[SQL] Faster loading of raisinbread test data

Dockerfile.test.db

@@ -17,8 +17,12 @@ RUN cat /sql/0000-00-00-schema.sql \
         /instruments_sql/*.sql \
         /test_instrument.sql \
         /RB_files/*.sql \
-    > /docker-entrypoint-initdb.d/0000-compiled.sql
+    > /RB_files/0000-compiled.sql
 
+RUN echo "#!/bin/bash" > /docker-entrypoint-initdb.d/0000-compiled.sh \
+    && echo "cd /RB_files" >> /docker-entrypoint-initdb.d/0000-compiled.sh \
+    && echo "mariadb --protocol=socket -uroot --password=\${MARIADB_ROOT_PASSWORD} -hlocalhost LorisTest < 0000-compiled.sql" >> /docker-entrypoint-initdb.d/0000-compiled.sh
+RUN chmod +x /docker-entrypoint-initdb.d/0000-compiled.sh
 RUN echo "USE LorisTest;" > /docker-entrypoint-initdb.d/0001-paths.sql \
     && echo "UPDATE Config SET Value='${BASE_DIR}/' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='base');" >> /docker-entrypoint-initdb.d/0001-paths.sql \
     && echo "CREATE USER IF NOT EXISTS 'SQLTestUser'@'%' IDENTIFIED BY 'TestPassword';" >> /docker-entrypoint-initdb.d/0001-paths.sql \

raisinbread/RB_files/CNV.sql

@@ -0,0 +1,6 @@
+SET FOREIGN_KEY_CHECKS=0;
+LOCK TABLE CNV WRITE;
+TRUNCATE TABLE CNV;
+LOAD DATA LOCAL INFILE 'CNV.tsv' INTO TABLE CNV
+ IGNORE 1 LINES;
+SET FOREIGN_KEY_CHECKS=1;

raisinbread/RB_files/CNV.tsv

@@ -0,0 +1,5 @@
+CNVID	CandidateID	Description	Type	EventName	Common_CNV	Characteristics	CopyNumChange	Inheritance	ArrayReport	Markers	ArrayReportDetail	ValidationMethod	PlatformID	Chromosome	Strand	EndLoc	StartLoc	Symbol	Name	NCBIID	OfficialSymbol	OfficialName
+1	326	\N	gain	\N	Y	Unknown	\N	unknown	Normal	\N	\N	\N	1	chr1	+	11007	11008	\N	\N	\N	\N	\N
+2	326	\N	unknown	\N	Y	Unknown	\N	unknown	Normal	\N	\N	\N	1	chr1	-	11009	11010	\N	\N	\N	\N	\N
+3	302	\N	unknown	\N	Y	Unknown	\N	unknown	Normal	\N	\N	\N	1	chr1	+	11007	11008	\N	\N	\N	\N	\N
+4	323	\N	unknown	\N	Y	Unknown	\N	unknown	Normal	\N	\N	\N	1	chr1	+	11007	11008	\N	\N	\N	\N	\N

raisinbread/RB_files/Config.sql

@@ -0,0 +1,6 @@
+SET FOREIGN_KEY_CHECKS=0;
+LOCK TABLE Config WRITE;
+TRUNCATE TABLE Config;
+LOAD DATA LOCAL INFILE 'Config.tsv' INTO TABLE Config
+ IGNORE 1 LINES;
+SET FOREIGN_KEY_CHECKS=1;

raisinbread/RB_files/Config.tsv

@@ -0,0 +1,113 @@
+1	2	1
+2	3	LORIS Demonstration Database
+3	42	<h3>Example Study Description</h3>\
+ <p>This is a sample description for this study, because it is a new LORIS install that has not yet customized this text.</p>\
+ <p>A LORIS administrator can customize this text in the configuration module, under the configuration option labeled "Study Description"</p>\
+ <h3>Useful Links</h3>\
+ <ul>\
+ <li><a href="https://github.com/aces/Loris" >LORIS GitHub Repository</a></li>\
+ <li><a href="https://github.com/aces/Loris/wiki/Setup" >LORIS Setup Guide</a></li>\
+ <li><a href="https://www.youtube.com/watch?v=2Syd_BUbl5A" >A video of a loris on YouTube</a></li>\
+ </ul>
+4	4	images/LORIS_logo.png
+5	5	false
+6	6	5
+7	7	99
+9	9	false
+10	10	2016
+11	11	2028
+12	13	false
+13	14	false
+15	16	false
+16	20	false
+17	21	true
+18	22	true
+19	23	0
+20	24	Customize this text with your citation policy (via Configuration module)
+22	12	Ymd
+23	27	/data-raisinbread/
+24	28	/home/driusan/Code/Loris/
+26	30	/PATH/TO/EXTERNAL/LIBRARY/
+29	33	tools/logs/
+30	34	/data/incoming/
+31	35	/data/demo/bin/mri/
+32	36	/data/incoming/
+33	37	/PATH/TO/Genomic-Data/
+34	38	/data/uploads/
+37	44	localhost
+39	48	This database provides an on-line mechanism to store both imaging and behavioural data collected from various locations. Within this framework, there are several tools that will make this process as efficient and simple as possible. For more detailed information regarding any aspect of the database, please click on the Help icon at the top right. Otherwise, feel free to contact us at the DCC. We strive to make data collection almost fun.
+40	51	[a-zA-Z]{3}[0-9]{4}_[0-9]{6}_[vV][0-9]+
+41	52	(?i).
+42	53	(?i)phantom
+43	54	(?i)phantom
+44	55	true
+45	56	t1
+46	56	t2
+47	58	radiology_review
+48	58	mri_parameter_form
+49	60	[email protected]
+50	61	[email protected]
+51	62	Produced by LorisDB
+52	66	S3cret
+53	71	demo
+54	72	[email protected]
+55	73	/data/demo/bin/mri/dicom-archive/get_dicom_info.pl
+56	74	1
+57	75	1
+58	76	dcm2mnc
+59	77	/data-raisinbread/tarchive/
+60	78	PatientName
+61	79	1
+62	80	1
+63	81	0
+64	82	65
+65	83	t1
+66	84	19
+67	85	/opt/niak-0.6.4.1/
+68	86	INTERLACE_outputDWIFileNameSuffix
+75	87	/issue_tracker
+76	88	localizer
+77	88	scout
+78	89	true
+79	90	0
+80	91	mri_parameter_form
+82	92	prod
+83	94	t1
+84	95	flair
+85	95	t1
+86	95	t2
+87	95	pd
+88	96	flair
+89	96	t1
+90	96	t2
+91	96	pd
+92	97	/data/publication_uploads/
+93	98	/data/publication_uploads/to_be_deleted/
+94	99	true
+95	49	1000
+96	100	environment
+97	70	/data-raisinbread/
+98	93	V1
+102	19	false
+103	102	/data/document_repository_uploads/
+104	103	/data/data_release_uploads/
+105	104	Ymd
+106	105	Y-m-d H:i:s
+107	106	/data/issue_tracker/
+108	107	
+113	112	warning
+114	113	warning
+115	114	none
+116	116	
+117	117	
+118	118	
+119	119	
+120	120	database_config.py
+121	125	false
+122	126	0
+126	129	365
+127	130	/var/www/loris/
+128	131	/data/EEGUploadIncomingPath/
+129	132	false
+130	133	EEGS3DataPath
+131	134	false

raisinbread/RB_files/ConfigI18n.sql

@@ -0,0 +1,6 @@
+SET FOREIGN_KEY_CHECKS=0;
+LOCK TABLE ConfigI18n WRITE;
+TRUNCATE TABLE ConfigI18n;
+LOAD DATA LOCAL INFILE 'ConfigI18n.tsv' INTO TABLE ConfigI18n
+ IGNORE 1 LINES;
+SET FOREIGN_KEY_CHECKS=1;

raisinbread/RB_files/ConfigSettings.sql

@@ -0,0 +1,6 @@
+SET FOREIGN_KEY_CHECKS=0;
+LOCK TABLE ConfigSettings WRITE;
+TRUNCATE TABLE ConfigSettings;
+LOAD DATA LOCAL INFILE 'ConfigSettings.tsv' INTO TABLE ConfigSettings
+ IGNORE 1 LINES;
+SET FOREIGN_KEY_CHECKS=1;