Add CSR test study

transmart-core-db/src/integration-test/groovy/org/transmartproject/db/multidimquery/AggregateDataServicePgSpec.groovy

@@ -72,6 +72,8 @@ class AggregateDataServicePgSpec extends Specification {
                 'TUMOR_NORMAL_SAMPLES',
                 'SURVEY1',
                 'SURVEY2',
+                '100_CATS',
+                'CSR'
         ] as Set
 
         then: "the result should have the correct counts for study EHR"

transmart-core-db/src/integration-test/groovy/org/transmartproject/db/multidimquery/QueryServicePgSpec.groovy

@@ -677,8 +677,11 @@ class QueryServicePgSpec extends Specification {
     void "test values of date type"() {
         def user = User.findByUsername('test-public-user-1')
 
-        Constraint constraint = new ValueConstraint(valueType: Type.DATE, operator: Operator.AFTER,
-                value: DATE_FORMAT.parse('1986-10-21 00:00:00'))
+        Constraint constraint = new AndConstraint([
+                new StudyNameConstraint(studyId: 'SURVEY1'),
+                new ValueConstraint(valueType: Type.DATE, operator: Operator.AFTER,
+                        value: DATE_FORMAT.parse('1986-10-21 00:00:00'))
+        ])
 
         when:
         def values = multiDimService.retrieveClinicalData(constraint, user).asList()*.value

transmart-core-db/src/integration-test/groovy/org/transmartproject/db/support/InQuerySpec.groovy

@@ -4,6 +4,7 @@ import grails.orm.HibernateCriteriaBuilder
 import grails.test.mixin.integration.Integration
 import grails.transaction.Rollback
 import org.transmartproject.db.i2b2data.PatientDimension
+import org.transmartproject.db.i2b2data.PatientMapping
 import spock.lang.Specification
 import spock.lang.Unroll
 
@@ -14,22 +15,32 @@ import java.util.function.Supplier
 class InQuerySpec extends Specification {
 
     @Unroll
-    void 'test postgres query splitting for list of #values.size() values'(Integer expectedCount, List<Long> values) {
-        when: 'Querying for patients'
+    void 'test listIn fetches requested entities'(Integer expectedCount, List<Long> values) {
+        when: 'Querying for patient mappings'
         Supplier<HibernateCriteriaBuilder> criteriaBuilderProducer = { ->
-            PatientDimension.createCriteria() as HibernateCriteriaBuilder
+            PatientMapping.createCriteria() as HibernateCriteriaBuilder
         }
-        List result = InQuery.listIn(criteriaBuilderProducer, 'id', values)
+        List result = InQuery.listIn(criteriaBuilderProducer, 'encryptedId', values)
 
-        then: 'The expected amount of objects is returned'
+        then: 'The expected amount of patient mappings is returned'
         result.size() == expectedCount
 
-        where: 'sizes range from 0 to more than 30000'
+        where:
         expectedCount | values
         0             | []
-        1             | [-40L]
-        3             | [-41L, -42L, -43L]
-        1250          | (-20000L .. 20000L)
+        1             | ['CV:40']
+        3             | ['CT:41', 'EHR:42', 'TNS:43']
+    }
+
+    void 'test listIn gets actual patients by wide range of ids'() {
+        when: 'Querying for patients'
+        Supplier<HibernateCriteriaBuilder> criteriaBuilderProducer = { ->
+            PatientDimension.createCriteria() as HibernateCriteriaBuilder
+        }
+        List result = InQuery.listIn(criteriaBuilderProducer, 'id', (-20000L..20000L))
+
+        then: 'The actual amount of patient is returned'
+        result.size() == PatientDimension.count()
     }
 
 }

transmart-core-db/src/integration-test/groovy/org/transmartproject/db/tree/TreeServiceSpec.groovy

@@ -64,9 +64,11 @@ class TreeServiceSpec extends Specification {
         then: "the top level should contain one node with all public studies as children"
         forest*.name == ['Public Studies']
         forest[0].children*.name == [
+                '100 CATS',
                 'CATEGORICAL_VALUES',
                 'CLINICAL_TRIAL',
                 'CLINICAL_TRIAL_HIGHDIM',
+                'CSR',
                 'EHR',
                 'EHR_HIGHDIM',
                 'MIX_HD',
@@ -77,7 +79,6 @@ class TreeServiceSpec extends Specification {
                 'SHARED_HD_CONCEPTS_STUDY_A',
                 'SHARED_HD_CONCEPTS_STUDY_B',
                 'TUMOR_NORMAL_SAMPLES'
-
         ]
     }
 

transmart-data/Makefile

@@ -17,6 +17,7 @@ postgres_test:
 	$(MAKE) -C ddl/postgres load
 	$(MAKE) -C data/postgres load_schema_amapp
 	$(MAKE) -C test_data/ postgres_test_data
+	$(MAKE) -C test_studies/ load
 	$(MAKE) -C data/postgres refresh_mvs
 
 oracle:
@@ -28,6 +29,7 @@ oracle_test:
 	$(MAKE) -C ddl/oracle load
 	$(MAKE) -C data/oracle load_schema_amapp
 	$(MAKE) -C test_data/ oracle_test_data
+	$(MAKE) -C test_studies/ load
 	$(MAKE) -C data/oracle refresh_mvs
 
 oracle_drop:

transmart-data/env/vars-ubuntu.php

@@ -11,5 +11,7 @@
 
 PATH=<?= realpath(__DIR__) ?>:$PATH
 
+TM_CZ_PWD=tm_cz
+
 export PGHOST PGPORT PGDATABASE PGUSER PGPASSWORD TABLESPACES PGSQL_BIN \
-	KETTLE_JOBS_PSQL KITCHEN PATH
+	KETTLE_JOBS_PSQL KITCHEN PATH TM_CZ_PWD

transmart-data/test_studies/.gitignore

@@ -0,0 +1 @@
+transmart-copy-*.jar

transmart-data/test_studies/CSR/README.md

@@ -0,0 +1,8 @@
+# Central Subject Registry
+
+CSR study has been composed to test sample-based features.
+Patient data has been made up.
+Novelty of the study that it stores observations over multiple level of entities: 
+Patient > Diagnosis > Biosource > Biomateral
+
+This realtion expressed by means of modifiers

transmart-data/test_studies/CSR/i2b2demodata/concept_dimension.tsv

@@ -0,0 +1,34 @@
+concept_blob	concept_cd	concept_path	download_date	import_date	name_char	sourcesystem_cd	table_name	update_date	upload_id
+	82fe43990271eabe4266c0392e99327f7b68d9a8	\Public Studies\CSR\03. Biosource information\01. Biosource parent\			01. Biosource parent				
+	1d92eaf563dcb89a4beca0698e983acf9b7c37a6	\Public Studies\CSR\04. Biomaterial information\02. Date of biomaterial\			02. Date of biomaterial				
+	1ce3fc1098b2b8179e5b486b8349a5c08f807898	\Public Studies\CSR\03. Biosource information\02. Date of biosource\			02. Date of biosource				
+	309c81ae7e5f3fdcb3d32721460fb1796d4b24c3	\Public Studies\CSR\03. Biosource information\06. Biosource dedicated for specific study\			06. Biosource dedicated for specific study				
+	60da92e9c0229b8ce64785ce3060f2ac7a2ce8ac	\Public Studies\CSR\01. Patient information\01. Date of birth\			01. Date of birth				
+	a7cfe8e9c9d0ee7d282ee4bc579d9ea2d2f5f167	\Public Studies\CSR\02. Diagnosis information\05. Center of treatment\			05. Center of treatment				
+	e27724a7b7c9e8ed0c653d9e27ee0b770563f98e	\Public Studies\CSR\01. Patient information\05. Date of death\			05. Date of death				
+	9a35d3ffc12c75bbd93a8804e27d31ea1ee20c93	\Public Studies\CSR\02. Diagnosis information\01. Date of diagnosis\			01. Date of diagnosis				
+	584786ca0ff21ee8ceb22dc1e0d7d6ca7b2a90e3	\Public Studies\CSR\03. Biosource information\04. Disease status\			04. Disease status				
+	e24277e1af6ded3d1a0b231f32e7723c566d5e67	\Public Studies\CSR\01. Patient information\02. Gender\			02. Gender				
+	246e7915066ee4a150322518b213181a7f3903d9	\Public Studies\CSR\01. Patient information\Informed consent\05. Informed consent data\			05. Informed consent data				
+	7816a9fbf89154bdbfadda6daded4b6c58dd37b3	\Public Studies\CSR\01. Patient information\Informed consent\06. Informed concent linking external database\			06. Informed concent linking external database				
+	0e87b77f99a0e9d444cf4729e88301231334630d	\Public Studies\CSR\01. Patient information\Informed consent\04. Informed consent material\			04. Informed consent material				
+	b64e4f7183e7b75a6faedb430285e326c5a30fde	\Public Studies\CSR\01. Patient information\Informed consent\01. Informed consent type\			01. Informed consent type				
+	e1ee31813ba7572cfd8ac3a36ec5a22a3d22512e	\Public Studies\CSR\01. Patient information\Informed consent\03. Date informed consent withdrawn\			03. Date informed consent withdrawn				
+	480736dfd7cc2d85ec65223382b7c480b32f455c	\Public Studies\CSR\01. Patient information\Informed consent\07. Report heriditary susceptibility\			07. Report heriditary susceptibility				
+	08e58306d0b4cf7e9b10dfe47135ef607d2bae3a	\Public Studies\CSR\04. Biomaterial information\01. Biomaterial parent\			01. Biomaterial parent				
+	debae43031f4a461b0e7a7fa0a0d89c793573df6	\Public Studies\CSR\01. Patient information\Taxonomy\			Taxonomy				
+	640e439053c924ca78f5ec339e4f6fe26bd4073d	\Public Studies\CSR\03. Biosource information\03. Tissue\			03. Tissue				
+	4f33eeb399622afda11f16c40a3e87dea82d6414	\Public Studies\CSR\02. Diagnosis information\03. Topography\			03. Topography				
+	c3bb4810113fc3daa877a2109c1a9c1358955021	\Public Studies\CSR\02. Diagnosis information\Treatment\			Treatment				
+	83faa63b282f9ff2e97312309b3b18760a6db97b	\Public Studies\CSR\03. Biosource information\05. Tumor percentage\			05. Tumor percentage				
+	7043ff91b2bd050feca89996be82eb1421a3372b	\Public Studies\CSR\02. Diagnosis information\04. Tumor stage\			04. Tumor stage				
+	4fc4afd045e321c824da01fae5c679cb34d71cac	\Public Studies\CSR\02. Diagnosis information\02. Tumor type\			02. Tumor type				
+	e0e1f2c1393ba80effa972e6f395566104fcce8e	\Public Studies\CSR\04. Biomaterial information\03. Biomaterial type\			03. Biomaterial type				
+	6b74b1eda880cca4473e2793e13e88869c0a03a5	\Public Studies\CSR\05. Study information\STD1\01. Study ID\			01. Study ID				
+	c18ba4a966d996090e78993dc087b24dfaeea87a	\Public Studies\CSR\05. Study information\STD1\04. Individual Study ID\			04. Individual Study ID				
+	1cbd83e436976dee45dd5c446290b2cb508b801e	\Public Studies\CSR\05. Study information\STD1\02. Study acronym\			02. Study acronym				
+	f79e5c3b50c3c3f889281a8567ba2db15c657a18	\Public Studies\CSR\05. Study information\STD1\03. Study title\			03. Study title				
+	f997c8d7bffdc73544e76688094f42b347fc8dac	\Public Studies\CSR\05. Study information\STD2\01. Study ID\			01. Study ID				
+	eecc1d9cbd2b8ac72e1fc9771e574b248931328c	\Public Studies\CSR\05. Study information\STD2\04. Individual Study ID\			04. Individual Study ID				
+	bb02b2fe41e213d2f2511228236e63c8144c2bd9	\Public Studies\CSR\05. Study information\STD2\02. Study acronym\			02. Study acronym				
+	e2823a4ea40466a199a724b967a1cd8f9f28b533	\Public Studies\CSR\05. Study information\STD2\03. Study title\			03. Study title				

transmart-data/test_studies/CSR/i2b2demodata/modifier_dimension.tsv

@@ -0,0 +1,4 @@
+modifier_path	modifier_cd	name_char	modifier_blob	update_date	download_date	import_date	sourcesystem_cd	upload_id	modifier_level	modifier_node_type
+\biomaterial_mod	CSR_BIOMATERIAL_MOD	Biomaterial ID								
+\biosource_mod	CSR_BIOSOURCE_MOD	Biosource ID								
+\diagnose_mod	CSR_DIAGNOSIS_MOD	Diagnosis ID