From e396301ba44c6dcb059694a4b57b72754e3778b3 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 13 Sep 2023 14:09:00 -0400
Subject: [PATCH 01/23] Update package.json

---
 package.json | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/package.json b/package.json
index 3bcb3133a..bd6b39419 100644
--- a/package.json
+++ b/package.json
@@ -12,20 +12,20 @@
     "dev:server": "cd pyflask && python -m flask run --port 4242",
     "build": "npm run build:app",
     "build:app": "electron-vite build --outDir build",
-    "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
-    "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
+    "build:win": "npm run build && npm run build:flask && npm run build:electron:win",
+    "build:mac": "npm run build && npm run build:flask && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all ndx_dandi_icephys --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator",
-    "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:.",
+    "build:flask": "python -m PyInstaller nwb-guide.spec",
+    "build:flask:spec:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
+    "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
+    "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",
     "test": "npm run test:app && npm run test:server",
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s",
-    "wait3s": "node -e \"setTimeout(() => process.exit(0),3000)\"",
-    "test:executable": "concurrently -n EXE,TEST --kill-others --success first \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"npm run wait3s && pytest pyflask/tests/ -s --target http://localhost:3434\"",
+    "test:executable": "concurrently -n EXE,TEST --kill-others \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"pytest pyflask/tests/ -s --target http://localhost:3434\"",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
     "coverage:server": "pytest pyflask/tests/ -s --cov=pyflask --cov-report=xml",
@@ -57,7 +57,7 @@
       {
         "ext": "nwb",
         "name": "NWB File",
-        "role": "Viewer"
+        "role": "Editor"
       }
     ],
     "files": [

From d5812fb45fcee2beb9440baa713a712cd4bd5607 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 13 Sep 2023 14:10:53 -0400
Subject: [PATCH 02/23] fix alterations

---
 package.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/package.json b/package.json
index bd6b39419..2b3d60ea6 100644
--- a/package.json
+++ b/package.json
@@ -25,6 +25,7 @@
     "test": "npm run test:app && npm run test:server",
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s",
+    "wait3s": "node -e \"setTimeout(() => process.exit(0),3000)\"",
     "test:executable": "concurrently -n EXE,TEST --kill-others \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"pytest pyflask/tests/ -s --target http://localhost:3434\"",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
@@ -57,7 +58,7 @@
       {
         "ext": "nwb",
         "name": "NWB File",
-        "role": "Editor"
+        "role": "Viewer"
       }
     ],
     "files": [

From 9e83ca7cad85855100418d2c5bdcaa2ec29d4205 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 13 Sep 2023 14:13:42 -0400
Subject: [PATCH 03/23] restore other

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 2b3d60ea6..d93b2d6d8 100644
--- a/package.json
+++ b/package.json
@@ -26,7 +26,7 @@
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s",
     "wait3s": "node -e \"setTimeout(() => process.exit(0),3000)\"",
-    "test:executable": "concurrently -n EXE,TEST --kill-others \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"pytest pyflask/tests/ -s --target http://localhost:3434\"",
+    "test:executable": "concurrently -n EXE,TEST --kill-others --success first \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"npm run wait3s && pytest pyflask/tests/ -s --target http://localhost:3434\"",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
     "coverage:server": "pytest pyflask/tests/ -s --cov=pyflask --cov-report=xml",

From cb98081e6567c581f9438eae927c16f57e345e43 Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 14:54:47 -0400
Subject: [PATCH 04/23] add spec file for windows

---
 .gitignore             |  2 --
 nwb-guide-windows.spec | 70 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 70 insertions(+), 2 deletions(-)
 create mode 100644 nwb-guide-windows.spec

diff --git a/.gitignore b/.gitignore
index 852548470..0cda7e019 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,8 +19,6 @@ semantic.json
 build/
 yarn.lock
 
-*.spec
-
 *.pyc
 src/.DS_Store
 .DS_Store
diff --git a/nwb-guide-windows.spec b/nwb-guide-windows.spec
new file mode 100644
index 000000000..09f97562f
--- /dev/null
+++ b/nwb-guide-windows.spec
@@ -0,0 +1,70 @@
+# -*- mode: python ; coding: utf-8 -*-
+import sys
+sys.setrecursionlimit(sys.getrecursionlimit() * 5)
+
+from PyInstaller.utils.hooks import collect_data_files
+from PyInstaller.utils.hooks import collect_all
+
+datas = [('./paths.config.json', '.'), ('./package.json', '.')]
+binaries = []
+hiddenimports = ['scipy._distributor_init', 'scipy._lib.messagestream', 'scipy._lib._ccallback', 'scipy._lib._testutils']
+datas += collect_data_files('jsonschema_specifications')
+tmp_ret = collect_all('nwbinspector')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('neuroconv')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('pynwb')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('hdmf')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('ci_info')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+
+
+block_cipher = None
+
+
+a = Analysis(
+    ['pyflask\\app.py'],
+    pathex=[],
+    binaries=binaries,
+    datas=datas,
+    hiddenimports=hiddenimports,
+    hookspath=[],
+    hooksconfig={},
+    runtime_hooks=[],
+    excludes=[],
+    win_no_prefer_redirects=False,
+    win_private_assemblies=False,
+    cipher=block_cipher,
+    noarchive=False,
+)
+pyz = PYZ(a.pure, a.zipped_data, cipher=block_cipher)
+
+exe = EXE(
+    pyz,
+    a.scripts,
+    [],
+    exclude_binaries=True,
+    name='nwb-guide',
+    debug=False,
+    bootloader_ignore_signals=False,
+    strip=False,
+    upx=True,
+    console=True,
+    disable_windowed_traceback=False,
+    argv_emulation=False,
+    target_arch=None,
+    codesign_identity=None,
+    entitlements_file=None,
+)
+coll = COLLECT(
+    exe,
+    a.binaries,
+    a.zipfiles,
+    a.datas,
+    strip=False,
+    upx=True,
+    upx_exclude=[],
+    name='nwb-guide',
+)

From 0e1e839b492f704299cd1b0ab7a787b8b47a9a1c Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 14:55:52 -0400
Subject: [PATCH 05/23] new commands

---
 package.json | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/package.json b/package.json
index d93b2d6d8..6e2db7464 100644
--- a/package.json
+++ b/package.json
@@ -12,12 +12,13 @@
     "dev:server": "cd pyflask && python -m flask run --port 4242",
     "build": "npm run build:app",
     "build:app": "electron-vite build --outDir build",
-    "build:win": "npm run build && npm run build:flask && npm run build:electron:win",
-    "build:mac": "npm run build && npm run build:flask && npm run build:electron:mac",
+    "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
+    "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask": "python -m PyInstaller nwb-guide.spec",
-    "build:flask:spec:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
-    "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
+    "build:flask:win": "python -m PyInstaller nwb-guide-windows.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils ./pyflask/app.py",
+    "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
+    "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",
     "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",

From 610de05202970455f985c8130de9f792cee2c9e5 Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 15:03:09 -0400
Subject: [PATCH 06/23] add other renames

---
 package.json | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/package.json b/package.json
index 6e2db7464..602798335 100644
--- a/package.json
+++ b/package.json
@@ -20,6 +20,12 @@
     "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
     "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",
     "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
+    "rename:spec:mac": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-mac.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
+    "build:flask:spec:mac": "npm run build:flask:spec:mac && npm run rename:spec:mac",
+    "rename:spec:mac-arm64": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-mac-arm64.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
+    "build:flask:spec:mac-arm64": "npm run build:flask:spec:mac-arm64 && npm run rename:spec:mac-arm64",
+    "rename:spec:linux": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-linux.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
+    "build:flask:spec:linux": "npm run build:flask:spec:unix && npm run rename:spec:linux",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",

From cf691191a8b7313c7f79b8719b1bb9bcf42ab63d Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 15:04:23 -0400
Subject: [PATCH 07/23] add other build calls

---
 package.json | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/package.json b/package.json
index 602798335..4f6278343 100644
--- a/package.json
+++ b/package.json
@@ -16,6 +16,9 @@
     "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
     "build:flask:win": "python -m PyInstaller nwb-guide-windows.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:flask:mac": "python -m PyInstaller nwb-guide-mac.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:flask:mac-arm64": "python -m PyInstaller nwb-guide-mac-arm64.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:flask:linux": "python -m PyInstaller nwb-guide-linux.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils ./pyflask/app.py",
     "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
     "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",

From a807e65c5fe33d08671d0feb9c96574dddf283eb Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 15:05:14 -0400
Subject: [PATCH 08/23] propagate to top level

---
 package.json | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 4f6278343..d475f4018 100644
--- a/package.json
+++ b/package.json
@@ -13,8 +13,9 @@
     "build": "npm run build:app",
     "build:app": "electron-vite build --outDir build",
     "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
-    "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
-    "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
+    "build:mac": "npm run build && npm run build:flask:mac && npm run build:electron:mac",
+    "build:mac-arm64": "npm run build && npm run build:flask:mac-arm64 && npm run build:electron:mac",
+    "build:linux": "npm run build && npm run build:flask:linux && npm run build:electron:linux",
     "build:flask:win": "python -m PyInstaller nwb-guide-windows.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:mac": "python -m PyInstaller nwb-guide-mac.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:mac-arm64": "python -m PyInstaller nwb-guide-mac-arm64.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",

From 69efd18daac7cddf7dbcc6371329d350be4c3471 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 13 Sep 2023 15:28:30 -0400
Subject: [PATCH 09/23] forgot hidden import

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index d475f4018..f8efae261 100644
--- a/package.json
+++ b/package.json
@@ -20,7 +20,7 @@
     "build:flask:mac": "python -m PyInstaller nwb-guide-mac.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:mac-arm64": "python -m PyInstaller nwb-guide-mac-arm64.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:linux": "python -m PyInstaller nwb-guide-linux.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils ./pyflask/app.py",
+    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator ./pyflask/app.py",
     "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
     "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",
     "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",

From 1f97066df8744344e58572664ed373e723c2d595 Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 15:55:06 -0400
Subject: [PATCH 10/23] update spec file, duh

---
 nwb-guide-windows.spec | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/nwb-guide-windows.spec b/nwb-guide-windows.spec
index 09f97562f..1b46759fa 100644
--- a/nwb-guide-windows.spec
+++ b/nwb-guide-windows.spec
@@ -1,13 +1,10 @@
 # -*- mode: python ; coding: utf-8 -*-
-import sys
-sys.setrecursionlimit(sys.getrecursionlimit() * 5)
-
 from PyInstaller.utils.hooks import collect_data_files
 from PyInstaller.utils.hooks import collect_all
 
 datas = [('./paths.config.json', '.'), ('./package.json', '.')]
 binaries = []
-hiddenimports = ['scipy._distributor_init', 'scipy._lib.messagestream', 'scipy._lib._ccallback', 'scipy._lib._testutils']
+hiddenimports = ['scipy._distributor_init', 'scipy._lib.messagestream', 'scipy._lib._ccallback', 'scipy._lib._testutils', 'email_validator']
 datas += collect_data_files('jsonschema_specifications')
 tmp_ret = collect_all('nwbinspector')
 datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]

From b3a68d68b52b81da266ce05adf68f38e5e53da53 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 13 Sep 2023 21:43:55 -0400
Subject: [PATCH 11/23] re-add recursion limit hack, duh

---
 nwb-guide-windows.spec | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nwb-guide-windows.spec b/nwb-guide-windows.spec
index 1b46759fa..e3a9a731d 100644
--- a/nwb-guide-windows.spec
+++ b/nwb-guide-windows.spec
@@ -1,4 +1,7 @@
 # -*- mode: python ; coding: utf-8 -*-
+import sys
+sys.setrecursionlimit(sys.getrecursionlimit() * 5)
+
 from PyInstaller.utils.hooks import collect_data_files
 from PyInstaller.utils.hooks import collect_all
 

From 6e1e1ef3b5f63c0fc13d4f241140f9948eb4176f Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 22:08:27 -0400
Subject: [PATCH 12/23] re-add ndx-icephys

---
 nwb-guide-windows.spec | 2 ++
 package.json           | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/nwb-guide-windows.spec b/nwb-guide-windows.spec
index e3a9a731d..93640b066 100644
--- a/nwb-guide-windows.spec
+++ b/nwb-guide-windows.spec
@@ -17,6 +17,8 @@ tmp_ret = collect_all('pynwb')
 datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
 tmp_ret = collect_all('hdmf')
 datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('ndx_dandi_icephys')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
 tmp_ret = collect_all('ci_info')
 datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
 
diff --git a/package.json b/package.json
index f8efae261..c6f5b1487 100644
--- a/package.json
+++ b/package.json
@@ -20,7 +20,7 @@
     "build:flask:mac": "python -m PyInstaller nwb-guide-mac.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:mac-arm64": "python -m PyInstaller nwb-guide-mac-arm64.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:linux": "python -m PyInstaller nwb-guide-linux.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator ./pyflask/app.py",
+    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ndx_dandi_icephys --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator ./pyflask/app.py",
     "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
     "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",
     "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",

From 7c1c3c0a7becd8b6ff5591c421df7d11c298db0e Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 23:46:00 -0400
Subject: [PATCH 13/23] simpify cross-platform; update workflows

---
 .github/workflows/Build-and-deploy-mac.yml    |  1 -
 .../pyflask-build-and-dist-tests.yml          | 17 ++---------
 nwb-guide-windows.spec => nwb-guide.spec      |  0
 package.json                                  | 23 ++++----------
 prepare_pyinstaller_spec.py                   | 30 +++++++++++++++++++
 5 files changed, 39 insertions(+), 32 deletions(-)
 rename nwb-guide-windows.spec => nwb-guide.spec (100%)
 create mode 100644 prepare_pyinstaller_spec.py

diff --git a/.github/workflows/Build-and-deploy-mac.yml b/.github/workflows/Build-and-deploy-mac.yml
index dd7a77988..7e8afcfe5 100644
--- a/.github/workflows/Build-and-deploy-mac.yml
+++ b/.github/workflows/Build-and-deploy-mac.yml
@@ -22,7 +22,6 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: nwb-guide
-          #mamba-version: "*"
           environment-file: environments/environment-MAC.yml
           auto-activate-base: false
 
diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 5fbea858d..b2b89d50b 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -30,19 +30,16 @@ jobs:
             os: ubuntu-latest
             label: environments/environment-Linux.yml
             prefix: /usr/share/miniconda3/envs/nwb-guide
-            shorthand: unix
 
-          - python-version: "3.10"
+          - python-version: "3.9"
             os: macos-latest
             label: environments/environment-Mac.yml
             prefix: /Users/runner/miniconda3/envs/nwb-guide
-            shorthand: unix
 
-          - python-version: "3.10"
+          - python-version: "3.9"
             os: windows-latest
             label: environments/environment-Windows.yml
             prefix: C:\Miniconda3\envs\nwb-guide
-            shorthand: win
 
     steps:
       - uses: actions/checkout@v3
@@ -88,15 +85,7 @@ jobs:
         run: rm -f /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
 
       - name: Build PyFlask distribution
-        run: npm run build:flask:${{ matrix.shorthand }}
-
-      #- if: matrix.os == 'windows-latest'
-      #  name: Run test on build executable
-      #  run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide.exe
-
-      #- if: matrix.os != 'windows-latest'
-      #  name: Run test on build executable
-      #  run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide
+        run: npm run build:flask
 
       - name: Run test on distributed executable
         run: node tests/testPyinstallerExecutable.js
diff --git a/nwb-guide-windows.spec b/nwb-guide.spec
similarity index 100%
rename from nwb-guide-windows.spec
rename to nwb-guide.spec
diff --git a/package.json b/package.json
index c6f5b1487..28727a469 100644
--- a/package.json
+++ b/package.json
@@ -11,25 +11,14 @@
     "dev:app": "vite src/renderer",
     "dev:server": "cd pyflask && python -m flask run --port 4242",
     "build": "npm run build:app",
+    "echo": "python -c \"print('hello')\"",
     "build:app": "electron-vite build --outDir build",
-    "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
-    "build:mac": "npm run build && npm run build:flask:mac && npm run build:electron:mac",
-    "build:mac-arm64": "npm run build && npm run build:flask:mac-arm64 && npm run build:electron:mac",
-    "build:linux": "npm run build && npm run build:flask:linux && npm run build:electron:linux",
-    "build:flask:win": "python -m PyInstaller nwb-guide-windows.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:mac": "python -m PyInstaller nwb-guide-mac.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:mac-arm64": "python -m PyInstaller nwb-guide-mac-arm64.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:linux": "python -m PyInstaller nwb-guide-linux.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:win": "npm run build && npm run build:flask && npm run build:electron:win",
+    "build:mac": "npm run build && npm run build:flask && npm run build:electron:mac",
+    "build:linux": "npm run build && npm run build:flask && npm run build:electron:linux",
+    "build:flask": "python -m PyInstaller nwb-guide.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
     "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ndx_dandi_icephys --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator ./pyflask/app.py",
-    "rename:spec:windows": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-windows.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
-    "build:flask:spec:win": "npm run build:flask:spec:base -- --add-data ./paths.config.json;. --add-data ./package.json;. && npm run rename:spec:windows",
-    "build:flask:spec:unix": "npm run build:flask:spec:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
-    "rename:spec:mac": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-mac.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
-    "build:flask:spec:mac": "npm run build:flask:spec:mac && npm run rename:spec:mac",
-    "rename:spec:mac-arm64": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-mac-arm64.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
-    "build:flask:spec:mac-arm64": "npm run build:flask:spec:mac-arm64 && npm run rename:spec:mac-arm64",
-    "rename:spec:linux": "node -e \"require('fs').rename('nwb-guide.spec', 'nwb-guide-linux.spec', function(err) { if (err) console.log(err); console.log('File successfully renamed!') })\"",
-    "build:flask:spec:linux": "npm run build:flask:spec:unix && npm run rename:spec:linux",
+    "build:flask:spec": "npm run build:flask:spec:base && python prepare_pyinstaller_spec.py",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",
diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
new file mode 100644
index 000000000..41d2cc6d6
--- /dev/null
+++ b/prepare_pyinstaller_spec.py
@@ -0,0 +1,30 @@
+"""
+Calling `pyi-makespec` regenerates the base spec file, but we need to extend the recursion limit.
+
+This script is run automatically as a part of `npm run build:flask:spec` after the `pyi-makespec` call.
+"""
+
+
+def test():
+    from pathlib import Path
+
+    with open(file=Path(__file__).parent / "nwb-guide.spec", mode="r") as io:
+        lines = io.readlines()
+
+    lines.insert(1, "import sys\n")
+    lines.insert(2, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
+    lines.insert(3, "\n")
+
+    # Originally this was a separate `npm` command per platform to account for CLI syntax differences between ; and :
+    # The spec file is, however, the same across platforms
+    data_line_index = lines.index("datas = []\n")
+    lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
+
+    with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
+        io.writelines(lines)
+
+    print("Sucessfully injected recursion depth extension and json paths!")
+
+
+if __name__ == "__main__":
+    test()

From a9ddea5f8f250dbff3208fdfaaa59673e3f1e436 Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Wed, 13 Sep 2023 23:48:18 -0400
Subject: [PATCH 14/23] simplify python

---
 prepare_pyinstaller_spec.py | 33 +++++++++++++--------------------
 1 file changed, 13 insertions(+), 20 deletions(-)

diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
index 41d2cc6d6..2e69cb49e 100644
--- a/prepare_pyinstaller_spec.py
+++ b/prepare_pyinstaller_spec.py
@@ -3,28 +3,21 @@
 
 This script is run automatically as a part of `npm run build:flask:spec` after the `pyi-makespec` call.
 """
+from pathlib import Path
 
+with open(file=Path(__file__).parent / "nwb-guide.spec", mode="r") as io:
+    lines = io.readlines()
 
-def test():
-    from pathlib import Path
+lines.insert(1, "import sys\n")
+lines.insert(2, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
+lines.insert(3, "\n")
 
-    with open(file=Path(__file__).parent / "nwb-guide.spec", mode="r") as io:
-        lines = io.readlines()
+# Originally this was a separate `npm` command per platform to account for CLI syntax differences between ; and :
+# The spec file is, however, the same across platforms
+data_line_index = lines.index("datas = []\n")
+lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
 
-    lines.insert(1, "import sys\n")
-    lines.insert(2, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
-    lines.insert(3, "\n")
+with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
+    io.writelines(lines)
 
-    # Originally this was a separate `npm` command per platform to account for CLI syntax differences between ; and :
-    # The spec file is, however, the same across platforms
-    data_line_index = lines.index("datas = []\n")
-    lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
-
-    with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
-        io.writelines(lines)
-
-    print("Sucessfully injected recursion depth extension and json paths!")
-
-
-if __name__ == "__main__":
-    test()
+print("Sucessfully injected recursion depth extension and json paths!")

From 1d5579b21220a023404c421840bb35cf0e2d729f Mon Sep 17 00:00:00 2001
From: Cody Baker <cbaker9@nd.edu>
Date: Thu, 14 Sep 2023 00:22:19 -0400
Subject: [PATCH 15/23] modify spec to be platform indepedent

---
 nwb-guide.spec              | 4 +++-
 prepare_pyinstaller_spec.py | 9 ++++++++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/nwb-guide.spec b/nwb-guide.spec
index 93640b066..8b4f5649d 100644
--- a/nwb-guide.spec
+++ b/nwb-guide.spec
@@ -1,5 +1,7 @@
 # -*- mode: python ; coding: utf-8 -*-
 import sys
+from pathlib import Path
+
 sys.setrecursionlimit(sys.getrecursionlimit() * 5)
 
 from PyInstaller.utils.hooks import collect_data_files
@@ -27,7 +29,7 @@ block_cipher = None
 
 
 a = Analysis(
-    ['pyflask\\app.py'],
+    [f"{Path('pyflask') / 'app.py'}"],
     pathex=[],
     binaries=binaries,
     datas=datas,
diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
index 2e69cb49e..db06d8e91 100644
--- a/prepare_pyinstaller_spec.py
+++ b/prepare_pyinstaller_spec.py
@@ -9,14 +9,21 @@
     lines = io.readlines()
 
 lines.insert(1, "import sys\n")
-lines.insert(2, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
+lines.insert(2, "from pathlib import Path\n")
 lines.insert(3, "\n")
+lines.insert(4, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
+lines.insert(5, "\n")
 
 # Originally this was a separate `npm` command per platform to account for CLI syntax differences between ; and :
 # The spec file is, however, the same across platforms
 data_line_index = lines.index("datas = []\n")
 lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
 
+# Another platform specific difference is the app.py location
+app_py_line_index = next(index for index, line in enumerate(lines) if "app.py" in line)
+app_py_line = "    [f\"{Path('pyflask') / 'app.py'}\"],\n"
+lines[app_py_line_index] = app_py_line
+
 with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
     io.writelines(lines)
 

From b99b3391edee2a546593a32f9ed7331dbe18a626 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 14 Sep 2023 10:07:12 -0700
Subject: [PATCH 16/23] DANDI upload updates

---
 schemas/json/dandi/global.json                | 22 ++++++++++++++-----
 src/renderer/src/stories/JSONSchemaForm.js    | 22 ++++++++++++++++---
 src/renderer/src/stories/JSONSchemaInput.js   |  3 ++-
 src/renderer/src/stories/forms/utils.ts       |  4 +++-
 src/renderer/src/stories/pages/Page.js        |  2 +-
 .../pages/guided-mode/data/GuidedMetadata.js  |  5 +++--
 .../guided-mode/data/GuidedSourceData.js      |  1 +
 .../stories/pages/settings/SettingsPage.js    |  4 ++--
 .../src/stories/pages/uploads/UploadsPage.js  | 11 +++++++---
 9 files changed, 55 insertions(+), 19 deletions(-)

diff --git a/schemas/json/dandi/global.json b/schemas/json/dandi/global.json
index c841a1cf8..1680fd34d 100644
--- a/schemas/json/dandi/global.json
+++ b/schemas/json/dandi/global.json
@@ -1,10 +1,20 @@
 {
+    "description": "Log in to DANDI, click on your user initials in the top-right corner, and copy your API key from the resulting pop-up. <br/><small><b>Note:</b> <a href='https://dandiarchive.org' target='_blank'>The main archive</a> and <a href='https://gui-staging.dandiarchive.org'  target='_blank'>the staging (testing) server</a> have different API keys.</small>",
     "properties": {
-        "api_key": {
-            "type": "string",
-            "format": "password",
-            "description": "Log in to DANDI, click on your user initials in the top-right corner, and copy your API key from the resulting pop-up. <br/><small><b>Note:</b> <a href='https://dandiarchive.org' target='_blank'>The main archive</a> and <a href='https://gui-staging.dandiarchive.org'  target='_blank'>the staging (testing) server</a> have different API keys.</small>"
+        "api_keys": {
+            "properties": {
+                "main_api_key": {
+                    "type": "string",
+                    "format": "password",
+                    "description": "From the <a href='https://dandiarchive.org' target='_blank'>main archive</a>"
+                },
+                "staging_api_key": {
+                    "type": "string",
+                    "format": "password",
+                    "description": "From the <a href='https://gui-staging.dandiarchive.org' target='_blank'>staging (testing) server</a>"
+                }
+            },
+            "required": ["main_api_key", "staging_api_key"]
         }
-    },
-    "required": ["api_key"]
+    }
 }
diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index aa2912722..bbd554182 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -114,6 +114,22 @@ pre {
   .required.conditional label:after {
     color: transparent;
   }
+
+  h4 { 
+    margin: 0;
+    margin-bottom: 5px;
+    padding-bottom: 5px;
+    border-bottom: 1px solid gainsboro;
+  }
+
+  .guided--text-input-instructions {
+    font-size: 13px;
+    width: 100%;
+    padding-top: 4px;
+    color: dimgray !important;
+    margin: 0 0 1em;
+    line-height: 1.4285em;
+}
 `;
 
 document.addEventListener("dragover", (e) => {
@@ -238,10 +254,10 @@ export class JSONSchemaForm extends LitElement {
 
         // NOTE: Forms with nested forms will handle their own state updates
         if (!value) {
-            delete resultParent[name];
+            if (fullPath.length === 1) delete resultParent[name];
             delete resolvedParent[name];
         } else {
-            resultParent[name] = value;
+            if (fullPath.length === 1) resultParent[name] = value;
             resolvedParent[name] = value;
         }
 
@@ -836,7 +852,7 @@ export class JSONSchemaForm extends LitElement {
 
         return html`
             <div>
-                ${false ? html`<h2>${schema.title}</h2>` : ""} ${false ? html`<p>${schema.description}</p>` : ""}
+                ${schema.description ? html`<h4>Description</h4><p class="guided--text-input-instructions">${unsafeHTML(schema.description)}</p>` : ""}
                 ${this.#render(schema, this.resolved, this.#requirements)}
             </div>
         `;
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index fde0b43af..0a6a7ea07 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -1,4 +1,5 @@
 import { LitElement, css, html } from "lit";
+import { unsafeHTML } from 'lit/directives/unsafe-html.js'
 import { FilesystemSelector } from "./FileSystemSelector";
 
 import { BasicTable } from "./BasicTable";
@@ -136,7 +137,7 @@ export class JSONSchemaInput extends LitElement {
             ${input}
             ${info.description
                 ? html`<p class="guided--text-input-instructions">
-                      ${capitalize(info.description)}${info.description.slice(-1)[0] === "." ? "" : "."}
+                      ${unsafeHTML(capitalize(info.description))}${info.description.slice(-1)[0] === "." ? "" : "."}
                   </p>`
                 : ""}
         `;
diff --git a/src/renderer/src/stories/forms/utils.ts b/src/renderer/src/stories/forms/utils.ts
index 8a1973675..30660bc4f 100644
--- a/src/renderer/src/stories/forms/utils.ts
+++ b/src/renderer/src/stories/forms/utils.ts
@@ -1,4 +1,6 @@
-export const capitalize = (str: string) => str[0].toUpperCase() + str.slice(1)
+const toCapitalizeAll = ['nwb', 'api', 'id']
+
+export const capitalize = (str: string) => toCapitalizeAll.includes(str.toLowerCase()) ? str.toUpperCase() : str[0].toUpperCase() + str.slice(1)
 
 
 export const header = (headerStr: string) => {
diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index c4a52659b..07d3ef6ea 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -17,7 +17,7 @@ export class Page extends LitElement {
     //     );
     // }
 
-    info = { globalState: {} };
+    info = { globalState: {}, states: { saved: false } };
 
     constructor(info = {}) {
         super();
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
index 583ccbee2..ab9ddeb7b 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
@@ -58,18 +58,19 @@ export class GuidedMetadataPage extends ManagedPage {
     createForm = ({ subject, session, info }) => {
         // const results = createResults({ subject, info }, this.info.globalState);
 
-        const globalState = this.info.globalState;
+        const { globalState } = this.info;
 
         const results = info.metadata; // Edited form info
 
         // Define the appropriate global metadata to fill empty values in the form
-        const aggregateGlobalMetadata = resolveGlobalOverrides(subject, this.info.globalState);
+        const aggregateGlobalMetadata = resolveGlobalOverrides(subject, globalState);
 
         // Define the correct instance identifier
         const instanceId = `sub-${subject}/ses-${session}`;
 
         // Ignore specific metadata in the form by removing their schema value
         const schema = globalState.schema.metadata[subject][session];
+        delete schema.description;
         delete schema.properties.NWBFile.properties.source_script;
         delete schema.properties.NWBFile.properties.source_script_file_name;
 
diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
index 5abb23272..eacd86b3a 100644
--- a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
+++ b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -104,6 +104,7 @@ export class GuidedSourceDataPage extends ManagedPage {
         const instanceId = `sub-${subject}/ses-${session}`;
 
         const schema = this.info.globalState.schema.source_data;
+        delete schema.description;
 
         const form = new JSONSchemaForm({
             identifier: instanceId,
diff --git a/src/renderer/src/stories/pages/settings/SettingsPage.js b/src/renderer/src/stories/pages/settings/SettingsPage.js
index c0ae474f8..69cef8a23 100644
--- a/src/renderer/src/stories/pages/settings/SettingsPage.js
+++ b/src/renderer/src/stories/pages/settings/SettingsPage.js
@@ -40,7 +40,7 @@ export class SettingsPage extends Page {
             const res = resolved[prop];
             if (propInfo) setUndefinedIfNotDeclared(propInfo, res);
         }
-        if (!("api_key" in resolved.DANDI)) resolved.DANDI.api_key = undefined;
+
         merge(this.form.resolved, global.data);
 
         global.save(); // Save the changes, even if invalid on the form
@@ -69,7 +69,7 @@ export class SettingsPage extends Page {
             onUpdate: () => (this.unsavedUpdates = true),
             validateOnChange: (name, parent) => {
                 const value = parent[name];
-                if (name === "api_key") return dandiAPITokenRegex.test(value);
+                if (name.includes("api_key")) return dandiAPITokenRegex.test(value);
                 return true;
             },
             onThrow,
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index 2e4691212..2ed2331d1 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -19,10 +19,15 @@ import { DandiResults } from "../../DandiResults.js";
 export const isStaging = (id) => parseInt(id) >= 100000;
 
 export async function uploadToDandi(info, type = "project" in info ? "" : "folder") {
-    const api_key = global.data.DANDI?.api_key;
+
+    const staging = isStaging(info.dandiset_id) // Automatically detect staging IDs
+
+    const whichAPIKey = staging ? 'staging_api_key' : 'main_api_key'
+    const api_key = global.data.DANDI?.api_keys?.[whichAPIKey];
+
     if (!api_key) {
         await Swal.fire({
-            title: "Your DANDI API key is not configured.",
+            title: `Your DANDI API key (${whichAPIKey}) is not configured.`,
             html: "Edit your settings to include this value.",
             icon: "warning",
             confirmButtonText: "Go to Settings",
@@ -35,7 +40,7 @@ export async function uploadToDandi(info, type = "project" in info ? "" : "folde
         type ? `upload/${type}` : "upload",
         {
             ...info,
-            staging: isStaging(info.dandiset_id), // Automatically detect staging IDs
+            staging,
             api_key,
         },
         { title: "Uploading to DANDI" }

From ec98679b49b4456d11430c21bb10f400356434e4 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 14 Sep 2023 10:10:08 -0700
Subject: [PATCH 17/23] Add description about staging derivation

---
 schemas/json/dandi/upload.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/schemas/json/dandi/upload.json b/schemas/json/dandi/upload.json
index 4ece77105..366e702e9 100644
--- a/schemas/json/dandi/upload.json
+++ b/schemas/json/dandi/upload.json
@@ -1,7 +1,8 @@
 {
     "properties": {
         "dandiset_id": {
-            "type": "string"
+            "type": "string",
+            "description": "The unique identifier for your dandiset. Will automatically determine whether to upload to the main or staging DANDI server."
         },
         "cleanup": {
             "type": "boolean",

From 59925b13604f7be0c2181def57cb88cce4a3e694 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 14 Sep 2023 17:11:19 +0000
Subject: [PATCH 18/23] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js            | 7 +++++--
 src/renderer/src/stories/JSONSchemaInput.js           | 2 +-
 src/renderer/src/stories/pages/uploads/UploadsPage.js | 5 ++---
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index bbd554182..bfd84feed 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -115,7 +115,7 @@ pre {
     color: transparent;
   }
 
-  h4 { 
+  h4 {
     margin: 0;
     margin-bottom: 5px;
     padding-bottom: 5px;
@@ -852,7 +852,10 @@ export class JSONSchemaForm extends LitElement {
 
         return html`
             <div>
-                ${schema.description ? html`<h4>Description</h4><p class="guided--text-input-instructions">${unsafeHTML(schema.description)}</p>` : ""}
+                ${schema.description
+                    ? html`<h4>Description</h4>
+                          <p class="guided--text-input-instructions">${unsafeHTML(schema.description)}</p>`
+                    : ""}
                 ${this.#render(schema, this.resolved, this.#requirements)}
             </div>
         `;
diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 0a6a7ea07..f5293a61b 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -1,5 +1,5 @@
 import { LitElement, css, html } from "lit";
-import { unsafeHTML } from 'lit/directives/unsafe-html.js'
+import { unsafeHTML } from "lit/directives/unsafe-html.js";
 import { FilesystemSelector } from "./FileSystemSelector";
 
 import { BasicTable } from "./BasicTable";
diff --git a/src/renderer/src/stories/pages/uploads/UploadsPage.js b/src/renderer/src/stories/pages/uploads/UploadsPage.js
index 2ed2331d1..7da82c9a6 100644
--- a/src/renderer/src/stories/pages/uploads/UploadsPage.js
+++ b/src/renderer/src/stories/pages/uploads/UploadsPage.js
@@ -19,10 +19,9 @@ import { DandiResults } from "../../DandiResults.js";
 export const isStaging = (id) => parseInt(id) >= 100000;
 
 export async function uploadToDandi(info, type = "project" in info ? "" : "folder") {
+    const staging = isStaging(info.dandiset_id); // Automatically detect staging IDs
 
-    const staging = isStaging(info.dandiset_id) // Automatically detect staging IDs
-
-    const whichAPIKey = staging ? 'staging_api_key' : 'main_api_key'
+    const whichAPIKey = staging ? "staging_api_key" : "main_api_key";
     const api_key = global.data.DANDI?.api_keys?.[whichAPIKey];
 
     if (!api_key) {

From ff45354e34121d6a0ecdcb5450d9e9939eca8c70 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <garrettmflynn@gmail.com>
Date: Thu, 14 Sep 2023 10:30:46 -0700
Subject: [PATCH 19/23] Update schemas/json/dandi/upload.json

Co-authored-by: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
---
 schemas/json/dandi/upload.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/schemas/json/dandi/upload.json b/schemas/json/dandi/upload.json
index 366e702e9..40f130e47 100644
--- a/schemas/json/dandi/upload.json
+++ b/schemas/json/dandi/upload.json
@@ -2,7 +2,7 @@
     "properties": {
         "dandiset_id": {
             "type": "string",
-            "description": "The unique identifier for your dandiset. Will automatically determine whether to upload to the main or staging DANDI server."
+            "description": "The unique identifier for your dandiset. Will automatically determine whether to upload to the main DANDI archive or the development staging server."
         },
         "cleanup": {
             "type": "boolean",

From a62a8e56c2a4bad945eed0881cfd54b6e1224e75 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 14 Sep 2023 13:34:47 -0700
Subject: [PATCH 20/23] Count fields properly (only interactive)

---
 src/renderer/src/stories/JSONSchemaForm.js | 41 +++++++++++++++++-----
 1 file changed, 32 insertions(+), 9 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index bfd84feed..d1a7967ea 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -484,18 +484,39 @@ export class JSONSchemaForm extends LitElement {
         }
     };
 
-    #getRenderable = (schema = {}, required, path) => {
+    #getRenderable = (schema = {}, required, path, recursive = false) => {
         const entries = Object.entries(schema.properties ?? {});
 
-        return entries.filter(([key, value]) => {
+        const isArrayOfArrays = (arr) => !!arr.find((v) => Array.isArray(v))
+
+        const flattenRecursedValues = (arr) => {
+            const newArr = []
+            arr.forEach((o) => {
+                if (isArrayOfArrays(o)) newArr.push(...o)
+                else newArr.push(o)
+            })
+
+            return newArr
+        }
+
+        const isRenderable = (key, value) => {
+            if (recursive && value.properties)  return this.#getRenderable(value, required[key], [...path, key], true)
+            
+            else return [key, value]
+        }
+
+        const res = entries.map(([key, value]) => {
             if (!value.properties && key === "definitions") return false; // Skip definitions
             if (this.ignore.includes(key)) return false;
-            if (this.showLevelOverride >= path.length) return true;
-            if (required[key]) return true;
-            if (this.#getLink([...this.#base, ...path, key])) return true;
-            if (!this.onlyRequired) return true;
+            if (this.showLevelOverride >= path.length) return isRenderable(key, value);
+            if (required[key]) return isRenderable(key, value);
+            if (this.#getLink([...this.#base, ...path, key])) return isRenderable(key, value);
+            if (!this.onlyRequired) return isRenderable(key, value);
             return false;
-        });
+        }).filter(o => !!o)
+
+        return flattenRecursedValues(res); // Flatten on the last pass
+
     };
 
     validateOnChange = () => {};
@@ -735,6 +756,7 @@ export class JSONSchemaForm extends LitElement {
             if (this.mode === "accordion" && hasMany) {
                 const headerName = header(name);
 
+
                 this.#nestedForms[name] = new JSONSchemaForm({
                     identifier: this.identifier,
                     schema: info,
@@ -770,10 +792,11 @@ export class JSONSchemaForm extends LitElement {
                     base: fullPath,
                 });
 
-                const accordion = new Accordion({
+
+                const accordion = new  Accordion({
                     sections: {
                         [headerName]: {
-                            subtitle: `${this.#getRenderable(info, required[name], fullPath).length} fields`,
+                            subtitle: `${this.#getRenderable(info, required[name], fullPath, true).length} fields`,
                             content: this.#nestedForms[name],
                         },
                     },

From 8b4291f710aaa26b24dd1536f4b78e34cec2a3cd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 14 Sep 2023 20:36:18 +0000
Subject: [PATCH 21/23] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaForm.js | 46 +++++++++++-----------
 1 file changed, 22 insertions(+), 24 deletions(-)

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
index d1a7967ea..e1902a2a3 100644
--- a/src/renderer/src/stories/JSONSchemaForm.js
+++ b/src/renderer/src/stories/JSONSchemaForm.js
@@ -487,36 +487,36 @@ export class JSONSchemaForm extends LitElement {
     #getRenderable = (schema = {}, required, path, recursive = false) => {
         const entries = Object.entries(schema.properties ?? {});
 
-        const isArrayOfArrays = (arr) => !!arr.find((v) => Array.isArray(v))
+        const isArrayOfArrays = (arr) => !!arr.find((v) => Array.isArray(v));
 
         const flattenRecursedValues = (arr) => {
-            const newArr = []
+            const newArr = [];
             arr.forEach((o) => {
-                if (isArrayOfArrays(o)) newArr.push(...o)
-                else newArr.push(o)
-            })
+                if (isArrayOfArrays(o)) newArr.push(...o);
+                else newArr.push(o);
+            });
 
-            return newArr
-        }
+            return newArr;
+        };
 
         const isRenderable = (key, value) => {
-            if (recursive && value.properties)  return this.#getRenderable(value, required[key], [...path, key], true)
-            
-            else return [key, value]
-        }
+            if (recursive && value.properties) return this.#getRenderable(value, required[key], [...path, key], true);
+            else return [key, value];
+        };
 
-        const res = entries.map(([key, value]) => {
-            if (!value.properties && key === "definitions") return false; // Skip definitions
-            if (this.ignore.includes(key)) return false;
-            if (this.showLevelOverride >= path.length) return isRenderable(key, value);
-            if (required[key]) return isRenderable(key, value);
-            if (this.#getLink([...this.#base, ...path, key])) return isRenderable(key, value);
-            if (!this.onlyRequired) return isRenderable(key, value);
-            return false;
-        }).filter(o => !!o)
+        const res = entries
+            .map(([key, value]) => {
+                if (!value.properties && key === "definitions") return false; // Skip definitions
+                if (this.ignore.includes(key)) return false;
+                if (this.showLevelOverride >= path.length) return isRenderable(key, value);
+                if (required[key]) return isRenderable(key, value);
+                if (this.#getLink([...this.#base, ...path, key])) return isRenderable(key, value);
+                if (!this.onlyRequired) return isRenderable(key, value);
+                return false;
+            })
+            .filter((o) => !!o);
 
         return flattenRecursedValues(res); // Flatten on the last pass
-
     };
 
     validateOnChange = () => {};
@@ -756,7 +756,6 @@ export class JSONSchemaForm extends LitElement {
             if (this.mode === "accordion" && hasMany) {
                 const headerName = header(name);
 
-
                 this.#nestedForms[name] = new JSONSchemaForm({
                     identifier: this.identifier,
                     schema: info,
@@ -792,8 +791,7 @@ export class JSONSchemaForm extends LitElement {
                     base: fullPath,
                 });
 
-
-                const accordion = new  Accordion({
+                const accordion = new Accordion({
                     sections: {
                         [headerName]: {
                             subtitle: `${this.#getRenderable(info, required[name], fullPath, true).length} fields`,

From 7e48322912da6cd8b4bcb5bfe532f3ffabc9897b Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 14 Sep 2023 13:39:56 -0700
Subject: [PATCH 22/23] Fix table validation

---
 src/renderer/src/stories/JSONSchemaInput.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 81c5fd6ae..3b0b67376 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -189,7 +189,7 @@ export class JSONSchemaInput extends LitElement {
 
                     // NOTE: This is likely an incorrect declaration of the table validation call
                     validateOnChange: (key, parent, v) => {
-                        return validateOnChange && this.#triggerValidation(key, this.form.tables[name], path); // this.form.validateOnChange(key, parent, fullPath, v);
+                        return validateOnChange && ( this.onValidate ? this.onValidate() : this.form ? this.form.validateOnChange(key, parent, fullPath, v) : '');
                     },
 
                     onStatusChange: () => this.form?.checkStatus(), // Check status on all elements

From cd85235dd1216025b3a630280241151a1edb04ef Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 14 Sep 2023 20:40:20 +0000
Subject: [PATCH 23/23] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/JSONSchemaInput.js | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
index 3b0b67376..467cdbb65 100644
--- a/src/renderer/src/stories/JSONSchemaInput.js
+++ b/src/renderer/src/stories/JSONSchemaInput.js
@@ -189,7 +189,14 @@ export class JSONSchemaInput extends LitElement {
 
                     // NOTE: This is likely an incorrect declaration of the table validation call
                     validateOnChange: (key, parent, v) => {
-                        return validateOnChange && ( this.onValidate ? this.onValidate() : this.form ? this.form.validateOnChange(key, parent, fullPath, v) : '');
+                        return (
+                            validateOnChange &&
+                            (this.onValidate
+                                ? this.onValidate()
+                                : this.form
+                                ? this.form.validateOnChange(key, parent, fullPath, v)
+                                : "")
+                        );
                     },
 
                     onStatusChange: () => this.form?.checkStatus(), // Check status on all elements