From 3c2e48c76c77906bb88c86cc262c3752aec8cc50 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Wed, 10 Apr 2024 12:31:15 -0700
Subject: [PATCH 1/2] Avoid setting units if not exists. Use global base
 directory in results

---
 schemas/base-metadata.schema.ts               | 25 +++++++++++--------
 .../guided-mode/data/GuidedPathExpansion.js   |  7 ++++++
 2 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index b9ed45eea..6dd46a272 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -156,16 +156,21 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
             order: ["channel_name", "group_name", "shank_electrode_number", ...UV_PROPERTIES]
         })
 
-        ecephys.properties["Units"].title = "Summarized Units"
-
-        updateEcephysTable("Units", copy, {
-            properties: {
-                clu_id: {
-                    title: 'Cluster ID',
-                }
-            },
-            order: ["unit_id", "unit_name", "clu_id", "group_id"]
-        })
+        if (ecephys.properties["Units"]) {
+
+            ecephys.properties["Units"].title = "Summarized Units"
+
+            
+            updateEcephysTable("Units", copy, {
+                properties: {
+                    clu_id: {
+                        title: 'Cluster ID',
+                    }
+                },
+                order: ["unit_id", "unit_name", "clu_id", "group_id"]
+            })
+
+        }
 
     }
 
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
index 8ea3ee24a..11dc925e1 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -329,6 +329,9 @@ export class GuidedPathExpansionPage extends Page {
 
         await this.form.validate();
 
+        const globalBaseDirectory = this.workflow.base_directory.value;
+
+
         const finalStructure = {};
         for (let key in structure) {
             const entry = { ...structure[key] };
@@ -337,9 +340,13 @@ export class GuidedPathExpansionPage extends Page {
             if (fstring.split(".").length > 1) entry.file_path = fstring;
             else entry.folder_path = fstring;
             delete entry.format_string_path;
+
+            if (!entry.base_directory && globalBaseDirectory) entry.base_directory = globalBaseDirectory
+
             finalStructure[key] = entry;
         }
 
+
         if (Object.keys(finalStructure).length === 0) {
             const message =
                 "Please configure at least one interface. <br/><small>Otherwise, revisit <b>Pipeline Workflow</b> to update your configuration.</small>";

From 851138d14417e16820b0aad144c136acb80b92a8 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 10 Apr 2024 19:32:26 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 schemas/base-metadata.schema.ts                               | 2 +-
 .../src/stories/pages/guided-mode/data/GuidedPathExpansion.js | 4 +---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/schemas/base-metadata.schema.ts b/schemas/base-metadata.schema.ts
index 6dd46a272..062d1a232 100644
--- a/schemas/base-metadata.schema.ts
+++ b/schemas/base-metadata.schema.ts
@@ -160,7 +160,7 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
 
             ecephys.properties["Units"].title = "Summarized Units"
 
-            
+
             updateEcephysTable("Units", copy, {
                 properties: {
                     clu_id: {
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
index 11dc925e1..4d39e77af 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js
@@ -331,7 +331,6 @@ export class GuidedPathExpansionPage extends Page {
 
         const globalBaseDirectory = this.workflow.base_directory.value;
 
-
         const finalStructure = {};
         for (let key in structure) {
             const entry = { ...structure[key] };
@@ -341,12 +340,11 @@ export class GuidedPathExpansionPage extends Page {
             else entry.folder_path = fstring;
             delete entry.format_string_path;
 
-            if (!entry.base_directory && globalBaseDirectory) entry.base_directory = globalBaseDirectory
+            if (!entry.base_directory && globalBaseDirectory) entry.base_directory = globalBaseDirectory;
 
             finalStructure[key] = entry;
         }
 
-
         if (Object.keys(finalStructure).length === 0) {
             const message =
                 "Please configure at least one interface. <br/><small>Otherwise, revisit <b>Pipeline Workflow</b> to update your configuration.</small>";