original mappings listed as belows:
88

99
(1) PT to UNII
10-
1110
(2) UNII to RxNORM
12-
1311
(3) PT to Drugbank
14-
1512
(4) PT to ChEBI
16-
1713
(5) RxNORM to OMOP
18-
1914
(6) RxNORM to DrOn
20-
2115
(7) RxNORM to NDFRT (EPC)
2216

2317
Outputs is a RDF/XML graph that represents all active moiety with linked resouces.
@@ -27,28 +21,10 @@ Outputs is a RDF/XML graph that represents all active moiety with linked resouce
2721
Procedures to get active moieties RDF graph
2822
################################################################################
2923

30-
<STEP 1>: prepare mappings in folder mappings/
31-
32-
----------------------------------------------
33-
mappings of PT to UNII (FDA)
34-
----------------------------------------------
24+
<1>: query to get omopid mapping and put in mapping folder
3525

36-
FROM "../../LinkedSPLs-update/data/FDA/FDAPreferredSubstanceToUNII.txt"
26+
mappings/active-ingredient-omopid-rxcui.dsv
3727

38-
----------------------------------------------
39-
mappings of UNII to RXCUI (UMLS)
40-
----------------------------------------------
41-
42-
FROM "../../LinkedSPLs-update/data/UMLS/UNIIs-Rxcuis-from-UMLS.txt"
43-
44-
----------------------------------------------
45-
mappings/dron-to-chebi-and-rxnorm.txt
46-
----------------------------------------------
47-
FROM "../../LinkedSPLs-update/mappings/DrOn-to-RxNorm/dron-to-chebi-and-rxnorm.txt"
48-
49-
----------------------------------------------
50-
mappings/active-ingredient-omopid-rxcui-09042015.dsv
51-
----------------------------------------------
5228

5329
query OMOP CDM V5 (GeriOMOP) by SQL query below:
5430
SELECT cpt.CONCEPT_ID as omopid, cpt.CONCEPT_CODE as rxcui FROM
@@ -60,21 +36,6 @@ cpt.CONCEPT_CLASS = 'Ingredient';
6036

6137
right click result table and export to csv ('|' delimited)
6238

63-
----------------------------------------------
64-
mappings/UNIIToChEBI-<DATE>.txt
65-
----------------------------------------------
66-
FROM "../../LinkedSPLs-update/mappings/PT-UNII-ChEBI-mapping/UNIIToChEBI-<DATE>.txt"
67-
68-
----------------------------------------------
69-
mappings/pt_drugbank-<DATE>.txt
70-
----------------------------------------------
71-
FROM "../../LinkedSPLs-update/mappings/ChEBI-DrugBank-bio2rdf-mapping/fda-substance-preferred-name-to-drugbank-<DATE>.txt"
72-
73-
----------------------------------------------
74-
mappings/EPC_extraction_most_recent_<DATE>.txt"
75-
----------------------------------------------
76-
FROM "../../LinkedSPLs-update/mappings/pharmacologic_class_indexing/EPC_extraction_most_recent_<DATE>.txt"
77-
7839

7940
<STEP 2>: run python script to merge those mappings together
8041

@@ -92,7 +53,7 @@ outputs: activeMoietySub-in-rdf.xml
9253

9354

9455
################################################################################
95-
PRE#REQUISITES:
56+
PRE-REQUISITES:
9657
################################################################################
9758

9859
python libraries:

‎linkedSPLs/LinkedSPLs-activeMoiety/mergeToActiveMoiety.py

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -20,12 +20,12 @@
2020
PT_UNII = "../LinkedSPLs-update/data/FDA/FDAPreferredSubstanceToUNII.txt"
2121
UNII_RXCUI = "../LinkedSPLs-update/data/UMLS/UNIIs-Rxcuis-from-UMLS.txt"
2222

23-
PT_CHEBI = "mappings/UNIIToChEBI-06102015.txt"
24-
PT_DRUGBANK = "mappings/fda-substance-preferred-name-to-drugbank-06102015.txt"
23+
PT_CHEBI = "../LinkedSPLs-update/mappings/PT-UNII-ChEBI-mapping/UNIIToChEBI.txt"
24+
PT_DRUGBANK = "../LinkedSPLs-update/mappings/ChEBI-DrugBank-bio2rdf-mapping/fda-substance-preferred-name-to-drugbank.txt"
2525

26-
UNII_NUI_PREFERRED_NAME_ROLE = "mappings/EPC_extraction_most_recent_06102015.txt"
27-
DRON_CHEBI_RXCUI = "mappings/cleaned-dron-chebi-rxcui-ingredient-06222015.txt"
28-
OMOP_RXCUI = "mappings/active-ingredient-omopid-rxcui-09042015.dsv"
26+
UNII_NUI_PREFERRED_NAME_ROLE = "../LinkedSPLs-update/mappings/pharmacologic_class_indexing/EPC_extraction_most_recent.txt"
27+
DRON_CHEBI_RXCUI = "../LinkedSPLs-update/mappings/DrOn-to-RxNorm/cleaned-dron-chebi-rxcui-ingredient.txt"
28+
OMOP_RXCUI = "mappings/active-ingredient-omopid-rxcui.dsv"
2929

3030
## Get UNII - PT - RXCUI
3131
unii_pt_cols = ['unii','pt']

‎linkedSPLs/LinkedSPLs-activeMoiety/mergedActiveMoiety.csv

Lines changed: 23924 additions & 9625 deletions
Large diffs are not rendered by default.

‎linkedSPLs/LinkedSPLs-clinicalDrug/README

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -37,14 +37,20 @@ converted_rxnorm_mappings_<DATE>.txt
3737

3838
Dailymed product label indexing mapping from "linkedSPLs/LinkedSPLs-update/mappings/RxNORM-mapping/converted_rxnorm_mappings_<DATE>"
3939

40-
$ cat converted_rxnorm_mappings_06262015.txt | cut -f1,2 -d\| | sort | uniq > setid_rxcui.txt
40+
$ cd mappings
41+
42+
$ cp ../../LinkedSPLs-update/mappings/RxNORM-mapping/converted_rxnorm_mappings_10132015.txt converted_rxnorm_mappings.txt
43+
44+
$ cat converted_rxnorm_mappings.txt | cut -f1,2 -d\| | sort | uniq > setid_rxcui.txt
4145

4246
----------------------------------------------------------
4347
mappings of FDA preferred term and setId
4448
----------------------------------------------------------
4549

4650
$ mysql -u <username> -p
4751

52+
$ use linkedSPLs;
53+
4854
SELECT setId, fullName FROM linkedSPLs.structuredProductLabelMetadata INTO OUTFILE '/tmp/setid_fullname.txt' FIELDS TERMINATED BY ',' ENCLOSED BY '"' LINES TERMINATED BY '\n';
4955

5056
$ cp /tmp/setid_fullname.txt ../linkedSPLs/LinkedSPLs-clinicalDrug/mappings/

‎linkedSPLs/LinkedSPLs-clinicalDrug/mergeToClinicalDrug.py

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -17,11 +17,12 @@
1717
RXNORM_BASE_URI = "http://purl.bioontology.org/ontology/RXNORM/"
1818

1919
## Define data inputs
20-
DRON_RXCUI = "mappings/cleaned-dron-to-rxcui-drug-06222015.txt"
21-
OMOP_RXCUI = "mappings/imeds_drugids_to_rxcuis.csv"
20+
DRON_RXCUI = "../LinkedSPLs-update/mappings/DrOn-to-RxNorm/cleaned-dron-to-rxcui-drug.txt"
2221
SETID_RXCUI = "mappings/setid_rxcui.txt"
2322
FULLNAME_SETID = "mappings/setid_fullname.txt"
24-
#OMOP_RXCUI = "mappings/clinical-drug-omopid-rxcui-09042015.dsv"
23+
24+
#OMOP_RXCUI = "mappings/imeds_drugids_to_rxcuis.csv"
25+
OMOP_RXCUI = "mappings/clinical-drug-omopid-rxcui-09042015.dsv"
2526

2627

2728

@@ -71,6 +72,6 @@
7172
output_DF = fullname_rxcui_setid_DF.merge(dron_omop_rxcui_DF, on=['rxcui'], how='left')
7273

7374
print output_DF.info()
74-
print output_DF
75+
#print output_DF
7576

7677
output_DF.to_csv('mergedClinicalDrug.tsv', sep='\t', index=False)

‎linkedSPLs/LinkedSPLs-update/build.xml

Lines changed: 33 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -210,7 +210,7 @@
210210
(6) mappings of RxNORM, NUI and NDFRT label
211211
(7) mappings of setId, UNII, NUI and PreferredNameAndRole
212212
213-
takes about 1 hour for update
213+
takes about 3 hour for update
214214
-->
215215

216216
<target name="linkedSPLs-update" depends="check-mapping-sources">
@@ -221,12 +221,13 @@
221221

222222
<!-- <antcall target="load-FDAPreferredSubstanceToUNII" /> -->
223223
<!-- <antcall target="load-FDA_UNII_to_ChEBI" /> -->
224-
<!-- <antcall target="load-FDAPreferredSubstanceToRxNORM" /> -->
225224
<!-- <antcall target="load-FDA_SUBSTANCE_TO_DRUGBANK_BIO2RDF" /> -->
225+
<!-- <antcall target="load-ChEBI_DRUGBANK_BIO2RDF" /> -->
226+
227+
<!-- <antcall target="load-FDAPreferredSubstanceToRxNORM" /> -->
226228
<!-- <antcall target="load-SPLSetIDToRxNORM" /> -->
227229
<!-- <antcall target="load-RXNORM_NDFRT_INGRED_Table" /> -->
228230
<!-- <antcall target="load-FDA_EPC_Table" /> -->
229-
<!-- <antcall target="load-ChEBI_DRUGBANK_BIO2RDF" /> -->
230231

231232
<!-- <antcall target="load-FDAPharmgxTable" /> -->
232233
<!-- <antcall target="load-FDAPharmgxTableToOntologyMap" /> -->
@@ -290,7 +291,7 @@
290291

291292
<target name="load-FDA_UNII_to_ChEBI">
292293

293-
<delete file="${PT-UNII-ChEBI-mapping}/UNIIToChEBI-${TODAY_US}.txt"/>
294+
<delete file="${PT-UNII-ChEBI-mapping}/UNIIToChEBI.txt"/>
294295

295296
<delete dir="${PT-UNII-ChEBI-mapping}/ChEBIJavaClient/bin"/>
296297
<mkdir dir="${PT-UNII-ChEBI-mapping}/ChEBIJavaClient/bin" />
@@ -316,7 +317,7 @@
316317
</manifest>
317318
</jar>
318319

319-
<echo>[INFO] : It takes about 4 hour ... </echo>
320+
<echo>[INFO] : It takes about 4 hours ... </echo>
320321

321322
<java classname="chebi.service.GetChEBIbyNames" fork="true" >
322323
<classpath>
@@ -326,13 +327,13 @@
326327
</java>
327328

328329
<!-- old apporach that query bioportal -->
329-
<!-- <exec executable="python" failonerror="true"> -->
330-
<!-- <arg line="${PT-UNII-ChEBI-mapping}/getChebiMappingsFromJSON.py data/FDA/FDAPreferredSubstanceToUNII.txt" /> -->
331-
<!-- <redirector append="true"> -->
332-
<!-- <outputmapper type="merge" to="${PT-UNII-ChEBI-mapping}/UNIIToChEBI-${TODAY_US}.txt"/> -->
333-
<!-- <errormapper type="merge" to="${ERROR_LOG}"/> -->
334-
<!-- </redirector> -->
335-
<!-- </exec> -->
330+
<exec executable="python" failonerror="true">
331+
<arg line="${PT-UNII-ChEBI-mapping}/getChebiMappingsFromJSON.py data/FDA/FDAPreferredSubstanceToUNII.txt" />
332+
<redirector append="true">
333+
<outputmapper type="merge" to="${PT-UNII-ChEBI-mapping}/UNIIToChEBI.txt"/>
334+
<errormapper type="merge" to="${ERROR_LOG}"/>
335+
</redirector>
336+
</exec>
336337

337338
<antcall target="set.timestamp">
338339
<param name="message" value="mappings of FDA preferred term and ChEBI is created at ${PT-UNII-ChEBI-mapping}/UNIIToChEBI.txt" />
@@ -368,7 +369,7 @@
368369

369370
<target name="load-FDA_SUBSTANCE_TO_DRUGBANK_BIO2RDF" >
370371

371-
<delete file="${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/Name_Syns_UNII_DbId_0_${TODAY_US}.txt"/>
372+
<delete file="${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/Name_Syns_UNII_DbId_0.txt"/>
372373

373374
<antcall target="set.timestamp">
374375
<param name="message" value="execute script to parse ${DRUGBANK_XML}, ${FDA_UNII_NAMES} and ${FDA_UNII_RECORDS} " />
@@ -379,26 +380,26 @@
379380
<exec executable="python" failonerror="true">
380381
<arg line="${ChEBI-DrugBank-bio2rdf-mapping}/scripts/parseDBIdBySynsInchiName.py 0 ${DRUGBANK_XML} ${FDA_UNII_NAMES} ${FDA_UNII_RECORDS}"/>
381382
<redirector append="true">
382-
<outputmapper type="merge" to="${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/Name_Syns_UNII_DbId_0_${TODAY_US}.txt"/>
383+
<outputmapper type="merge" to="${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/Name_Syns_UNII_DbId_0.txt"/>
383384
<errormapper type="merge" to="${ERROR_LOG}"/>
384385
</redirector>
385386
</exec>
386387

387-
<delete file="${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/INCHI-OR-Syns-OR-Name-${TODAY_US}.txt"/>
388+
<delete file="${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/INCHI-OR-Syns-OR-Name.txt"/>
388389

389390
<exec executable="bash">
390391
<arg value="-c" />
391-
<arg value ='cat ${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/Name_Syns_UNII_DbId_0_${TODAY_US}.txt | cut -f1,3,4,5 | sort | uniq > ${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/INCHI-OR-Syns-OR-Name-${TODAY_US}.txt' />
392+
<arg value ='cat ${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/Name_Syns_UNII_DbId_0.txt | cut -f1,3,4,5 | sort | uniq > ${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/INCHI-OR-Syns-OR-Name.txt' />
392393
</exec>
393394

394395
<antcall target="set.timestamp">
395-
<param name="message" value="mappings of perferred term, UNII and drugbank URI is created at ${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/INCHI-OR-Syns-OR-Name-${TODAY_US}.txt" />
396+
<param name="message" value="mappings of perferred term, UNII and drugbank URI is created at ${ChEBI-DrugBank-bio2rdf-mapping}/UNII-data/INCHI-OR-Syns-OR-Name.txt" />
396397
</antcall>
397398

398399
<delete file="${ChEBI-DrugBank-bio2rdf-mapping}/fda-substance-preferred-name-to-drugbank.txt"/>
399400

400401
<exec executable="python" dir="${ChEBI-DrugBank-bio2rdf-mapping}/scripts" output="${ChEBI-DrugBank-bio2rdf-mapping}/fda-substance-preferred-name-to-drugbank.txt">
401-
<arg line="addBio2rdf_UNII_to_DrugBank.py ../UNII-data/INCHI-OR-Syns-OR-Name-${TODAY_US}.txt"/>
402+
<arg line="addBio2rdf_UNII_to_DrugBank.py ../UNII-data/INCHI-OR-Syns-OR-Name.txt"/>
402403
</exec>
403404

404405
<antcall target="set.timestamp">
@@ -520,15 +521,15 @@
520521

521522
<target name="load-SPLSetIDToRxNORM" >
522523

523-
<delete file="${RxNORM-mapping}/converted_rxnorm_mappings_${TODAY_US}.txt"/>
524+
<delete file="${RxNORM-mapping}/converted_rxnorm_mappings.txt"/>
524525

525526
<exec executable="bash">
526527
<arg value="-c" />
527-
<arg value ='tail -n +2 ${RXNORM_SETID} | cut -f 1,3,4 -d "|" | sort > ${RxNORM-mapping}/converted_rxnorm_mappings_${TODAY_US}.txt' />
528+
<arg value ='tail -n +2 ${RXNORM_SETID} | cut -f 1,3,4 -d "|" | sort > ${RxNORM-mapping}/converted_rxnorm_mappings.txt' />
528529
</exec>
529530

530531
<antcall target="set.timestamp">
531-
<param name="message" value="mappings of setid, RxCui and RxClinicalDrug is created at ${RxNORM-mapping}/converted_rxnorm_mappings_${TODAY_US}.txt" />
532+
<param name="message" value="mappings of setid, RxCui and RxClinicalDrug is created at ${RxNORM-mapping}/converted_rxnorm_mappings.txt" />
532533
</antcall>
533534

534535
<sql
@@ -541,7 +542,7 @@
541542
</classpath>
542543
<transaction>
543544
truncate SPLSetIDToRxNORM;
544-
LOAD DATA LOCAL INFILE '${RxNORM-mapping}/converted_rxnorm_mappings_${TODAY_US}.txt' INTO TABLE `SPLSetIDToRxNORM` FIELDS TERMINATED BY '|' LINES TERMINATED BY '\n' (setId, RxCUI, RxClinicalDrug);
545+
LOAD DATA LOCAL INFILE '${RxNORM-mapping}/converted_rxnorm_mappings.txt' INTO TABLE `SPLSetIDToRxNORM` FIELDS TERMINATED BY '|' LINES TERMINATED BY '\n' (setId, RxCUI, RxClinicalDrug);
545546
</transaction>
546547
</sql>
547548

@@ -559,29 +560,29 @@
559560

560561
<target name="load-RXNORM_NDFRT_INGRED_Table" >
561562

562-
<delete file="${NDFRT-to-RxNorm}/rxnorm-to-ndfrt-chemical-ingredient-mapping-${TODAY_US}.txt"/>
563+
<delete file="${NDFRT-to-RxNorm}/rxnorm-to-ndfrt-chemical-ingredient-mapping.txt"/>
563564

564565
<exec executable="bash">
565566
<arg value="-c" />
566-
<arg value ='cat ${RXNCONSO_RRF} | grep "Chemical/Ingredient" | cut -f 1,14,15 -d "|" > ${NDFRT-to-RxNorm}/rxnorm-to-ndfrt-chemical-ingredient-mapping-${TODAY_US}.txt' />
567+
<arg value ='cat ${RXNCONSO_RRF} | grep "Chemical/Ingredient" | cut -f 1,14,15 -d "|" > ${NDFRT-to-RxNorm}/rxnorm-to-ndfrt-chemical-ingredient-mapping.txt' />
567568
</exec>
568569

569570
<antcall target="set.timestamp">
570-
<param name="message" value="mappings of RxNORM, NUI and NDFRT label is created at ${NDFRT-to-RxNorm}/rxnorm-to-ndfrt-chemical-ingredient-mapping-${TODAY_US}.txt" />
571+
<param name="message" value="mappings of RxNORM, NUI and NDFRT label is created at ${NDFRT-to-RxNorm}/rxnorm-to-ndfrt-chemical-ingredient-mapping.txt" />
571572
</antcall>
572573

573-
<delete file="${NDFRT-to-RxNorm}/converted-rxnorm-to-ndfrt-chemical-ingredient-${TODAY_US}.txt"/>
574+
<delete file="${NDFRT-to-RxNorm}/converted-rxnorm-to-ndfrt-chemical-ingredient.txt"/>
574575

575576
<exec executable="python" failonerror="true">
576-
<arg line="${NDFRT-to-RxNorm}/convertNDFRTandRXNORM_UUIDsToPurls.py ${NDFRT-to-RxNorm}/rxnorm-to-ndfrt-chemical-ingredient-mapping-${TODAY_US}.txt" />
577+
<arg line="${NDFRT-to-RxNorm}/convertNDFRTandRXNORM_UUIDsToPurls.py ${NDFRT-to-RxNorm}/rxnorm-to-ndfrt-chemical-ingredient-mapping.txt" />
577578
<redirector append="true">
578-
<outputmapper type="merge" to="${NDFRT-to-RxNorm}/converted-rxnorm-to-ndfrt-chemical-ingredient-${TODAY_US}.txt"/>
579+
<outputmapper type="merge" to="${NDFRT-to-RxNorm}/converted-rxnorm-to-ndfrt-chemical-ingredient.txt"/>
579580
<errormapper type="merge" to="${ERROR_LOG}"/>
580581
</redirector>
581582
</exec>
582583

583584
<antcall target="set.timestamp">
584-
<param name="message" value="post-processed mappings of RxNORM, NUI and NDFRT label is created at ${NDFRT-to-RxNorm}/converted-rxnorm-to-ndfrt-chemical-ingredient-${TODAY_US}.txt" />
585+
<param name="message" value="post-processed mappings of RxNORM, NUI and NDFRT label is created at ${NDFRT-to-RxNorm}/converted-rxnorm-to-ndfrt-chemical-ingredient.txt" />
585586
</antcall>
586587

587588
<sql
@@ -594,7 +595,7 @@
594595
</classpath>
595596
<transaction>
596597
truncate RXNORM_NDFRT_INGRED_Table;
597-
LOAD DATA LOCAL INFILE "${NDFRT-to-RxNorm}/converted-rxnorm-to-ndfrt-chemical-ingredient-${TODAY_US}.txt" INTO TABLE RXNORM_NDFRT_INGRED_Table(RXNORM, NUI, NDFRT_LABEL);
598+
LOAD DATA LOCAL INFILE "${NDFRT-to-RxNorm}/converted-rxnorm-to-ndfrt-chemical-ingredient.txt" INTO TABLE RXNORM_NDFRT_INGRED_Table(RXNORM, NUI, NDFRT_LABEL);
598599
</transaction>
599600
</sql>
600601

@@ -612,10 +613,10 @@
612613

613614
<target name="load-FDA_EPC_Table" >
614615

615-
<delete file="${pharmacologic_class_indexing}/EPC_extraction_most_recent_${TODAY_US}.txt"/>
616+
<delete file="${pharmacologic_class_indexing}/EPC_extraction_most_recent.txt"/>
616617

617618
<exec executable="python" failonerror="true">
618-
<arg line="${pharmacologic_class_indexing}/parseEPCfromXMLs.py ${PG_CLASS_INDEXING_SPLS}" />
619+
<arg line="${pharmacologic_class_indexing}/parseEPCfromXMLs.py ${PG_CLASS_INDEXING_SPLS}" />
619620
<redirector append="true">
620621
<outputmapper type="merge" to="${pharmacologic_class_indexing}/EPC_extraction_most_recent.txt"/>
621622
<errormapper type="merge" to="${ERROR_LOG}"/>

‎linkedSPLs/LinkedSPLs-update/load-dailymed-spls/loadDailymedToSql.py

Lines changed: 6 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -391,7 +391,6 @@ def run(logger, spls, limit=None):
391391
continue
392392

393393
try:
394-
395394

396395
insert_active_moieties(tags['activeMoieties'], tags['activeMoietyUNIIs'])
397396
insertQuery = "INSERT INTO structuredProductLabelMetadata(setId, versionNumber, fullName, routeOfAdministration, genericMedicine, representedOrganization, effectiveTime, filename) VALUES(%s,%s,%s,%s,%s,%s,%s,%s)"
@@ -410,7 +409,7 @@ def run(logger, spls, limit=None):
410409
for code in splSections:
411410

412411
cursor.execute("SELECT table_name FROM loinc WHERE loinc='{0}'".format(code))
413-
res = cursor.fetchone()
412+
res = cursor.fetchone
414413
if res:
415414
table = cursor.fetchone()[0]
416415
else:
@@ -440,11 +439,11 @@ def run(logger, spls, limit=None):
440439
con.commit()
441440
os.rename ("spls/{0}".format(splF),"problematic-spls/{0}".format(splF))
442441
continue
443-
# except:
444-
# print "Unexpected error:", sys.exc_info()[0]
445-
# con.rollback()
446-
# con.commit()
447-
# continue
442+
except:
443+
print "Unexpected error:", sys.exc_info()[0]
444+
con.rollback()
445+
con.commit()
446+
continue
448447

449448

450449
##Create custom logger

0 commit comments

Comments
 (0)