From 9555309b6c853f2de36e778af59500b23486d54c Mon Sep 17 00:00:00 2001
From: Morgan Taylor <marymorg@broadinstitute.org>
Date: Mon, 23 Sep 2024 13:12:35 -0400
Subject: [PATCH 1/2] redefine service-provided input paths

---
 service/src/main/resources/db/changelog.xml   |  1 +
 ...240923_update_input_defs_bucket_paths.yaml | 30 +++++++++++++++++++
 2 files changed, 31 insertions(+)
 create mode 100644 service/src/main/resources/db/changesets/20240923_update_input_defs_bucket_paths.yaml

diff --git a/service/src/main/resources/db/changelog.xml b/service/src/main/resources/db/changelog.xml
index 5eb0cbca..d317e086 100644
--- a/service/src/main/resources/db/changelog.xml
+++ b/service/src/main/resources/db/changelog.xml
@@ -27,6 +27,7 @@
   <include file="changesets/20240903_rename_workspace_project.yaml" relativeToChangelogFile="true"/>
   <include file="changesets/20240906_add_wdl_version_to_pipeline_run.yaml" relativeToChangelogFile="true"/>
   <include file="changesets/20240911_remove_isSuccess.yaml" relativeToChangelogFile="true"/>
+  <include file="changesets/20240923_update_input_defs_bucket_paths.yaml" relativeToChangelogFile="true"/>
 
   <include file="changesets/20240412-testdata.yaml" relativeToChangelogFile="true"/>
 
diff --git a/service/src/main/resources/db/changesets/20240923_update_input_defs_bucket_paths.yaml b/service/src/main/resources/db/changesets/20240923_update_input_defs_bucket_paths.yaml
new file mode 100644
index 00000000..8f3632ce
--- /dev/null
+++ b/service/src/main/resources/db/changesets/20240923_update_input_defs_bucket_paths.yaml
@@ -0,0 +1,30 @@
+# Update input definitions bucket paths for service provided inputs
+databaseChangeLog:
+  - changeSet:
+      id: Update input definitions bucket paths for service provided inputs
+      author: mma
+      changes:
+        # update geneticMapsPath default_value from /plink-genetic-maps/GRCh38_fixed/
+        - update:
+            tableName: pipeline_input_definitions
+            where: id=3 AND name='geneticMapsPath'
+            columns:
+              - column:
+                  name: default_value
+                  value: "/hg38/plink-genetic-maps/"
+        # update refDict default_value from /hg38/Homo_sapiens_assembly38.dict
+        - update:
+            tableName: pipeline_input_definitions
+            where: id=4 AND name='refDict'
+            columns:
+              - column:
+                  name: default_value
+                  value: "/hg38/ref_dict/Homo_sapiens_assembly38.dict"
+        # update referencePanelPathPrefix default_value from /hg38/1000G_HGDP_no_singletons_ref_panel/hgdp.tgp.gwaspy.merged.merged.AN_added.bcf.ac2
+        - update:
+            tableName: pipeline_input_definitions
+            where: id=5 AND name='referencePanelPathPrefix'
+            columns:
+              - column:
+                  name: default_value
+                  value: "/hg38/ref_panels/1000G_HGDP_no_singletons/hgdp.tgp.gwaspy.merged.merged.AN_added.bcf.ac2"

From f894663c92fe62514283c6c6ef5e782640b7a73d Mon Sep 17 00:00:00 2001
From: Morgan Taylor <marymorg@broadinstitute.org>
Date: Mon, 23 Sep 2024 14:25:15 -0400
Subject: [PATCH 2/2] pr comment suggestion

---
 .../changesets/20240923_update_input_defs_bucket_paths.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/service/src/main/resources/db/changesets/20240923_update_input_defs_bucket_paths.yaml b/service/src/main/resources/db/changesets/20240923_update_input_defs_bucket_paths.yaml
index 8f3632ce..c06739d8 100644
--- a/service/src/main/resources/db/changesets/20240923_update_input_defs_bucket_paths.yaml
+++ b/service/src/main/resources/db/changesets/20240923_update_input_defs_bucket_paths.yaml
@@ -7,7 +7,7 @@ databaseChangeLog:
         # update geneticMapsPath default_value from /plink-genetic-maps/GRCh38_fixed/
         - update:
             tableName: pipeline_input_definitions
-            where: id=3 AND name='geneticMapsPath'
+            where: name='geneticMapsPath' AND pipeline_id=(SELECT id FROM pipelines WHERE name='imputation_beagle')
             columns:
               - column:
                   name: default_value
@@ -15,7 +15,7 @@ databaseChangeLog:
         # update refDict default_value from /hg38/Homo_sapiens_assembly38.dict
         - update:
             tableName: pipeline_input_definitions
-            where: id=4 AND name='refDict'
+            where: name='refDict' AND pipeline_id=(SELECT id FROM pipelines WHERE name='imputation_beagle')
             columns:
               - column:
                   name: default_value
@@ -23,7 +23,7 @@ databaseChangeLog:
         # update referencePanelPathPrefix default_value from /hg38/1000G_HGDP_no_singletons_ref_panel/hgdp.tgp.gwaspy.merged.merged.AN_added.bcf.ac2
         - update:
             tableName: pipeline_input_definitions
-            where: id=5 AND name='referencePanelPathPrefix'
+            where: name='referencePanelPathPrefix' AND pipeline_id=(SELECT id FROM pipelines WHERE name='imputation_beagle')
             columns:
               - column:
                   name: default_value