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Now dm+d sources are updated separately
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Timur
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Feb 3, 2021
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| /************************************************************************** | ||
| * Copyright 2016 Observational Health Data Sciences and Informatics (OHDSI) | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| * | ||
| * Authors: Timur Vakhitov | ||
| * Date: 2021 | ||
| **************************************************************************/ | ||
|
|
||
| DROP TABLE IF EXISTS SOURCES.F_LOOKUP2,SOURCES.F_INGREDIENT2,SOURCES.F_VTM2,SOURCES.F_VMP2,SOURCES.F_AMP2,SOURCES.F_VMPP2,SOURCES.F_AMPP2,SOURCES.DMDBONUS; | ||
| CREATE TABLE SOURCES.F_LOOKUP2 (xmlfield XML, vocabulary_date DATE, vocabulary_version VARCHAR (200)); | ||
| CREATE TABLE SOURCES.F_INGREDIENT2 (xmlfield XML); | ||
| CREATE TABLE SOURCES.F_VTM2 (xmlfield XML); | ||
| CREATE TABLE SOURCES.F_VMP2 (xmlfield XML); | ||
| CREATE TABLE SOURCES.F_VMPP2 (xmlfield XML); | ||
| CREATE TABLE SOURCES.F_AMP2 (xmlfield XML); | ||
| CREATE TABLE SOURCES.F_AMPP2 (xmlfield XML); | ||
| CREATE TABLE SOURCES.DMDBONUS (xmlfield XML); |
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65 changes: 65 additions & 0 deletions
65
working/packages/vocabulary_download/bash_functions_dmd.sql
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| --DMD part | ||
| DO $_$ | ||
| DECLARE | ||
| z text; | ||
| BEGIN | ||
| z:=$FUNCTIONBODY$ | ||
| CREATE OR REPLACE FUNCTION vocabulary_download.get_dmd_prepare_dmd (iPath text, iFilename text) | ||
| RETURNS void AS | ||
| $BODY$#!/bin/bash | ||
| #set permissions=775 by default | ||
| umask 002 && \ | ||
| cd "$1/work" && \ | ||
| unzip -oqj "$2" "f_ampp2_*.xml" -d . && \ | ||
| unzip -oqj "$2" "f_amp2_*.xml" -d . && \ | ||
| unzip -oqj "$2" "f_vmpp2_*.xml" -d . && \ | ||
| unzip -oqj "$2" "f_vmp2_*.xml" -d . && \ | ||
| unzip -oqj "$2" "f_lookup2_*.xml" -d . && \ | ||
| unzip -oqj "$2" "f_vtm2_*.xml" -d . && \ | ||
| unzip -oqj "$2" "f_ingredient2_*.xml" -d . | ||
|
|
||
| #move result to original folder | ||
| cd "$1" | ||
| rm -f *.xml | ||
| mv work/f_ampp2_*.xml "f_ampp2.xml" && \ | ||
| mv work/f_amp2_*.xml "f_amp2.xml" && \ | ||
| mv work/f_vmpp2_*.xml "f_vmpp2.xml" && \ | ||
| mv work/f_vmp2_*.xml "f_vmp2.xml" && \ | ||
| mv work/f_lookup2_*.xml "f_lookup2.xml" && \ | ||
| mv work/f_vtm2_*.xml "f_vtm2.xml" && \ | ||
| mv work/f_ingredient2_*.xml "f_ingredient2.xml" | ||
| $BODY$ | ||
| LANGUAGE 'plsh' | ||
| SECURITY DEFINER; | ||
| $FUNCTIONBODY$; | ||
| --convert CRLF to LF for bash | ||
| EXECUTE REPLACE(z,E'\r',''); | ||
| END $_$; | ||
|
|
||
| --DMD bonus part | ||
| DO $_$ | ||
| DECLARE | ||
| z text; | ||
| BEGIN | ||
| z:=$FUNCTIONBODY$ | ||
| CREATE OR REPLACE FUNCTION vocabulary_download.get_dmd_prepare_dmdbonus (iPath text, iFilename text) | ||
| RETURNS void AS | ||
| $BODY$#!/bin/bash | ||
| #set permissions=775 by default | ||
| umask 002 && \ | ||
| cd "$1/work" && \ | ||
| unzip -oqj "$2" "*.zip" -d . && \ | ||
| unzip -oqj "week*BNF.zip" "f_bnf1_*.xml" -d . && \ | ||
| rm -f week*BNF.zip | ||
|
|
||
| #move result to original folder | ||
| cd "$1" | ||
| rm -f dmdbonus.xml | ||
| mv work/f_bnf1_*.xml "dmdbonus.xml" | ||
| $BODY$ | ||
| LANGUAGE 'plsh' | ||
| SECURITY DEFINER; | ||
| $FUNCTIONBODY$; | ||
| --convert CRLF to LF for bash | ||
| EXECUTE REPLACE(z,E'\r',''); | ||
| END $_$; |
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