Merge pull request #68 from PytorchConnectomics/refactor

file handling

Author: akgohain

.gitignore

@@ -5,6 +5,7 @@
 *.png
 node_modules/
 pytc/
+pytorch_connectomics/
 logs/
 data/
 outputs/

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "pytorch_connectomics"]
-	path = pytorch_connectomics
-	url = https://github.com/zudi-lin/pytorch_connectomics.git

Dockerfile

@@ -1,10 +1,11 @@
 #centOS
 FROM nvidia/cuda:11.1.1-devel-ubi8
 
-# Enable AppStream and install Python 3.9
+# Enable AppStream and install Python 3.9 and git
 RUN yum -y module enable python39 && \
     yum install -y python39-3.9.2 && \
     yum install -y python39-devel-3.9.2 && \
+    yum install -y git && \
     yum clean all && \ 
     (python3.9 --version || echo "Python installation failed" && exit 1)
 
@@ -21,7 +22,11 @@ WORKDIR /app
 # Install dependencies
 RUN pip3 install --no-cache-dir torch==1.9.0 torchvision==0.10.0 cuda-python==11.1.1
 
-COPY ./pytorch_connectomics /app/pytorch_connectomics
+# Download pytorch_connectomics at specific commit (version 1.0)
+RUN git clone https://github.com/zudi-lin/pytorch_connectomics.git /app/pytorch_connectomics && \
+    cd /app/pytorch_connectomics && \
+    git checkout 20ccfde
+
 COPY ./samples_pytc /app/samples_pytc
 COPY ./server_pytc /app/server_pytc
 COPY ./server_api /app/server_api
@@ -35,9 +40,10 @@ WORKDIR /app/server_api
 RUN pip3 install --no-cache-dir -r requirements.txt
 
 WORKDIR /app
-# Copies the startup script, and runs it at CMD
+# Copies the startup scripts, and runs it at CMD
 COPY ./start.sh /app/
-RUN chmod +x start.sh
+COPY ./setup_pytorch_connectomics.sh /app/
+RUN chmod +x start.sh setup_pytorch_connectomics.sh
 
 # Expose ports
 EXPOSE 4242 4243 4244 6006

README.md

@@ -62,8 +62,17 @@ pip install -r requirements.txt
 
 In root folder,
 ```bash
+# The setup script will automatically download pytorch_connectomics at commit 20ccfde (version 1.0)
+./setup_pytorch_connectomics.sh
+cd pytorch_connectomics
+pip install --editable .
+```
+
+Alternatively, you can run this manually:
+```bash
 git clone https://github.com/zudi-lin/pytorch_connectomics.git
 cd pytorch_connectomics
+git checkout 20ccfde
 pip install --editable .
 ```
 

client/package-lock.json

@@ -11,7 +11,7 @@
     "antd": "^5.18.1",
     "axios": "^1.7.2",
     "buffer": "^6.0.3",
-    "electron": "^31.2.1",
+    "electron": "^38.3.0",
     "js-yaml": "^4.1.0",
     "localforage": "^1.10.0",
     "nth-check": "^2.1.1",
@@ -20,7 +20,7 @@
     "react": "^18.3.1",
     "react-dom": "^18.3.1",
     "react-router-dom": "^6.23.1",
-    "react-scripts": "5.0.1",
+    "react-scripts": "^5.0.1",
     "utif": "^3.1.0",
     "web-vitals": "^4.1.1"
   },
@@ -58,6 +58,7 @@
   "overrides": {
     "nth-check": "$nth-check",
     "resolve-url-loader": "^5.0.0",
-    "svgo": "^3.3.2"
+    "svgo": "^3.3.2",
+    "webpack-dev-server": "^5.2.1"
   }
 }

client/package.json

@@ -1,15 +1,44 @@
+import { useContext, useEffect, useState } from 'react'
 import './App.css'
 import Views from './views/Views'
-import { ContextWrapper } from './contexts/GlobalContext'
+import { AppContext, ContextWrapper } from './contexts/GlobalContext'
 import { YamlContextWrapper } from './contexts/YamlContext'
 
+function CacheBootstrapper ({ children }) {
+  const { resetFileState } = useContext(AppContext)
+  const [isCacheCleared, setIsCacheCleared] = useState(false)
+
+  useEffect(() => {
+    let isMounted = true
+    const clearCache = async () => {
+      await resetFileState()
+      if (isMounted) {
+        setIsCacheCleared(true)
+      }
+    }
+
+    clearCache()
+    return () => {
+      isMounted = false
+    }
+  }, [resetFileState])
+
+  if (!isCacheCleared) {
+    return null
+  }
+
+  return children
+}
+
 function App () {
   return (
     <ContextWrapper>
       <YamlContextWrapper>
-        <div className='App'>
-          <Views />
-        </div>
+        <CacheBootstrapper>
+          <div className='App'>
+            <Views />
+          </div>
+        </CacheBootstrapper>
       </YamlContextWrapper>
     </ContextWrapper>
   )