Fixes for Oracle.

thehyve · Apr 16, 2016 · 30cf873 · 30cf873
1 parent 8fff877
commit 30cf873
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Showing 5 changed files with 12 additions and 10 deletions.
diff --git a/...ain/groovy/org/transmartproject/batch/browsetag/BrowseTagAssociationDatabaseReader.groovy b/...ain/groovy/org/transmartproject/batch/browsetag/BrowseTagAssociationDatabaseReader.groovy
@@ -114,7 +114,7 @@ class BrowseTagAssociationDatabaseReader implements ItemStreamReader<BrowseTagAs
                 INNER JOIN $Tables.AM_TAG_ITEM ati
                 ON ata.tag_item_id = ati.tag_item_id
                 INNER JOIN $Tables.BIO_CONCEPT_CODE bcc
-                ON ata.object_uid = concat(bcc.code_type_name, ':', bcc.bio_concept_code)
+                ON ata.object_uid = concat(bcc.code_type_name, concat(':', bcc.bio_concept_code))
                 LEFT OUTER JOIN $Tables.FM_FOLDER fp
                 ON f.parent_id = fp.folder_id
                 WHERE ata.object_type = 'BIO_CONCEPT_CODE')

diff --git a/src/main/groovy/org/transmartproject/batch/browsetag/BrowseTagTypeDatabaseReader.groovy b/src/main/groovy/org/transmartproject/batch/browsetag/BrowseTagTypeDatabaseReader.groovy
@@ -70,6 +70,7 @@ class BrowseTagTypeDatabaseReader implements ItemStreamReader<BrowseTagType> {
                 ON bcc.code_type_name = ati.code_type_name
                 INNER JOIN $Tables.AM_TAG_TEMPLATE att
                 ON ati.tag_template_id = att.tag_template_id
+                ORDER BY display_name ASC
         """
     }
 
@@ -112,6 +113,7 @@ class BrowseTagTypeDatabaseReader implements ItemStreamReader<BrowseTagType> {
                 INNER JOIN $Tables.AM_TAG_TEMPLATE att
                 ON ati.tag_template_id = att.tag_template_id
                 WHERE ati.tag_item_id = $tagType.id
+                ORDER BY bcc.code_description ASC
         """
     }
 

diff --git a/src/main/groovy/org/transmartproject/batch/tag/TagTypeService.groovy b/src/main/groovy/org/transmartproject/batch/tag/TagTypeService.groovy
@@ -73,7 +73,7 @@ class TagTypeService {
                 'node_type',
                 'value_type',
                 'shown_if_empty',
-                'index'
+                '"index"'
         ).executeBatch(
                 items.collect { TagType tagType ->
                     log.debug "Tag type: ${tagType}"

diff --git a/src/test-func/groovy/org/transmartproject/batch/browsetag/BrowseTagExportJobTests.groovy b/src/test-func/groovy/org/transmartproject/batch/browsetag/BrowseTagExportJobTests.groovy
@@ -71,8 +71,8 @@ class BrowseTagExportJobTests {
                         'Lead optimization',
                         'Hit finding',
                         'Target identification / validation'
-                ].join(','),
-                '4'
+                ].sort().join(','),
+                '9'
         ].join('\t')
         assertThat readExportedTagTypes(), hasItems(
             expected

diff --git a/src/test-func/groovy/org/transmartproject/batch/tag/TagTypesLoadJobTests.groovy b/src/test-func/groovy/org/transmartproject/batch/tag/TagTypesLoadJobTests.groovy
@@ -63,10 +63,10 @@ class TagTypesLoadJobTests implements JobRunningTestTrait {
     void testTagTypesAreLoaded() {
         assertThat fetchAllTagTypes(), contains(
             allOf(
-                hasEntry('tag_type', 'Test tag'),
+                hasEntry('tag_type', 'Programming language'),
             ),
             allOf(
-                hasEntry('tag_type', 'Programming language'),
+                hasEntry('tag_type', 'Test tag'),
             ),
         )
     }
@@ -85,14 +85,14 @@ class TagTypesLoadJobTests implements JobRunningTestTrait {
     void testTagOptionsAreLoaded() {
         assertThat fetchAllTagOptions(),
             allOf(
-                hasEntry(
-                    is('Test tag'),
-                    contains('Test option 1', 'Test option 2', 'Test option 3')
-                ),
                 hasEntry(
                     is('Programming language'),
                     contains('C', 'Haskell', 'Java', 'Javascript', 'Pascal', 'Python', 'R')
                 ),
+                hasEntry(
+                        is('Test tag'),
+                        contains('Test option 1', 'Test option 2', 'Test option 3')
+                ),
             )
     }