From aad84f0b05e37e99366dfab31c83ea03df938e32 Mon Sep 17 00:00:00 2001
From: Nathan Vieira Marcelino <nathan.v.marcelino@gmail.com>
Date: Fri, 19 Jul 2024 15:07:27 -0300
Subject: [PATCH 1/6] feat: use new vame version

---
 .github/workflows/build-and-release-linux.yml |  9 ++-------
 .github/workflows/build-and-release-mac.yml   |  9 ++-------
 .github/workflows/build-and-release-win.yml   |  7 +------
 .github/workflows/test-build-linux.yml        |  2 +-
 .github/workflows/test-build-mac.yml          |  2 +-
 .github/workflows/test-build-win.yml          |  2 +-
 src/renderer/src/@types/index.d.ts            |  1 +
 .../components/DynamicForm/DynamicInput.tsx   |  2 ++
 .../src/components/DynamicForm/index.tsx      | 11 ++++++++++-
 .../src/components/DynamicForm/styles.ts      |  2 +-
 src/renderer/src/context/Projects/index.tsx   |  1 +
 .../pages/Project/Tabs/CommunityAnalysis.tsx  |  5 +++--
 .../pages/Project/Tabs/CommunityVideos.tsx    | 17 +++++++++++------
 src/renderer/src/pages/Project/Tabs/Model.tsx |  4 ++--
 .../src/pages/Project/Tabs/MotifVideos.tsx    | 19 ++++++++++++-------
 .../src/pages/Project/Tabs/Organize.tsx       |  2 +-
 .../Project/Tabs/ProjectConfiguration.tsx     |  2 +-
 .../src/pages/Project/Tabs/Segmentation.tsx   |  2 +-
 .../pages/Project/Tabs/UMAPVisualization.tsx  | 17 +++++++++++------
 src/renderer/src/pages/Project/index.tsx      | 12 ++++++++----
 .../src/utils/extractDefaultValues.ts         |  2 +-
 src/schema/community-videos.schema.json       | 13 +++++++++++++
 src/schema/community.schema.json              |  5 +++++
 src/schema/config.schema.json                 |  9 ++++++---
 src/schema/motif-videos.schema.json           | 13 +++++++++++++
 src/schema/umap.schema.json                   | 14 ++++++++++++++
 26 files changed, 125 insertions(+), 59 deletions(-)
 create mode 100644 src/schema/community-videos.schema.json
 create mode 100644 src/schema/motif-videos.schema.json
 create mode 100644 src/schema/umap.schema.json

diff --git a/.github/workflows/build-and-release-linux.yml b/.github/workflows/build-and-release-linux.yml
index b924117..54e9cbf 100644
--- a/.github/workflows/build-and-release-linux.yml
+++ b/.github/workflows/build-and-release-linux.yml
@@ -38,12 +38,7 @@ jobs:
       - name: Install dependencies
         run: npm install
 
-      - name: Build
+      - name: Build and deploy on Linux(Debian)
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: npm run build:linux
-      
-      - name: Deploy Linux
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: npm run publish -- --publish=always
+        run: npm run build:linux --publish=always
diff --git a/.github/workflows/build-and-release-mac.yml b/.github/workflows/build-and-release-mac.yml
index ea5a2f3..0f6417d 100644
--- a/.github/workflows/build-and-release-mac.yml
+++ b/.github/workflows/build-and-release-mac.yml
@@ -43,12 +43,7 @@ jobs:
           p12-file-base64: ${{ secrets.MACOS_CERTIFICATE }}
           p12-password: ${{ secrets.MACOS_CERTIFICATE_PWD }}
 
-      - name: Build Mac
+      - name: Build and deploy on MacOS
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: npm run build:mac
-
-      - name: Deploy Mac
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: npm run publish -- --publish=always
\ No newline at end of file
+        run: npm run build:mac -- --publish=always
diff --git a/.github/workflows/build-and-release-win.yml b/.github/workflows/build-and-release-win.yml
index 29fa425..15d65b9 100644
--- a/.github/workflows/build-and-release-win.yml
+++ b/.github/workflows/build-and-release-win.yml
@@ -41,9 +41,4 @@ jobs:
       - name: Build and deploy on Windows
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: npm run build:win
-
-      - name: Deploy Windows
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: npm run publish -- --publish=always
+        run: npm run build:win -- --publish=always
diff --git a/.github/workflows/test-build-linux.yml b/.github/workflows/test-build-linux.yml
index 05f2ab5..3f27188 100644
--- a/.github/workflows/test-build-linux.yml
+++ b/.github/workflows/test-build-linux.yml
@@ -33,4 +33,4 @@ jobs:
         run: npm install
 
       - name: Build
-        run: npm run build:linux
+        run: npm run build:linux -- --publish=never
diff --git a/.github/workflows/test-build-mac.yml b/.github/workflows/test-build-mac.yml
index b7a0e8f..7739a23 100644
--- a/.github/workflows/test-build-mac.yml
+++ b/.github/workflows/test-build-mac.yml
@@ -33,4 +33,4 @@ jobs:
         run: npm install
 
       - name: Build and deploy on Mac
-        run: npm run build:mac
\ No newline at end of file
+        run: npm run build:mac -- --publish=never
\ No newline at end of file
diff --git a/.github/workflows/test-build-win.yml b/.github/workflows/test-build-win.yml
index b54a1a9..911a722 100644
--- a/.github/workflows/test-build-win.yml
+++ b/.github/workflows/test-build-win.yml
@@ -33,4 +33,4 @@ jobs:
         run: npm install
 
       - name: Build and deploy on Windows
-        run: npm run build:win
+        run: npm run build:win -- --publish=never
diff --git a/src/renderer/src/@types/index.d.ts b/src/renderer/src/@types/index.d.ts
index eee6aff..e5c4554 100644
--- a/src/renderer/src/@types/index.d.ts
+++ b/src/renderer/src/@types/index.d.ts
@@ -227,6 +227,7 @@ declare global {
   export type EnumProperty = DefaultPropertyAttrs &  {
     type: "string";
     enum: string[];
+    multiple?: boolean;
     default?: string;
   };
 
diff --git a/src/renderer/src/components/DynamicForm/DynamicInput.tsx b/src/renderer/src/components/DynamicForm/DynamicInput.tsx
index f964b22..8421c1a 100644
--- a/src/renderer/src/components/DynamicForm/DynamicInput.tsx
+++ b/src/renderer/src/components/DynamicForm/DynamicInput.tsx
@@ -41,9 +41,11 @@ const DynamicInput: React.FC<DynamicInputProps> = ({
 
   // Handle select fields
   if (type === "enum") {
+    const enumProperty = property as EnumProperty
     return (
       <select
         {...register(itemKey, { required, disabled: readOnly })}
+        multiple={enumProperty.multiple}
       >
         {(property as EnumProperty)!.enum.map((option) => (
           <option key={option} value={option}>
diff --git a/src/renderer/src/components/DynamicForm/index.tsx b/src/renderer/src/components/DynamicForm/index.tsx
index 99cf30c..0660ec7 100644
--- a/src/renderer/src/components/DynamicForm/index.tsx
+++ b/src/renderer/src/components/DynamicForm/index.tsx
@@ -21,7 +21,11 @@ const DynamicForm: React.FC<DynamicFormProps> = ({
   initialValues,
   submitText = "Submit",
 }) => {
-  const defaultValues = initialValues && !isEmpty(initialValues) ? initialValues : extractDefaultValues(schema)
+
+  const defaultValues = {
+    ...extractDefaultValues(schema),
+    ...initialValues
+  }
 
   const methods = useForm({
     disabled: blockSubmission,
@@ -31,6 +35,11 @@ const DynamicForm: React.FC<DynamicFormProps> = ({
   const properties = Object.entries(schema.properties)
   const readOnly = !properties.some(([_,p])=> !p.readOnly)
 
+  // const handleSubmit = (data) => {
+  //   console.log(data)
+  //   onFormSubmit(data)
+  // }
+
   return (
     <FormProvider {...methods}>
 
diff --git a/src/renderer/src/components/DynamicForm/styles.ts b/src/renderer/src/components/DynamicForm/styles.ts
index f39363a..2123724 100644
--- a/src/renderer/src/components/DynamicForm/styles.ts
+++ b/src/renderer/src/components/DynamicForm/styles.ts
@@ -149,4 +149,4 @@ export const FileListItem = styled.li`
   align-items: center;
   padding: 5px 0;
   overflow: auto;
-`;
\ No newline at end of file
+`;
diff --git a/src/renderer/src/context/Projects/index.tsx b/src/renderer/src/context/Projects/index.tsx
index b02a239..a6c6c30 100644
--- a/src/renderer/src/context/Projects/index.tsx
+++ b/src/renderer/src/context/Projects/index.tsx
@@ -177,6 +177,7 @@ export const ProjectsProvider: React.FC<{ children: ReactNode }> = ({
   }, [])
 
   const createMotifVideos = useCallback(async (data) => {
+    console.log(data)
     const res = await createMotifVideosVAMEProject(data)
     await refresh()
     return res
diff --git a/src/renderer/src/pages/Project/Tabs/CommunityAnalysis.tsx b/src/renderer/src/pages/Project/Tabs/CommunityAnalysis.tsx
index f773709..7547a7f 100644
--- a/src/renderer/src/pages/Project/Tabs/CommunityAnalysis.tsx
+++ b/src/renderer/src/pages/Project/Tabs/CommunityAnalysis.tsx
@@ -3,6 +3,7 @@ import { useState } from "react"
 import DynamicForm from "../../../components/DynamicForm"
 
 import communitySchema from '../../../../../schema/community.schema.json'
+
 import { TabProps } from "./types"
 import TerminalModal from "../../../components/TerminalModal"
 import { ControlButton } from "@renderer/pages/Home/styles"
@@ -19,7 +20,7 @@ export const CommunityAnalysis = ({
 }: TabProps) => {
   const [terminal, setTerminal] = useState(false)
 
-  const schema = structuredClone(communitySchema) as Schema
+  const schema = structuredClone(communitySchema) as unknown as Schema
 
   const communitiesCreated = project.workflow.communities_created
   const states = project.states?.["community"]
@@ -47,7 +48,7 @@ export const CommunityAnalysis = ({
         content={blockTooltip}
         placement="bottom"
         hideOnClick={false}
-        onShow={() => !blockSubmission as false}
+        disabled={!blockSubmission || !blockTooltip}
       >
         <>
           <DynamicForm
diff --git a/src/renderer/src/pages/Project/Tabs/CommunityVideos.tsx b/src/renderer/src/pages/Project/Tabs/CommunityVideos.tsx
index 5366494..c978660 100644
--- a/src/renderer/src/pages/Project/Tabs/CommunityVideos.tsx
+++ b/src/renderer/src/pages/Project/Tabs/CommunityVideos.tsx
@@ -9,6 +9,9 @@ import { ControlButton } from "@renderer/pages/Home/styles"
 import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"
 import { faTerminal } from "@fortawesome/free-solid-svg-icons"
 
+import CommunityVideosSchema from "../../../../../schema/community-videos.schema.json"
+import DynamicForm from "@renderer/components/DynamicForm"
+
 const CommunityVideos = ({
   project,
   onFormSubmit,
@@ -17,6 +20,8 @@ const CommunityVideos = ({
 }: TabProps) => {
   const [terminal, setTerminal] = useState(false)
 
+  const schema = structuredClone(CommunityVideosSchema) as unknown as Schema
+
   const hasCommunityVideos = project.workflow.community_videos_created
 
   if (!hasCommunityVideos) return (
@@ -42,12 +47,12 @@ const CommunityVideos = ({
         disabled={!blockSubmission}
       >
         <span>
-          <Button
-            disabled={blockSubmission}
-            onClick={onFormSubmit}
-          >
-            Create Community Videos
-          </Button>
+          <DynamicForm
+            schema={schema}
+            blockSubmission={blockSubmission}
+            submitText={"Create Community Videos"}
+            onFormSubmit={onFormSubmit}
+          />
         </span>
       </Tippy>
     </PaddedTab>
diff --git a/src/renderer/src/pages/Project/Tabs/Model.tsx b/src/renderer/src/pages/Project/Tabs/Model.tsx
index bf5ea0e..786c386 100644
--- a/src/renderer/src/pages/Project/Tabs/Model.tsx
+++ b/src/renderer/src/pages/Project/Tabs/Model.tsx
@@ -65,7 +65,7 @@ const Model = ({
           content={blockTooltip}
           placement="bottom"
           hideOnClick={false}
-          onShow={() => !blockSubmission as false}
+          disabled={!blockSubmission || !blockTooltip}
         >
           <span>
 
@@ -102,7 +102,7 @@ const Model = ({
         content={blockTooltip}
         placement="bottom"
         hideOnClick={false}
-        onShow={() => !blockSubmission as false}
+        disabled={!blockSubmission || !blockTooltip}
       >
         <span>
 
diff --git a/src/renderer/src/pages/Project/Tabs/MotifVideos.tsx b/src/renderer/src/pages/Project/Tabs/MotifVideos.tsx
index e291d1a..0670b01 100644
--- a/src/renderer/src/pages/Project/Tabs/MotifVideos.tsx
+++ b/src/renderer/src/pages/Project/Tabs/MotifVideos.tsx
@@ -8,6 +8,9 @@ import { ControlButton } from "@renderer/pages/Home/styles"
 import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"
 import { faTerminal } from "@fortawesome/free-solid-svg-icons"
 import Tippy from "@tippyjs/react"
+import DynamicForm from "@renderer/components/DynamicForm"
+
+import motifVideosSchema from '../../../../../schema/motif-videos.schema.json'
 
 const MotifVideos = ({
   project,
@@ -17,6 +20,8 @@ const MotifVideos = ({
 }: TabProps) => {
   const [terminal, setTerminal] = useState(false)
 
+  const schema = structuredClone(motifVideosSchema) as unknown as Schema
+
   const hasMotifVideos = project.workflow.motif_videos_created
 
   if (!hasMotifVideos) return (
@@ -33,15 +38,15 @@ const MotifVideos = ({
         content={blockTooltip}
         placement="bottom"
         hideOnClick={false}
-        onShow={() => !blockSubmission as false}
+        disabled={!blockSubmission || !blockTooltip}
       >
         <span>
-          <Button
-            disabled={blockSubmission}
-            onClick={() => onFormSubmit({})}
-          >
-            Generate Motif Videos
-          </Button>
+          <DynamicForm
+            schema={schema}
+            blockSubmission={blockSubmission}
+            submitText={"Generate Motif Videos"}
+            onFormSubmit={onFormSubmit}
+          />
         </span>
       </Tippy>
     </PaddedTab>
diff --git a/src/renderer/src/pages/Project/Tabs/Organize.tsx b/src/renderer/src/pages/Project/Tabs/Organize.tsx
index 1e37761..1b74957 100644
--- a/src/renderer/src/pages/Project/Tabs/Organize.tsx
+++ b/src/renderer/src/pages/Project/Tabs/Organize.tsx
@@ -68,7 +68,7 @@ const Organize = ({
         content={blockTooltip}
         placement="bottom"
         hideOnClick={false}
-        onShow={() => !blockSubmission as false}
+        disabled={!blockSubmission || !blockTooltip}
       >
         <>
           <DynamicForm
diff --git a/src/renderer/src/pages/Project/Tabs/ProjectConfiguration.tsx b/src/renderer/src/pages/Project/Tabs/ProjectConfiguration.tsx
index 9f71060..80bf2c5 100644
--- a/src/renderer/src/pages/Project/Tabs/ProjectConfiguration.tsx
+++ b/src/renderer/src/pages/Project/Tabs/ProjectConfiguration.tsx
@@ -55,7 +55,7 @@ const ProjectConfiguration = ({
         content={blockTooltip}
         placement="bottom"
         hideOnClick={false}
-        onShow={() => !blockSubmission as false}
+        disabled={!blockSubmission || !blockTooltip}
       >
         <>
           <DynamicForm
diff --git a/src/renderer/src/pages/Project/Tabs/Segmentation.tsx b/src/renderer/src/pages/Project/Tabs/Segmentation.tsx
index 5204075..205a0ad 100644
--- a/src/renderer/src/pages/Project/Tabs/Segmentation.tsx
+++ b/src/renderer/src/pages/Project/Tabs/Segmentation.tsx
@@ -48,7 +48,7 @@ const Segmentation = ({
             content={blockTooltip}
             placement="bottom"
             hideOnClick={false}
-            onShow={() => !blockSubmission as false}
+            disabled={!blockSubmission || !blockTooltip}
           >
             <span>
               <Button
diff --git a/src/renderer/src/pages/Project/Tabs/UMAPVisualization.tsx b/src/renderer/src/pages/Project/Tabs/UMAPVisualization.tsx
index 85d0ba3..7ed37b9 100644
--- a/src/renderer/src/pages/Project/Tabs/UMAPVisualization.tsx
+++ b/src/renderer/src/pages/Project/Tabs/UMAPVisualization.tsx
@@ -11,6 +11,9 @@ import { faTerminal } from "@fortawesome/free-solid-svg-icons"
 import { useProjects } from "@renderer/context/Projects"
 import Tippy from "@tippyjs/react"
 
+import UMAPSchema from "../../../../../schema/umap.schema.json"
+import DynamicForm from "@renderer/components/DynamicForm"
+
 const FlexGrid = styled.div`
     display: flex;
     flex-wrap: wrap;
@@ -37,6 +40,8 @@ const UMAPVisualization = ({
   const hasUmaps = project.workflow.umaps_created
   const [terminal, setTerminal] = useState(false)
 
+  const schema = structuredClone(UMAPSchema) as unknown as Schema
+
   const { getAssetsPath } = useProjects()
 
   const images = useMemo(() => {
@@ -94,12 +99,12 @@ const UMAPVisualization = ({
         disabled={!blockSubmission}
       >
         <span>
-          <Button
-            disabled={blockSubmission}
-            onClick={() => onFormSubmit({ evaluate: true })}
-          >
-            Create UMAP Visualization
-          </Button>
+          <DynamicForm
+            schema={schema}
+            blockSubmission={blockSubmission}
+            submitText={"Create UMAP Visualization"}
+            onFormSubmit={onFormSubmit}
+          />
         </span>
       </Tippy>
     </PaddedTab>
diff --git a/src/renderer/src/pages/Project/index.tsx b/src/renderer/src/pages/Project/index.tsx
index a3f6275..840c3b7 100644
--- a/src/renderer/src/pages/Project/index.tsx
+++ b/src/renderer/src/pages/Project/index.tsx
@@ -207,10 +207,11 @@ const Project: React.FC = () => {
         project={project}
         blockSubmission={blockSubmit}
         blockTooltip="Waiting VAME to be ready."
-        onFormSubmit={() => submitTab(async () => {
+        onFormSubmit={(data) => submitTab(async () => {
           const projectPath = project.config.project_path
           await createMotifVideos({
             project: projectPath,
+            ...data,
           })
         }, "motifs-videos")}
       />
@@ -232,7 +233,8 @@ const Project: React.FC = () => {
             project: projectPath,
             cohort: data.cohort,
             cut_tree: data.cut_tree,
-            show_umap: data.show_umap
+            show_umap: data.show_umap,
+            parametrization: data.parametrization,
           })
         }, "community-videos")}
       />
@@ -247,10 +249,11 @@ const Project: React.FC = () => {
         project={project}
         blockSubmission={blockSubmit}
         blockTooltip="Waiting VAME to be ready."
-        onFormSubmit={() => submitTab(async () => {
+        onFormSubmit={(data: any) => submitTab(async () => {
           const projectPath = project.config.project_path
           await createCommunityVideos({
             project: projectPath,
+            parametrization: data.parametrization, 
           })
         }, "community-videos")}
       />
@@ -265,10 +268,11 @@ const Project: React.FC = () => {
         project={project}
         blockSubmission={blockSubmit}
         blockTooltip="Waiting VAME to be ready."
-        onFormSubmit={() => submitTab(async () => {
+        onFormSubmit={(data) => submitTab(async () => {
           const projectPath = project.config.project_path
           await createUMAPVisualization({
             project: projectPath,
+            ...data
           })
         }, "umap-visualization")}
       />
diff --git a/src/renderer/src/utils/extractDefaultValues.ts b/src/renderer/src/utils/extractDefaultValues.ts
index 649da7d..c60f639 100644
--- a/src/renderer/src/utils/extractDefaultValues.ts
+++ b/src/renderer/src/utils/extractDefaultValues.ts
@@ -15,7 +15,7 @@ export function extractDefaultValues(schema: Schema): Record<string, any> {
     }
   };
 
-  if (schema.properties) {
+  if (schema?.properties) {
     extractDefaults(schema.properties);
   }
 
diff --git a/src/schema/community-videos.schema.json b/src/schema/community-videos.schema.json
new file mode 100644
index 0000000..ed43f24
--- /dev/null
+++ b/src/schema/community-videos.schema.json
@@ -0,0 +1,13 @@
+{
+    "title": "Community Videos",
+    "type": "object",
+    "properties": {
+        "parametrization": {
+            "type": "string",
+            "enum": ["hmm", "kmeans"]
+        }
+    },
+    "required": [
+        "parametrization"
+    ]
+}
\ No newline at end of file
diff --git a/src/schema/community.schema.json b/src/schema/community.schema.json
index 622c36e..92d96a4 100644
--- a/src/schema/community.schema.json
+++ b/src/schema/community.schema.json
@@ -12,9 +12,14 @@
             "title": "Cut Line for Tree",
             "description": "Cut line for tree.",
             "default": 2
+        },
+        "parametrization": {
+            "type": "string",
+            "enum": ["hmm", "kmeans"]
         }
     },
     "required": [
+        "parametrization",
         "cohort",
         "cut_tree"
     ]
diff --git a/src/schema/config.schema.json b/src/schema/config.schema.json
index 4741001..a9c93e3 100644
--- a/src/schema/config.schema.json
+++ b/src/schema/config.schema.json
@@ -39,9 +39,12 @@
       "type": "integer",
       "description": "Please set to 1/2 of video fps. Value should be even, round up if needed"
     },
-    "parametrization": {
+    "parametrizations":{
+      "description": "Hold down the Ctrl (windows) or Command (Mac) button to select multiple options.",
       "type": "string",
-      "description": "Motif clustering method"
+      "multiple": true,
+      "enum": ["hmm","kmeans"],
+      "default": ["hmm","kmeans"]
     },
     "max_epochs": {
       "type": "integer",
@@ -205,7 +208,7 @@
     "time_window",
     "max_epochs",
     "zdims",
-    "parametrization",
+    "parametrizations",
     "advanced_options"
   ]
 }
\ No newline at end of file
diff --git a/src/schema/motif-videos.schema.json b/src/schema/motif-videos.schema.json
new file mode 100644
index 0000000..57fc315
--- /dev/null
+++ b/src/schema/motif-videos.schema.json
@@ -0,0 +1,13 @@
+{
+    "title": "Motifs Videos",
+    "type": "object",
+    "properties": {
+        "parametrization": {
+            "type": "string",
+            "enum": ["hmm", "kmeans"]
+        }
+    },
+    "required": [
+        "parametrization"
+    ]
+}
\ No newline at end of file
diff --git a/src/schema/umap.schema.json b/src/schema/umap.schema.json
new file mode 100644
index 0000000..a568d4f
--- /dev/null
+++ b/src/schema/umap.schema.json
@@ -0,0 +1,14 @@
+{
+  "title": "UMAP Visualization",
+  "type": "object",
+  "properties": {
+      "parametrization": {
+          "type": "string",
+          "enum": ["hmm", "kmeans"],
+          "default": "hmm"
+      }
+  },
+  "required": [
+      "parametrization"
+  ]
+}
\ No newline at end of file

From f97aa994b1e8c5819fbf6d26262f1d5ff5b8253b Mon Sep 17 00:00:00 2001
From: Nathan Vieira Marcelino <nathan.v.marcelino@gmail.com>
Date: Mon, 22 Jul 2024 08:52:24 -0300
Subject: [PATCH 2/6] feat: use vame from dev

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 68538fd..b2486f8 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,4 +4,4 @@ flask-restx==1.3.0
 numpy==1.26.4
 pyinstaller==6.8.0
 pyinstaller-hooks-contrib==2024.6
-vame-py==0.3.1
+vame-py@git+https://github.com/EthoML/VAME.git@dev

From b9acda6220f16b7f017845a88844b296b6d52f40 Mon Sep 17 00:00:00 2001
From: Nathan Vieira Marcelino <nathan.v.marcelino@gmail.com>
Date: Mon, 22 Jul 2024 08:53:00 -0300
Subject: [PATCH 3/6] update version

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

diff --git a/package.json b/package.json
index 94b990d..2d420d6 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "vame-desktop",
   "main": "./out/main/index.js",
-  "version": "0.2.0",
+  "version": "0.3.0",
   "description": "An open-source machine learning tool for behavioral segmentation and analyses.",
   "license": "GPL-3.0-only",
   "author": "Catalyst Neuro <hello@catalystneuro.com>, Nathan Vieira <nathan.v.marcelino@gmail.com>, Garrett Flynn <garrettmflynn@gmail.com>",

From 9c7aae6202f0f981671ef2aa04957805ecb411fa Mon Sep 17 00:00:00 2001
From: Nathan Vieira Marcelino <nathan.v.marcelino@gmail.com>
Date: Thu, 25 Jul 2024 23:03:52 -0300
Subject: [PATCH 4/6] fix kmeans and hmm showing

---
 main.spec                                     |   2 +-
 package-lock.json                             |   4 +-
 requirements.txt                              |   2 +-
 src/main/index.ts                             |   6 +-
 src/main/process/runChildProcess.ts           |   6 +-
 src/renderer/src/@types/index.d.ts            |  15 +-
 .../pages/Project/Tabs/CommunityVideos.tsx    |  65 ++----
 .../src/pages/Project/Tabs/MotifVideos.tsx    |  49 ++---
 .../pages/Project/Tabs/UMAPVisualization.tsx  |  53 ++---
 src/services/vameApi/app/__init__.py          |  38 ++++
 src/services/vameApi/app/config.py            |   7 +
 src/services/vameApi/app/routes/__init__.py   |  14 ++
 src/services/vameApi/app/routes/file.py       |  36 ++++
 .../vameApi/app/routes/health_check.py        |  13 ++
 src/services/vameApi/app/routes/project.py    |  94 ++++++++
 src/services/vameApi/app/routes/vame.py       | 201 ++++++++++++++++++
 src/services/vameApi/app/services/__init__.py |   0
 .../vameApi/app/services/file_service.py      |  15 ++
 .../vameApi/app/services/project_service.py   | 184 ++++++++++++++++
 .../vameApi/app/services/vame_service.py      |   1 +
 src/services/vameApi/app/utils/__init__.py    |   0
 src/services/vameApi/app/utils/get_assets.py  |  76 +++++++
 src/services/vameApi/app/utils/get_files.py   |   8 +
 .../utils/get_pose_ref_index_description.py   |  22 ++
 .../vameApi/app/utils/get_project_path.py     |  21 ++
 .../app/utils/not_bad_request_exception.py    |   5 +
 .../vameApi/app/utils/resolve_request_util.py |   8 +
 src/services/vameApi/main.py                  |  38 ++++
 28 files changed, 859 insertions(+), 124 deletions(-)
 create mode 100644 src/services/vameApi/app/__init__.py
 create mode 100644 src/services/vameApi/app/config.py
 create mode 100644 src/services/vameApi/app/routes/__init__.py
 create mode 100644 src/services/vameApi/app/routes/file.py
 create mode 100644 src/services/vameApi/app/routes/health_check.py
 create mode 100644 src/services/vameApi/app/routes/project.py
 create mode 100644 src/services/vameApi/app/routes/vame.py
 create mode 100644 src/services/vameApi/app/services/__init__.py
 create mode 100644 src/services/vameApi/app/services/file_service.py
 create mode 100644 src/services/vameApi/app/services/project_service.py
 create mode 100644 src/services/vameApi/app/services/vame_service.py
 create mode 100644 src/services/vameApi/app/utils/__init__.py
 create mode 100644 src/services/vameApi/app/utils/get_assets.py
 create mode 100644 src/services/vameApi/app/utils/get_files.py
 create mode 100644 src/services/vameApi/app/utils/get_pose_ref_index_description.py
 create mode 100644 src/services/vameApi/app/utils/get_project_path.py
 create mode 100644 src/services/vameApi/app/utils/not_bad_request_exception.py
 create mode 100644 src/services/vameApi/app/utils/resolve_request_util.py
 create mode 100644 src/services/vameApi/main.py

diff --git a/main.spec b/main.spec
index d3aac15..cfb7eb2 100644
--- a/main.spec
+++ b/main.spec
@@ -9,7 +9,7 @@ datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
 
 
 a = Analysis(
-    ['src/services/main.py'],
+    ['src/services/vameApi/main.py'],
     pathex=[],
     binaries=binaries,
     datas=datas,
diff --git a/package-lock.json b/package-lock.json
index a6953c9..31e3fc3 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "vame-desktop",
-  "version": "0.2.0",
+  "version": "0.3.0",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "vame-desktop",
-      "version": "0.2.0",
+      "version": "0.3.0",
       "hasInstallScript": true,
       "license": "GPL-3.0-only",
       "dependencies": {
diff --git a/requirements.txt b/requirements.txt
index b2486f8..ae02b9f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,4 +4,4 @@ flask-restx==1.3.0
 numpy==1.26.4
 pyinstaller==6.8.0
 pyinstaller-hooks-contrib==2024.6
-vame-py@git+https://github.com/EthoML/VAME.git@dev
+vame-py==0.4.0
diff --git a/src/main/index.ts b/src/main/index.ts
index 5e6f798..859c3a5 100644
--- a/src/main/index.ts
+++ b/src/main/index.ts
@@ -48,7 +48,7 @@ app.whenReady().then(() => {
   folderHandler()
 
   if (is.dev) {
-    backend = runChildProcess("python", [join(__dirname, "..", "..", "src", "services", "main.py")])
+    backend = runChildProcess("python", [join(__dirname, "..", "..", "src", "services", "vameApi", "main.py")])
 
     backend?.stdout.on("data", (data) => {
       if (data?.toString().includes("Flask server started at")) {
@@ -89,10 +89,6 @@ app.on("window-all-closed", () => {
 app.on("before-quit", (event) => {
   if (backend && backend.exitCode === null) {
     event.preventDefault(); // Prevent the default behavior of quitting immediately
-    backend.once("exit", (code) => {
-      console.log(`[electron]: Process exited with code ${code}`)
-      app.exit(code ?? 0); // Quit the app after the child process exits
-    });
     backend.kill("SIGTERM"); // Send SIGTERM to the child process
   } else if (backend && backend.exitCode !== null) {
     console.log(`[electron]: Process exited with code ${backend.exitCode}`)
diff --git a/src/main/process/runChildProcess.ts b/src/main/process/runChildProcess.ts
index 8611731..31bdead 100644
--- a/src/main/process/runChildProcess.ts
+++ b/src/main/process/runChildProcess.ts
@@ -1,3 +1,4 @@
+import { app } from "electron";
 
 export function runChildProcess(exec: string, path?: string[]) {
   let stdoutChunks = [], stderrChunks = [];
@@ -9,9 +10,10 @@ export function runChildProcess(exec: string, path?: string[]) {
     }
   });
 
-  child.on('exit', (code) =>
+  child.on('exit', (code) => {
     console.log(`[${exec}]: Process exited with code ${code}`)
-  );
+    app.exit(code ?? -1)
+  });
 
   child.stdout.on('data', (data) => {
     console.log(`[${exec}]:`, data.toString());
diff --git a/src/renderer/src/@types/index.d.ts b/src/renderer/src/@types/index.d.ts
index e5c4554..b3b8151 100644
--- a/src/renderer/src/@types/index.d.ts
+++ b/src/renderer/src/@types/index.d.ts
@@ -137,11 +137,20 @@ declare global {
     assets: {
       images: {
         evaluation: string[];
-        visualization: Record<string,string[]>;
+        visualization: {
+          hmm: Record<string,string[]>,
+          kmeans: Record<string,string[]>
+        };
       };
       videos: {
-        community: Record<string,string[]>;
-        motif: Record<string,string[]>;
+        community: {
+          hmm: Record<string,string[]>,
+          kmeans: Record<string,string[]>
+        };
+        motif: {
+          hmm: Record<string,string[]>,
+          kmeans: Record<string,string[]>
+        };
       };
     };
     created_at: string;
diff --git a/src/renderer/src/pages/Project/Tabs/CommunityVideos.tsx b/src/renderer/src/pages/Project/Tabs/CommunityVideos.tsx
index c978660..f84609f 100644
--- a/src/renderer/src/pages/Project/Tabs/CommunityVideos.tsx
+++ b/src/renderer/src/pages/Project/Tabs/CommunityVideos.tsx
@@ -22,52 +22,18 @@ const CommunityVideos = ({
 
   const schema = structuredClone(CommunityVideosSchema) as unknown as Schema
 
-  const hasCommunityVideos = project.workflow.community_videos_created
-
-  if (!hasCommunityVideos) return (
-    <PaddedTab>
-      <span>
-        Open logs:{" "}
-        <ControlButton onClick={() => setTerminal(true)}>
-          <FontAwesomeIcon icon={faTerminal} />
-        </ControlButton>
-      </span>
-
-      <TerminalModal
-        projectPath={project.config.project_path}
-        logName={["community_videos"]}
-        isOpen={terminal}
-        onClose={() => setTerminal(false)}
-      />
-
-      <Tippy
-        content={blockTooltip}
-        placement="bottom"
-        hideOnClick={false}
-        disabled={!blockSubmission}
-      >
-        <span>
-          <DynamicForm
-            schema={schema}
-            blockSubmission={blockSubmission}
-            submitText={"Create Community Videos"}
-            onFormSubmit={onFormSubmit}
-          />
-        </span>
-      </Tippy>
-    </PaddedTab>
-  )
-
-
   const { videos } = project.assets
 
   const communityVideos = videos?.community ?? {}
 
-  const organizedVideos = Object.entries(communityVideos).reduce((acc, [label, videos]) => {
-    acc[label] = videos.map((videoPath: string) => {
-      const number = videoPath.split('-').pop()?.split('_').pop()?.split('.')[0]
-      return { path: videoPath, label: `Community ${number}`, idx: Number(number) }
-    }).sort((a, b) => a.idx - b.idx)
+  const organizedVideos = Object.entries(communityVideos).reduce((acc, [label, videosObj]) => {
+    Object.entries(videosObj).forEach(([parametrization, videos]) => {
+
+      acc[`${label}-${parametrization}`] = videos.map((videoPath: string) => {
+        const number = videoPath.split('-').pop()?.split('_').pop()?.split('.')[0]
+        return { path: videoPath, label: `Community ${number}`, idx: Number(number) }
+      }).sort((a, b) => a.idx - b.idx)
+    })
 
     return acc
   }, {} as Record<string, VideoType[]>)
@@ -81,6 +47,21 @@ const CommunityVideos = ({
       </ControlButton>
     </span>
 
+    <Tippy
+      content={blockTooltip}
+      placement="bottom"
+      hideOnClick={false}
+      disabled={!blockSubmission}
+    >
+      <span>
+        <DynamicForm
+          schema={schema}
+          blockSubmission={blockSubmission}
+          submitText={"Create Community Videos"}
+          onFormSubmit={onFormSubmit}
+        />
+      </span>
+    </Tippy>
 
     <TerminalModal
       projectPath={project.config.project_path}
diff --git a/src/renderer/src/pages/Project/Tabs/MotifVideos.tsx b/src/renderer/src/pages/Project/Tabs/MotifVideos.tsx
index 0670b01..eefef7f 100644
--- a/src/renderer/src/pages/Project/Tabs/MotifVideos.tsx
+++ b/src/renderer/src/pages/Project/Tabs/MotifVideos.tsx
@@ -22,10 +22,23 @@ const MotifVideos = ({
 
   const schema = structuredClone(motifVideosSchema) as unknown as Schema
 
-  const hasMotifVideos = project.workflow.motif_videos_created
+  const { videos } = project.assets
+  const motifVideos = videos?.motif ?? {}
+
+  const organizedVideos = Object.entries(motifVideos).reduce((acc, [videoLabel, videosObj]) => {
+    Object.entries(videosObj).forEach(([parametrization,videos])=>{
+      acc[`${videoLabel}-${parametrization}`] = videos.map((videoPath: string) => {
+        const num = videoPath.split("-").pop()?.split("_").pop()?.split(".")[0]!
+        
+        return { path: videoPath, label: `Motif ${num}`, idx: Number(num) }
+      }).sort((a, b) => a.idx - b.idx)
+      
+    })
+    return acc
+  }, {} as Record<string, VideoType[]>)
 
-  if (!hasMotifVideos) return (
-    <PaddedTab>
+
+  return <PaddedTab>
       <span>
         Open logs:{" "}
         <ControlButton onClick={() => setTerminal(true)}>
@@ -49,37 +62,7 @@ const MotifVideos = ({
           />
         </span>
       </Tippy>
-    </PaddedTab>
-  )
-
-  const { videos } = project.assets
-  const motifVideos = videos?.motif ?? {}
 
-  const organizedVideos = Object.entries(motifVideos).reduce((acc, [label, videos]) => {
-    acc[label] = videos.map((videoPath: string) => {
-      const num = videoPath.split("-").pop()?.split("_").pop()?.split(".")[0]!
-
-      return { path: videoPath, label: `Motif ${num}`, idx: Number(num) }
-    }).sort((a, b) => a.idx - b.idx)
-
-    return acc
-  }, {} as Record<string, VideoType[]>)
-
-
-  return <PaddedTab>
-    <span>
-      Open logs:{" "}
-      <ControlButton onClick={() => setTerminal(true)}>
-        <FontAwesomeIcon icon={faTerminal} />
-      </ControlButton>
-    </span>
-
-    <TerminalModal
-      projectPath={project.config.project_path}
-      logName={["motif_videos"]}
-      isOpen={terminal}
-      onClose={() => setTerminal(false)}
-    />
 
     <VideoGrid
       videos={organizedVideos}
diff --git a/src/renderer/src/pages/Project/Tabs/UMAPVisualization.tsx b/src/renderer/src/pages/Project/Tabs/UMAPVisualization.tsx
index 7ed37b9..64dbd2d 100644
--- a/src/renderer/src/pages/Project/Tabs/UMAPVisualization.tsx
+++ b/src/renderer/src/pages/Project/Tabs/UMAPVisualization.tsx
@@ -4,7 +4,6 @@ import { header } from "../../../utils/text"
 import TerminalModal from "../../../components/TerminalModal"
 import { useMemo, useState } from "react"
 import { PaddedTab } from "@renderer/components/Tabs/styles"
-import { Button } from "@renderer/components/DynamicForm/styles"
 import { ControlButton } from "@renderer/pages/Home/styles"
 import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"
 import { faTerminal } from "@fortawesome/free-solid-svg-icons"
@@ -37,7 +36,6 @@ const UMAPVisualization = ({
   blockSubmission,
   blockTooltip,
 }: TabProps) => {
-  const hasUmaps = project.workflow.umaps_created
   const [terminal, setTerminal] = useState(false)
 
   const schema = structuredClone(UMAPSchema) as unknown as Schema
@@ -45,41 +43,22 @@ const UMAPVisualization = ({
   const { getAssetsPath } = useProjects()
 
   const images = useMemo(() => {
-    return Object.entries(project.assets.images.visualization).map(([video_set, images]) => (
-      images.map((umapPath) => {
-        const label = umapPath.split('umap_vis_label_')[1].split(`_${video_set}`)[0]
-        const uniqueKey = `${video_set}_${label}`
-
-        return (
-          <ImageContainer key={uniqueKey}>
-            <img src={getAssetsPath(project.config.project_path, umapPath)} alt={uniqueKey} />
-            <small><b>{video_set}:</b> {header(label)}</small>
-          </ImageContainer>
-        )
-      })
-    )).flat(1);
+    return Object.entries(project.assets.images.visualization).map(([video_set, imagesObj]) => (
+      Object.entries(imagesObj).flatMap(([p, images]) =>
+        images.map((umapPath) => {
+          const label = umapPath.split('umap_vis_label_')[1].split(`_${video_set}`)[0]
+          const uniqueKey = `${video_set}_${label}`
+
+          return (
+            <ImageContainer key={uniqueKey}>
+              <img src={getAssetsPath(project.config.project_path, umapPath)} alt={uniqueKey} />
+              <small><b>{video_set}:</b> {header(label)}</small>
+            </ImageContainer>
+          )
+        })
+      ))).flat(1);
   }, [project])
 
-  if (hasUmaps) {
-    return (
-      <PaddedTab>
-        <span>
-          Open logs:{" "}
-          <ControlButton onClick={() => setTerminal(true)}>
-            <FontAwesomeIcon icon={faTerminal} />
-          </ControlButton>
-        </span>
-
-        <TerminalModal projectPath={project.config.project_path} logName={["visualization"]} isOpen={terminal} onClose={() => setTerminal(false)} />
-
-        <FlexGrid>
-          {images}
-        </FlexGrid>
-      </PaddedTab>
-    )
-  }
-
-
   return (
     <PaddedTab>
       <span>
@@ -107,6 +86,10 @@ const UMAPVisualization = ({
           />
         </span>
       </Tippy>
+
+      <FlexGrid>
+        {images}
+      </FlexGrid>
     </PaddedTab>
   )
 }
diff --git a/src/services/vameApi/app/__init__.py b/src/services/vameApi/app/__init__.py
new file mode 100644
index 0000000..b303d27
--- /dev/null
+++ b/src/services/vameApi/app/__init__.py
@@ -0,0 +1,38 @@
+from flask import Flask
+from flask_cors import CORS
+from flask_restx import Api
+from logging.config import dictConfig
+
+def create_app():
+    app = Flask("VAME API")
+    CORS(app)
+    app.config['CORS_HEADERS'] = 'Content-Type'
+
+    dictConfig({
+        'version': 1,
+        'formatters': {'default': {
+            'format': '%(message)s',
+        }},
+        'handlers': {'wsgi': {
+            'class': 'logging.StreamHandler',
+            'stream': 'ext://sys.stdout',
+            'formatter': 'default'
+        }},
+        'root': {
+            'level': 'INFO',
+            'handlers': ['wsgi']
+        }
+    })
+  
+    api = Api(app, version='2.0', title='VAME API', description="The REST API for VAME.")
+
+    from app.routes import project, file, health_check, vame
+
+    api.add_namespace(health_check.api)
+    api.add_namespace(file.api)
+    api.add_namespace(project.api)
+    api.add_namespace(vame.api)
+
+    return app
+
+
diff --git a/src/services/vameApi/app/config.py b/src/services/vameApi/app/config.py
new file mode 100644
index 0000000..d61a220
--- /dev/null
+++ b/src/services/vameApi/app/config.py
@@ -0,0 +1,7 @@
+from pathlib import Path
+
+VAME_APP_DIRECTORY = Path.home() / 'vame-desktop'
+VAME_PROJECTS_DIRECTORY = VAME_APP_DIRECTORY / 'projects'
+VAME_LOG_DIRECTORY = VAME_APP_DIRECTORY / 'logs'
+GLOBAL_SETTINGS_FILE = VAME_APP_DIRECTORY / 'settings.json'
+GLOBAL_STATES_FILE = VAME_APP_DIRECTORY / 'states.json'
diff --git a/src/services/vameApi/app/routes/__init__.py b/src/services/vameApi/app/routes/__init__.py
new file mode 100644
index 0000000..abcf2e7
--- /dev/null
+++ b/src/services/vameApi/app/routes/__init__.py
@@ -0,0 +1,14 @@
+from flask_restx import Namespace
+import traceback
+from flask import jsonify
+
+api = Namespace('/', description='Main API Namespace')
+
+@api.errorhandler(Exception)
+def exception_handler(error):
+    exception_data = traceback.format_exception(type(error), error, error.__traceback__)
+    response = {
+        "message": exception_data[-1].strip(),
+        "traceback": "".join(exception_data)
+    }
+    return jsonify(response), 500
\ No newline at end of file
diff --git a/src/services/vameApi/app/routes/file.py b/src/services/vameApi/app/routes/file.py
new file mode 100644
index 0000000..a5ac211
--- /dev/null
+++ b/src/services/vameApi/app/routes/file.py
@@ -0,0 +1,36 @@
+from flask_restx import Resource
+from flask import send_from_directory, request
+from app.routes import api
+from app.services.file_service import check_file_exists, log_file
+from app.config import VAME_PROJECTS_DIRECTORY
+from pathlib import Path
+
+@api.route('/files/<path:project>/<path:path>')
+class Files(Resource):
+    def get(self, project, path):
+        return send_from_directory(VAME_PROJECTS_DIRECTORY, Path(project) / path)
+
+@api.route('/exists/<path:project>/<path:path>')
+class FileExists(Resource):
+    def get(self, project, path):
+        return check_file_exists(Path(project), path)
+
+@api.route('/log/<path:log_name>')
+class ProjectLog(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request",404: "Not found", 500: "Internal server error"})
+    def get(self, log_name):
+
+        project_path = request.args.get('project')
+        project_path = Path(project_path)
+
+        try:
+            if(log_name):
+                return log_file(project_path, log_name)
+            else:
+                return "missing log_name", 400
+        except:
+                return f"{log_name} log not found.", 404
+
+        
+
+# Add other file-related routes here
diff --git a/src/services/vameApi/app/routes/health_check.py b/src/services/vameApi/app/routes/health_check.py
new file mode 100644
index 0000000..23cdc35
--- /dev/null
+++ b/src/services/vameApi/app/routes/health_check.py
@@ -0,0 +1,13 @@
+from flask_restx import Resource
+from . import api
+
+@api.route('/connected')
+class Connected(Resource):
+    def get(self):
+        return {"payload": True}
+
+@api.route('/ready')
+class VAMEReady(Resource):
+    def get(self):
+        import vame
+        return {"payload": True}
diff --git a/src/services/vameApi/app/routes/project.py b/src/services/vameApi/app/routes/project.py
new file mode 100644
index 0000000..9932255
--- /dev/null
+++ b/src/services/vameApi/app/routes/project.py
@@ -0,0 +1,94 @@
+from flask_restx import Resource
+from flask import request, jsonify
+from pathlib import Path
+import json
+from . import api
+from app.utils.resolve_request_util import resolve_request_data
+from app.services.project_service import get_projects, get_recent_projects, is_project_ready, register_recent_projetc, load_project, create_project,delete_project, configure_project
+
+from app.utils.not_bad_request_exception import not_bad_request_exception
+
+@api.route('/projects')
+class Projects(Resource):
+    def get(self):
+        projects = get_projects()
+        return jsonify(projects)
+    
+@api.route('/projects/recent')
+class RecentProjects(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def get(self):
+        recent_projects = get_recent_projects()
+        return jsonify(recent_projects)
+
+@api.route('/project_ready')
+class ProjectReady(Resource):
+    def post(self):
+        _, project_path = resolve_request_data(request)
+        return jsonify(is_project_ready(project_path))
+    
+@api.route('/project/register')
+class RegisterProject(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        try:
+            _, project_path = resolve_request_data(request)
+            return register_recent_projetc(project_path)
+
+        except Exception as exception:
+            # TODO: Should lock access to the file
+            pass
+
+@api.route('/create', methods=['POST'])
+class Create(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        try:
+            data = json.loads(request.data) if request.data else {}
+
+            project = create_project(data)
+
+            return jsonify(project)
+
+        except Exception as exception:
+            print("exception", exception)
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+@api.route('/delete_project', methods=['POST'])
+class DeleteProject(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        try:
+            _, project_path = resolve_request_data(request)
+            res = delete_project(project_path)
+            return jsonify(res)
+
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+
+@api.route('/configure', methods=['POST'])
+class ConfigureProject(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        try:
+            data, project_path = resolve_request_data(request)
+            configuration = configure_project(data, project_path)
+
+            return jsonify(configuration)
+
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+    
+@api.route('/load')
+class Load(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        _, project_path = resolve_request_data(request)
+
+        loaded_project = load_project(Path(project_path))
+        return jsonify(loaded_project)
\ No newline at end of file
diff --git a/src/services/vameApi/app/routes/vame.py b/src/services/vameApi/app/routes/vame.py
new file mode 100644
index 0000000..81a8aef
--- /dev/null
+++ b/src/services/vameApi/app/routes/vame.py
@@ -0,0 +1,201 @@
+from flask_restx import Resource
+from flask import request, jsonify
+from pathlib import Path
+from . import api
+from app.utils.resolve_request_util import resolve_request_data
+from app.utils.get_assets import get_evaluation_images, get_visualization_images
+from app.utils.not_bad_request_exception import not_bad_request_exception
+
+@api.route('/align', methods=['POST'])
+class Align(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        try:
+
+            data, project_path = resolve_request_data(request)
+
+            # If your experiment is by design egocentrical (e.g. head-fixed experiment on treadmill etc)
+            # you can use the following to convert your .csv to a .npy array, ready to train vame on it
+            egocentric_data = data.pop('egocentric_data', None)
+
+
+            if egocentric_data:
+                vame.csv_to_numpy(
+                    project_path / 'config.yaml',
+                    save_logs=True
+                )
+
+            else:
+                vame.egocentric_alignment(
+                    **data,
+                    save_logs=True
+                )
+
+
+            return jsonify(dict(result='success'))
+
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+
+@api.route("/create_trainset")
+class CreateTrainset(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        try:
+            data, project_path = resolve_request_data(request)
+
+            result = vame.create_trainset(
+                **data,
+                save_logs=True
+            )
+
+            return dict(result=result)
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+@api.route('/train', methods=['POST'])
+class TrainModel(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        try:
+            data, project_path = resolve_request_data(request)
+
+            result = vame.train_model(
+                **data,
+                save_logs=True
+            )
+
+            return dict(result=result)
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+@api.route('/evaluate', methods=['POST'])
+class EvaluateModel(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        import matplotlib
+        matplotlib.use('agg')
+        try:
+            data, project_path = resolve_request_data(request)
+            vame.evaluate_model(
+                **data,
+                save_logs=True
+            )
+            return dict(result=get_evaluation_images(project_path))
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+@api.route('/segment', methods=['POST'])
+class Segment(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        try:
+            data, project_path = resolve_request_data(request)
+            result = vame.pose_segmentation(
+                **data,
+                save_logs=True
+            )
+            return dict(result=result)
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+@api.route('/motif_videos', methods=['POST'])
+class MotifVideos(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        try:
+            data, project_path = resolve_request_data(request)
+            result = vame.motif_videos(
+                **data,
+                save_logs=True
+            )
+            return dict(result=result)
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+@api.route('/community', methods=['POST'])
+class Community(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        try:
+            data, project_path = resolve_request_data(request)
+            result = vame.community(
+                **data,
+                save_logs=True
+            )
+            return dict(result=result)
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+@api.route('/community_videos', methods=['POST'])
+class CommunityVideos(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        try:
+            data, project_path = resolve_request_data(request)
+            result = vame.community_videos(
+                **data,
+                save_logs=True
+            )
+            return dict(result=result)
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+@api.route('/visualization', methods=['POST'])
+class Visualization(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        try:
+            data, project_path = resolve_request_data(request)
+            vame.visualization(
+                **data,
+                save_logs=True
+            )
+            return dict(result=get_visualization_images(project_path))
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+@api.route('/generative_model', methods=['POST'])
+class GenerativeModel(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        try:
+            data, project_path = resolve_request_data(request)
+            result = vame.generative_model(**data)
+            return dict(result=result)
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
+
+@api.route('/gif', methods=['POST'])
+class CreateGif(Resource):
+    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        import vame
+        try:
+            data, project_path = resolve_request_data(request)
+            result = vame.gif(**data)
+            return dict(result=result)
+        except Exception as exception:
+            if not_bad_request_exception(exception):
+                api.abort(500, str(exception))
diff --git a/src/services/vameApi/app/services/__init__.py b/src/services/vameApi/app/services/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/services/vameApi/app/services/file_service.py b/src/services/vameApi/app/services/file_service.py
new file mode 100644
index 0000000..226eadc
--- /dev/null
+++ b/src/services/vameApi/app/services/file_service.py
@@ -0,0 +1,15 @@
+from flask import jsonify
+from pathlib import Path
+from app.config import VAME_PROJECTS_DIRECTORY
+
+def check_file_exists(project: Path, path: str):
+  full_path = VAME_PROJECTS_DIRECTORY / project / path
+  return jsonify(dict(exists=full_path.exists()))
+
+def log_file(project: Path, log_name: str):
+  log_path = Path(project) / "logs" / f"{log_name}.log"
+  if log_path.is_file():
+    log = open(log_path, "r").read()
+    return log
+  else:
+    raise BaseException("Not found.")
\ No newline at end of file
diff --git a/src/services/vameApi/app/services/project_service.py b/src/services/vameApi/app/services/project_service.py
new file mode 100644
index 0000000..0b4e538
--- /dev/null
+++ b/src/services/vameApi/app/services/project_service.py
@@ -0,0 +1,184 @@
+import json
+import yaml
+import os
+from pathlib import Path
+
+from app.config import VAME_PROJECTS_DIRECTORY,GLOBAL_STATES_FILE
+
+from app.utils.get_files import get_files
+from app.utils.get_project_path import get_project_path
+from app.utils.get_assets import get_evaluation_images, get_visualization_images, get_motif_videos, get_community_videos, get_video_results_path
+from app.utils.get_pose_ref_index_description import get_pose_ref_index_description
+
+def get_projects():
+    projects = [str(project) for project in VAME_PROJECTS_DIRECTORY.glob('*') if project.is_dir()]
+    return projects
+
+def get_recent_projects():
+    with open(GLOBAL_STATES_FILE, "r") as inp:
+        states = json.load(fp=inp)
+    # states = json.loads(open(GLOBAL_STATES_FILE, "r").read())
+    recent_projects = states.get("recent_projects", [])
+
+    # Filter those that no longer exist
+    recent_projects = [ str(project) for project in recent_projects if (VAME_PROJECTS_DIRECTORY / project).exists() ]
+    states["recent_projects"] = recent_projects
+    with open(GLOBAL_STATES_FILE, "w") as file:
+        json.dump(states, file)
+
+    return recent_projects
+
+def is_project_ready(project_path: Path):
+  states_path = Path(project_path) / "states" / "states.json"
+
+  with open(states_path, "r") as file:
+      states = json.load(fp=file)
+
+  if states is None:
+      return dict(is_ready=True)
+
+  for _, value in states.items():
+      execution_state = value.get("execution_state", None)
+      if execution_state == "running":
+          return dict(is_ready=False)
+
+  return dict(is_ready=True)
+
+def register_recent_projetc(project_path: Path):
+    with open(GLOBAL_STATES_FILE, "r") as inp:
+        states = json.load(fp=inp)
+
+    recent_projects = states.get("recent_projects", [])
+
+    project_path = str(project_path)
+
+    if project_path in recent_projects:
+        recent_projects.remove(project_path)
+
+    recent_projects.append(project_path)
+
+    if len(recent_projects) > 5:
+        recent_projects = recent_projects[-5:]
+
+    with open(GLOBAL_STATES_FILE, "w") as file:
+        json.dump({
+            **states,
+            "recent_projects": recent_projects
+        }, file)
+
+    return recent_projects
+
+def create_project(data):
+    import vame
+    project_path = get_project_path(data["project"], VAME_PROJECTS_DIRECTORY)
+
+    created = not project_path.exists()
+
+    config_path = Path(vame.init_new_project(
+        working_directory=VAME_PROJECTS_DIRECTORY,
+        **data
+    ))
+
+    return dict(
+        project=str(config_path.parent),
+        created=created,
+        config=yaml.safe_load(open(config_path, "r"))
+    )
+
+def delete_project(project_path):
+    if project_path.exists():
+        import shutil
+        shutil.rmtree(project_path, ignore_errors=True)
+        return (dict(project=str(project_path), deleted=True))
+
+    return dict(project=str(project_path), deleted=False)
+
+def configure_project(data, project_path: Path):
+    from vame.util import auxiliary
+    config_path = project_path / "config.yaml"
+
+    if config_path.exists():
+        with open(config_path, "r") as file:
+            config = yaml.safe_load(file)
+            config_update = data["config"]
+
+            if config_update:
+                config.update(config_update)
+                auxiliary.write_config(config_path, config)
+
+            return dict(config=config)
+
+    return dict(config=None)
+
+def load_project(project_path: Path):
+    config_path = project_path / "config.yaml"
+
+    # Create a symlink to the project directory if it isn't in the VAME_PROJECTS_DIRECTORY
+    if project_path.parent != VAME_PROJECTS_DIRECTORY:
+        symlink = VAME_PROJECTS_DIRECTORY / project_path.name
+        if not symlink.exists():
+            symlink.symlink_to(project_path)
+
+    states_path = Path(project_path) / "states" / "states.json"
+
+    states = json.load(open(states_path)) if os.path.exists(states_path) else None
+
+    config = yaml.safe_load(open(config_path, "r")) if config_path.exists() else None
+
+    images = dict(
+        evaluation=get_evaluation_images(project_path),
+        visualization=dict(
+            hmm=get_visualization_images(project_path, 'hmm-15'),
+            kmeans=get_visualization_images(project_path, 'kmeans-15')
+        )
+    )
+
+    videos = dict(
+        motif=dict(
+            hmm=get_motif_videos(project_path, 'hmm-15'),
+            kmeans=get_motif_videos(project_path, 'kmeans-15')
+        ),
+        community=dict(
+            hmm=get_community_videos(project_path, 'hmm-15'),
+            kmeans=get_community_videos(project_path, 'kmeans-15')
+        )
+    )
+
+    has_latent_vector_files = False
+    if config:
+        has_latent_vector_files = all(map(lambda video: (get_video_results_path(video, project_path) / f"latent_vector_{video}.npy").exists(), config["video_sets"]))
+
+    has_communities = (project_path / 'cohort_community_label.npy').exists()
+
+    original_videos_location = project_path / 'videos'
+    original_csvs_location = original_videos_location / 'pose_estimation'
+
+    # Get all files in the original data directory
+    original_videos = list(map(lambda file: str(file), get_files(original_videos_location)))
+    original_csvs = list(map(lambda file: str(file), get_files(original_csvs_location)))
+
+    # Provide project workflow status
+    workflow = dict(
+        organized = (project_path / 'data' / 'train').exists(),
+        pose_ref_index_description=get_pose_ref_index_description(original_csvs[0]),
+        modeled = len(images["evaluation"]) > 0,
+        segmented = has_latent_vector_files,
+        motif_videos_created_hmm = all(map(lambda videos: len(videos) > 0, videos["motif"]["hmm"].values())),
+        motif_videos_created_kmeans = all(map(lambda videos: len(videos) > 0, videos["motif"]["kmeans"].values())),
+        communities_created = has_communities,
+        community_videos_created = all(map(lambda videos: len(videos) > 0, videos["community"].values())),
+        umaps_created = any(map(lambda videos: len(videos) > 0, images["visualization"].values())),
+    )
+
+    return dict(
+        project=str(config_path.parent),
+        config=config,
+        assets=dict(
+            images=images,
+            videos=videos
+        ),
+        videos=original_videos,
+        csvs=original_csvs,
+        workflow=workflow,
+        states=states
+    )
\ No newline at end of file
diff --git a/src/services/vameApi/app/services/vame_service.py b/src/services/vameApi/app/services/vame_service.py
new file mode 100644
index 0000000..27e7ac8
--- /dev/null
+++ b/src/services/vameApi/app/services/vame_service.py
@@ -0,0 +1 @@
+# TODO: Move vame business rules to this file.
\ No newline at end of file
diff --git a/src/services/vameApi/app/utils/__init__.py b/src/services/vameApi/app/utils/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/services/vameApi/app/utils/get_assets.py b/src/services/vameApi/app/utils/get_assets.py
new file mode 100644
index 0000000..c724767
--- /dev/null
+++ b/src/services/vameApi/app/utils/get_assets.py
@@ -0,0 +1,76 @@
+from pathlib import Path
+from typing import Union
+import yaml
+
+def get_evaluation_images(project_path: Path):
+    evaluation_output = project_path / 'model' / 'evaluate'
+    png_files = list(evaluation_output.glob('*.png'))
+    return [ str(png_file.relative_to(project_path)) for png_file in png_files ]
+
+def get_visualization_images(project_path, parametrization):
+    community_subfolders = get_video_related_asset(
+        project_path,
+        subpath=Path(parametrization) / 'community',
+        validate=True
+    )
+
+    visualization_images = dict()
+
+    for video_set, community_subfolder in community_subfolders.items():
+        if community_subfolder:
+            visualization_images[video_set] = [ str(image.relative_to(project_path)) for image in community_subfolder.glob('umap_*.png') ]
+        else:
+            visualization_images[video_set] = []
+
+
+    return visualization_images
+
+def get_video_related_asset(
+        project_path,
+        subpath: Union[str, callable],
+        return_path = True,
+        validate = False
+    ):
+
+    results_location = project_path / 'results'
+    config = yaml.safe_load(open(project_path / 'config.yaml', "r"))
+
+    video_sets = config["video_sets"]
+    model_name = config["model_name"]
+
+    video_related_assets = dict()
+
+    for video_set in video_sets:
+        video_set_subpath = subpath(video_set) if callable(subpath) else subpath
+        asset_path = results_location / video_set / model_name / video_set_subpath
+        video_related_assets[video_set] = asset_path if return_path else str(asset_path)
+        if validate and not asset_path.exists():
+            video_related_assets[video_set] = None
+
+    return video_related_assets
+
+def get_motif_videos(project_path, algorithm):
+    return get_videos(project_path, Path(algorithm) / 'cluster_videos')
+
+def get_community_videos(project_path, algorithm):
+    return get_videos(project_path, Path(algorithm) / 'community_videos')
+
+def get_videos(
+        project_path,
+        subfolder
+    ):
+
+    video_subfolders = get_video_related_asset(project_path, subfolder)
+
+    output_videos = dict()
+
+    for video_set, video_subfolder in video_subfolders.items():
+        if video_subfolder.exists():
+            output_videos[video_set] = [ str(video.relative_to(project_path)) for video in video_subfolder.glob('*.mp4') ]
+        else:
+            output_videos[video_set] = []
+
+    return output_videos
+
+def get_video_results_path(video, project_path):
+    return project_path / 'results' / video / "VAME" / 'hmm-15'
\ No newline at end of file
diff --git a/src/services/vameApi/app/utils/get_files.py b/src/services/vameApi/app/utils/get_files.py
new file mode 100644
index 0000000..c6b73e4
--- /dev/null
+++ b/src/services/vameApi/app/utils/get_files.py
@@ -0,0 +1,8 @@
+from pathlib import Path
+
+FILES_TO_IGNORE = [ '.DS_Store' ]
+
+def get_files(folder_to_search):
+    folder_to_search = Path(folder_to_search)
+    ignore_glob = set(FILES_TO_IGNORE)
+    return [ file for file in folder_to_search.glob('*') if file.is_file() and file.name not in ignore_glob ]
\ No newline at end of file
diff --git a/src/services/vameApi/app/utils/get_pose_ref_index_description.py b/src/services/vameApi/app/utils/get_pose_ref_index_description.py
new file mode 100644
index 0000000..79fbd35
--- /dev/null
+++ b/src/services/vameApi/app/utils/get_pose_ref_index_description.py
@@ -0,0 +1,22 @@
+import csv
+
+def get_pose_ref_index_description(csv_file_path: str) -> str:
+    with open(csv_file_path) as csv_file:
+        csv_reader = csv.reader(csv_file, delimiter=',')
+        body_parts = []
+
+        # loop to iterate through the rows of csv
+        for row in csv_reader:
+            if row[0] == "bodyparts":
+                body_parts = list(dict.fromkeys(row[1:]))  # Extract body parts starting from the second element and remove duplicates
+                break
+
+        if len(body_parts) == 0:
+            print("No body parts headers found in CSV.")
+            return ""
+
+        # Create the string based on body parts
+        body_parts_string = ", ".join([f"{i}-{part}" for i, part in enumerate(body_parts)])
+
+    return body_parts_string
+
diff --git a/src/services/vameApi/app/utils/get_project_path.py b/src/services/vameApi/app/utils/get_project_path.py
new file mode 100644
index 0000000..fca90dd
--- /dev/null
+++ b/src/services/vameApi/app/utils/get_project_path.py
@@ -0,0 +1,21 @@
+from datetime import datetime
+from pathlib import Path
+
+def get_project_path(
+        project: str,
+        working_directory: str = None
+    ):
+
+    date = datetime.today()
+    month = date.strftime("%B")
+    day = date.day
+    year = date.year
+    d = str(month[0:3]+str(day))
+    date = datetime.today().strftime('%Y-%m-%d')
+
+    if working_directory == None:
+        working_directory = '.'
+
+    wd = Path(working_directory).resolve()
+    project_name = '{pn}-{date}'.format(pn=project, date=d+'-'+str(year))
+    return wd / project_name
diff --git a/src/services/vameApi/app/utils/not_bad_request_exception.py b/src/services/vameApi/app/utils/not_bad_request_exception.py
new file mode 100644
index 0000000..c943c74
--- /dev/null
+++ b/src/services/vameApi/app/utils/not_bad_request_exception.py
@@ -0,0 +1,5 @@
+def not_bad_request_exception(exception):
+    """
+    Check if the exception is a generic exception.
+    """
+    return type(exception).__name__ not in ["BadRequest", "Forbidden", "Unauthorized"]
\ No newline at end of file
diff --git a/src/services/vameApi/app/utils/resolve_request_util.py b/src/services/vameApi/app/utils/resolve_request_util.py
new file mode 100644
index 0000000..d8da178
--- /dev/null
+++ b/src/services/vameApi/app/utils/resolve_request_util.py
@@ -0,0 +1,8 @@
+import json
+from pathlib import Path
+
+def resolve_request_data(request):
+    data = json.loads(request.data) if request.data else {}
+    project_path = Path(data.pop("project") if "project" in data else Path(data["config"].parent))
+    data["config"] = str(project_path / 'config.yaml') if "config" not in data else data["config"]
+    return data, project_path
diff --git a/src/services/vameApi/main.py b/src/services/vameApi/main.py
new file mode 100644
index 0000000..31afb01
--- /dev/null
+++ b/src/services/vameApi/main.py
@@ -0,0 +1,38 @@
+import json
+import os
+import signal
+
+from app.config import VAME_PROJECTS_DIRECTORY,VAME_LOG_DIRECTORY,GLOBAL_SETTINGS_FILE, GLOBAL_STATES_FILE
+
+from app import create_app
+
+def signal_handler(sig, frame):
+    print('Received SIGTERM, shutting down...')
+    os._exit(0)
+
+signal.signal(signal.SIGTERM, signal_handler)
+
+app = create_app()
+
+if __name__ == "__main__":
+    env_port = os.getenv('PORT')
+    PORT = int(env_port) if env_port else 8641
+    HOST = os.getenv('HOST') or 'localhost'
+
+    VAME_PROJECTS_DIRECTORY.mkdir(exist_ok=True, parents=True) # Create the VAME_PROJECTS_DIRECTORY if it doesn't exist
+    VAME_LOG_DIRECTORY.mkdir(exist_ok=True, parents=True)  # Create the VAME_LOG_DIRECTORY if it doesn't exist
+
+    # Create the global files if they don't exist
+    global_files = [GLOBAL_STATES_FILE, GLOBAL_SETTINGS_FILE]
+    for file in global_files:
+        if not file.exists():
+            with open(file, "w") as f:
+                json.dump({}, f)
+
+    try:
+        print(f"Flask server started at {HOST}:{PORT}")
+        app.run(host=HOST, port = PORT)
+
+    except Exception as e:
+        print(f"An error occurred that closed the server: {e}")
+        raise e

From 0cc4ff7f84df3778bde0209fb959f45f15740b9b Mon Sep 17 00:00:00 2001
From: Nathan Vieira Marcelino <nathan.v.marcelino@gmail.com>
Date: Fri, 26 Jul 2024 11:10:53 -0300
Subject: [PATCH 5/6] docs: how to download builded versions

---
 README.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/README.md b/README.md
index 9e004fd..1843e6c 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,13 @@ A desktop application for the Variational Animal Motion Encoding (VAME) project.
 VAME Desktop has been designed to run each step of a VAME project **only once**. This is to ensure that the project is reproducible and that the data is not accidentally overwritten.
 
 ## Installation
+
+### Download builded versions:
+
+You can find the builed versions of VAME Desktop on the [release page](https://github.com/catalystneuro/vame-desktop/releases).
+
+## Development mode
+
 ### Python
 You will need to have [miniconda](https://docs.conda.io/en/latest/miniconda.html) installed on your machine OR [pyenv](https://github.com/pyenv/pyenv).
 

From 204880a5b14300acfefa22d1e57180eab2bb1c01 Mon Sep 17 00:00:00 2001
From: Nathan Vieira Marcelino <nathan.v.marcelino@gmail.com>
Date: Mon, 29 Jul 2024 15:18:15 -0300
Subject: [PATCH 6/6] fix: minor issues

---
 src/renderer/src/context/Projects/index.tsx   |   1 -
 src/renderer/src/pages/Project/index.tsx      |   4 +-
 src/services/main.py                          | 765 ------------------
 src/services/vameApi/app/routes/vame.py       |  20 +
 .../vameApi/app/services/project_service.py   |  19 +-
 5 files changed, 36 insertions(+), 773 deletions(-)
 delete mode 100644 src/services/main.py

diff --git a/src/renderer/src/context/Projects/index.tsx b/src/renderer/src/context/Projects/index.tsx
index a6c6c30..b02a239 100644
--- a/src/renderer/src/context/Projects/index.tsx
+++ b/src/renderer/src/context/Projects/index.tsx
@@ -177,7 +177,6 @@ export const ProjectsProvider: React.FC<{ children: ReactNode }> = ({
   }, [])
 
   const createMotifVideos = useCallback(async (data) => {
-    console.log(data)
     const res = await createMotifVideosVAMEProject(data)
     await refresh()
     return res
diff --git a/src/renderer/src/pages/Project/index.tsx b/src/renderer/src/pages/Project/index.tsx
index 840c3b7..9ffd194 100644
--- a/src/renderer/src/pages/Project/index.tsx
+++ b/src/renderer/src/pages/Project/index.tsx
@@ -57,7 +57,6 @@ const Project: React.FC = () => {
 
       if (tab) {
         const localItem = `selected-tab-${project?.config.Project}`
-        console.log("localItem",localItem)
         localStorage.setItem(localItem, tab)
         setSelectedTab(tab)
       }
@@ -109,6 +108,7 @@ const Project: React.FC = () => {
     segmented,
     motif_videos_created,
     community_videos_created,
+    umaps_created,
   } = project.workflow
 
   const {
@@ -261,7 +261,7 @@ const Project: React.FC = () => {
     {
       id: 'umap-visualization',
       label: '7. UMAP Visualization',
-      completed: visualization?.execution_state==="success",
+      complete: umaps_created,
       disabled: !segmented,
       tooltip: "Need segmentation.",
       content: <UMAPVisualization
diff --git a/src/services/main.py b/src/services/main.py
deleted file mode 100644
index 9d23c7a..0000000
--- a/src/services/main.py
+++ /dev/null
@@ -1,765 +0,0 @@
-import sys
-import os
-import yaml
-import json
-import csv
-from pathlib import Path
-import sys
-import signal
-from logging.config import dictConfig
-
-import traceback
-from flask import Flask, request, jsonify
-from flask_cors import CORS
-from flask_restx import Api, Resource
-
-# Type hinting
-from typing import Union
-
-# Logging dependencies
-import queue
-import threading
-from datetime import datetime
-
-# Plotting configuration
-import matplotlib
-matplotlib.use('Agg')  # Non-interactive matplotlib backend
-
-FILES_TO_IGNORE = [ '.DS_Store' ]
-
-def get_files(folder_to_search):
-    folder_to_search = Path(folder_to_search)
-    ignore_glob = set(FILES_TO_IGNORE)
-    return [ file for file in folder_to_search.glob('*') if file.is_file() and file.name not in ignore_glob ]
-
-    # Queue to hold stdout messages
-    log_queue = queue.Queue()
-
-    # Save the original stdout
-    original_stdout = sys.stdout
-    original_stderr = sys.stderr
-
-    # Custom stream handler to put stdout into the queue and print to console
-    class QueueStream:
-        def __init__(self, q, stream):
-            self.q = q
-            self.stream = stream
-
-        def write(self, msg):
-            if isinstance(msg, bytes):
-                msg = msg.decode('utf-8')  # Decode bytes to string if necessary
-            if msg.strip():  # Avoid writing empty messages
-                self.q.put(msg)
-                self.stream.write(msg)  # Print to console
-
-        def flush(self):
-            self.stream.flush()
-
-    # Logging thread function
-    def log_writer(q, log_file):
-        with open(log_file, 'a') as f:
-            while True:
-                msg = q.get()
-                if msg == 'STOP':  # Stop signal for the thread
-                    break
-                f.write(msg)
-                f.flush()
-
-    # Redirect stdout to the queue and console
-    sys.stdout = QueueStream(log_queue, original_stdout)
-    sys.stderr = QueueStream(log_queue, original_stderr)
-
-    # Start the logging thread
-    log_thread = threading.Thread(target=log_writer, args=(log_queue, log_file))
-    log_thread.start()
-
-    def close():
-        # Stop the logging thread
-        log_queue.put('STOP')
-        log_thread.join()
-
-        # Reset stdout and stderr
-        sys.stdout = original_stdout
-        sys.stderr = original_stderr
-
-    return dict(
-        close=close
-    )
-
-VAME_APP_DIRECTORY = Path.home() / 'vame-desktop'
-VAME_PROJECTS_DIRECTORY = VAME_APP_DIRECTORY / 'projects'
-VAME_LOG_DIRECTORY = VAME_APP_DIRECTORY / 'logs'
-GLOBAL_SETTINGS_FILE = VAME_APP_DIRECTORY / 'settings.json'
-GLOBAL_STATES_FILE = VAME_APP_DIRECTORY / 'states.json'
-
-dictConfig({
-    'version': 1,
-    'formatters': {'default': {
-        'format': '%(message)s',
-    }},
-    'handlers': {'wsgi': {
-        'class': 'logging.StreamHandler',
-        'stream': 'ext://sys.stdout',  # <-- Solution
-        'formatter': 'default'
-    }},
-    'root': {
-        'level': 'INFO',
-        'handlers': ['wsgi']
-    }
-})
-
-app = Flask(__name__)
-cors = CORS(app)
-app.config['CORS_HEADERS'] = 'Content-Type'
-
-api = Api(
-    app,
-    version='1.0',
-    title='VAME API',
-    description="The REST API for VAME.",
-)
-
-@api.errorhandler(Exception)
-def exception_handler(error):
-    exceptiondata = traceback.format_exception(type(error), error, error.__traceback__)
-    return {"message": exceptiondata[-1], "traceback": "".join(exceptiondata)}
-
-
-def notBadRequestException(exception):
-    """
-    Check if the exception is a generic exception.
-    """
-    return type(exception).__name__ not in ["BadRequest", "Forbidden", "Unauthorized"]
-
-def get_project_path(
-        project: str,
-        working_directory: str = None
-    ):
-
-    date = datetime.today()
-    month = date.strftime("%B")
-    day = date.day
-    year = date.year
-    d = str(month[0:3]+str(day))
-    date = datetime.today().strftime('%Y-%m-%d')
-
-    if working_directory == None:
-        working_directory = '.'
-
-    wd = Path(working_directory).resolve()
-    project_name = '{pn}-{date}'.format(pn=project, date=d+'-'+str(year))
-    return wd / project_name
-
-def resolve_request_data(request):
-    data = json.loads(request.data) if request.data else {}
-    project_path = Path( data.pop("project") if "project" in data else Path(data["config"].parent) )
-    data["config"] = str(project_path / 'config.yaml') if "config" not in data else data["config"]
-    return data, project_path
-
-
-def get_evaluation_images(project_path):
-    evaluation_output = project_path / 'model' / 'evaluate'
-    png_files = list(evaluation_output.glob('*.png'))
-    return [ str(png_file.relative_to(project_path)) for png_file in png_files ]
-
-
-def get_visualization_images(project_path):
-    community_subfolders = get_video_related_asset(
-        project_path,
-        subpath='community',
-        validate=True
-    )
-
-    visualization_images = dict()
-
-    for video_set, community_subfolder in community_subfolders.items():
-        if community_subfolder:
-            visualization_images[video_set] = [ str(image.relative_to(project_path)) for image in community_subfolder.glob('umap_*.png') ]
-        else:
-            visualization_images[video_set] = []
-
-
-    return visualization_images
-
-
-
-def get_video_related_asset(
-        project_path,
-        subpath: Union[str, callable],
-        return_path = True,
-        validate = False
-    ):
-
-    results_location = project_path / 'results'
-    config = yaml.safe_load(open(project_path / 'config.yaml', "r"))
-
-    video_sets = config["video_sets"]
-    model_name = config["model_name"]
-
-    video_related_assets = dict()
-
-    for video_set in video_sets:
-        video_set_subpath = subpath(video_set) if callable(subpath) else subpath
-        asset_path = results_location / video_set / model_name / 'hmm-15' / video_set_subpath
-        video_related_assets[video_set] = asset_path if return_path else str(asset_path)
-        if validate and not asset_path.exists():
-            video_related_assets[video_set] = None
-
-    return video_related_assets
-
-def get_videos(
-        project_path,
-        subfolder
-    ):
-
-    video_subfolders = get_video_related_asset(project_path, subfolder)
-
-    output_videos = dict()
-
-    for video_set, video_subfolder in video_subfolders.items():
-        if video_subfolder.exists():
-            output_videos[video_set] = [ str(video.relative_to(project_path)) for video in video_subfolder.glob('*.mp4') ]
-        else:
-            output_videos[video_set] = []
-
-    return output_videos
-
-
-def get_video_results_path(video, project_path):
-    return project_path / 'results' / video / "VAME" / 'hmm-15'
-
-
-def get_motif_videos(project_path):
-    return get_videos(project_path, 'cluster_videos')
-
-def get_community_videos(project_path):
-    return get_videos(project_path, 'community_videos')
-
-def get_pose_ref_index_description(csv_file_path: str) -> str:
-    with open(csv_file_path) as csv_file:
-        csv_reader = csv.reader(csv_file, delimiter=',')
-        body_parts = []
-
-        # loop to iterate through the rows of csv
-        for row in csv_reader:
-            if row[0] == "bodyparts":
-                body_parts = list(dict.fromkeys(row[1:]))  # Extract body parts starting from the second element and remove duplicates
-                break
-
-        if len(body_parts) == 0:
-            print("No body parts headers found in CSV.")
-            return ""
-
-        # Create the string based on body parts
-        body_parts_string = ", ".join([f"{i}-{part}" for i, part in enumerate(body_parts)])
-
-    return body_parts_string
-
-
-@api.route('/connected')
-class Connected(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def get(self):
-        return jsonify({ "payload": True })
-
-
-@api.route('/ready')
-class VAMEReady(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def get(self):
-        import vame
-        return jsonify({ "payload": True })
-
-@api.route('/project_ready')
-class ProjectReady(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        data, project_path = resolve_request_data(request)
-
-        states_path = Path(project_path) / "states" / "states.json"
-
-        with open(states_path, "r") as file:
-            states = json.load(fp=file)
-
-        if states is None:
-            return jsonify({ "is_ready": True })
-
-        for _, value in states.items():
-            execution_state = value.get("execution_state", None)
-            if execution_state == "running":
-                return jsonify({ "is_ready": False })
-
-        return jsonify({ "is_ready": True })
-
-@api.route('/settings')
-class Settings(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def get(self):
-        return json.loads(open(GLOBAL_SETTINGS_FILE, "r").read())
-
-
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        data = json.loads(request.data) if request.data else {}
-        with open(GLOBAL_SETTINGS_FILE, "w") as file:
-            json.dump(data, file)
-        return jsonify(data)
-
-@api.route('/files/<path:project>/<path:path>')
-class Files(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def get(self, project, path):
-        from flask import send_from_directory
-        return send_from_directory(VAME_PROJECTS_DIRECTORY, Path(project) / path)
-
-
-@api.route('/exists/<path:project>/<path:path>')
-class FileExists(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def get(self, project, path):
-        full_path = VAME_PROJECTS_DIRECTORY / project / path
-        return jsonify(dict(exists=full_path.exists()))
-
-
-@api.route('/projects')
-class Projects(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def get(self):
-        projects = [ str(project) for project in VAME_PROJECTS_DIRECTORY.glob('*') if project.is_dir() ]
-        return jsonify(projects)
-
-@api.route('/projects/recent')
-class RecentProjects(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def get(self):
-        with open(GLOBAL_STATES_FILE, "r") as inp:
-            states = json.load(fp=inp)
-        # states = json.loads(open(GLOBAL_STATES_FILE, "r").read())
-        recent_projects = states.get("recent_projects", [])
-
-        # Filter those that no longer exist
-        recent_projects = [ str(project) for project in recent_projects if (VAME_PROJECTS_DIRECTORY / project).exists() ]
-        states["recent_projects"] = recent_projects
-        with open(GLOBAL_STATES_FILE, "w") as file:
-            json.dump(states, file)
-
-        return jsonify(recent_projects)
-
-@api.route('/project/register')
-class RegisterProject(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-
-        try:
-            with open(GLOBAL_STATES_FILE, "r") as inp:
-                states = json.load(fp=inp)
-
-            recent_projects = states.get("recent_projects", [])
-
-            _, project_path = resolve_request_data(request)
-
-            project_path = str(project_path)
-
-            if project_path in recent_projects:
-                recent_projects.remove(project_path)
-
-            recent_projects.append(project_path)
-
-            if len(recent_projects) > 5:
-                recent_projects = recent_projects[-5:]
-
-            with open(GLOBAL_STATES_FILE, "w") as file:
-                json.dump({
-                    **states,
-                    "recent_projects": recent_projects
-                }, file)
-
-            return jsonify(recent_projects)
-
-        except Exception as exception:
-            # TODO: Should lock access to the file
-            pass
-
-@api.route('/log/<path:log_name>')
-class ProjectLog(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request",404: "Not found", 500: "Internal server error"})
-    def get(self, log_name):
-
-        project_path = request.args.get('project')
-        project_path = Path(project_path)
-
-        if(log_name):
-            log_path = Path(project_path) / "logs" / f"{log_name}.log"
-            if log_path.is_file():
-                log = open(log_path, "r").read()
-                return log
-            else:
-                return f"{log_name} log not found.", 404
-
-        return "missing log_name", 400
-
-@api.route('/load')
-class Load(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-
-        _, project_path = resolve_request_data(request)
-        config_path = project_path / "config.yaml"
-
-        # Create a symlink to the project directory if it isn't in the VAME_PROJECTS_DIRECTORY
-        if project_path.parent != VAME_PROJECTS_DIRECTORY:
-            symlink = VAME_PROJECTS_DIRECTORY / project_path.name
-            if not symlink.exists():
-                symlink.symlink_to(project_path)
-
-        states_path = Path(project_path) / "states" / "states.json"
-
-        states = json.load(open(states_path)) if os.path.exists(states_path) else None
-
-        config = yaml.safe_load(open(config_path, "r")) if config_path.exists() else None
-
-        images = dict(
-            evaluation=get_evaluation_images(project_path),
-            visualization=get_visualization_images(project_path)
-        )
-
-        videos = dict(
-            motif=get_motif_videos(project_path),
-            community=get_community_videos(project_path)
-        )
-
-        has_latent_vector_files = False
-        if config:
-            has_latent_vector_files = all(map(lambda video: (get_video_results_path(video, project_path) / f"latent_vector_{video}.npy").exists(), config["video_sets"]))
-
-        has_communities = (project_path / 'cohort_community_label.npy').exists()
-
-        original_videos_location = project_path / 'videos'
-        original_csvs_location = original_videos_location / 'pose_estimation'
-
-        # Get all files in the original data directory
-        original_videos = list(map(lambda file: str(file), get_files(original_videos_location)))
-        original_csvs = list(map(lambda file: str(file), get_files(original_csvs_location)))
-
-        # Provide project workflow status
-        workflow = dict(
-            organized = (project_path / 'data' / 'train').exists(),
-            pose_ref_index_description=get_pose_ref_index_description(original_csvs[0]),
-            modeled = len(images["evaluation"]) > 0,
-            segmented = has_latent_vector_files,
-            motif_videos_created = all(map(lambda videos: len(videos) > 0, videos["motif"].values())),
-            communities_created = has_communities,
-            community_videos_created = all(map(lambda videos: len(videos) > 0, videos["community"].values())),
-            umaps_created = any(map(lambda videos: len(videos) > 0, images["visualization"].values())),
-        )
-
-        return jsonify(dict(
-            project=str(config_path.parent),
-            config=config,
-            assets=dict(
-                images=images,
-                videos=videos
-            ),
-            videos=original_videos,
-            csvs=original_csvs,
-            workflow=workflow,
-            states=states
-        ))
-
-@api.route('/create', methods=['POST'])
-class Create(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-
-            data = json.loads(request.data) if request.data else {}
-
-            project_path = get_project_path(data["project"], VAME_PROJECTS_DIRECTORY)
-
-            created = not project_path.exists()
-
-            config_path = Path(vame.init_new_project(
-                working_directory=VAME_PROJECTS_DIRECTORY,
-                **data
-            ))
-
-            return jsonify(dict(
-                project=str(config_path.parent),
-                created=created,
-                config=yaml.safe_load(open(config_path, "r"))
-            ))
-
-        except Exception as exception:
-            print("exception", exception)
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-@api.route('/delete_project', methods=['POST'])
-class DeleteProject(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        try:
-            data, project_path = resolve_request_data(request)
-
-            if project_path.exists():
-                import shutil
-                shutil.rmtree(project_path, ignore_errors=True)
-                return jsonify(dict(project=str(project_path), deleted=True))
-
-            return jsonify(dict(project=str(project_path), deleted=False))
-
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-
-@api.route('/configure', methods=['POST'])
-class ConfigureProject(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        from vame.util import auxiliary
-
-        try:
-            data, project_path = resolve_request_data(request)
-            config_path = project_path / "config.yaml"
-
-            if config_path.exists():
-                with open(config_path, "r") as file:
-                    config = yaml.safe_load(file)
-                    config_update = data["config"]
-
-                    if config_update:
-                        config.update(config_update)
-                        auxiliary.write_config(config_path, config)
-
-                    return jsonify(dict(config=config))
-
-            return jsonify(dict(config=None))
-
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-
-@api.route('/align', methods=['POST'])
-class Align(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-
-            data, project_path = resolve_request_data(request)
-
-            # If your experiment is by design egocentrical (e.g. head-fixed experiment on treadmill etc)
-            # you can use the following to convert your .csv to a .npy array, ready to train vame on it
-            egocentric_data = data.pop('egocentric_data', None)
-
-
-            if egocentric_data:
-                vame.csv_to_numpy(
-                    project_path / 'config.yaml',
-                    save_logs=True
-                )
-
-            else:
-                vame.egocentric_alignment(
-                    **data,
-                    save_logs=True
-                )
-
-
-            return jsonify(dict(result='success'))
-
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-
-@api.route("/create_trainset")
-class CreateTrainset(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-            data, project_path = resolve_request_data(request)
-
-            result = vame.create_trainset(
-                **data,
-                save_logs=True
-            )
-
-            return dict(result=result)
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-@api.route('/train', methods=['POST'])
-class TrainModel(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-            data, project_path = resolve_request_data(request)
-
-            result = vame.train_model(
-                **data,
-                save_logs=True
-            )
-
-            return dict(result=result)
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-@api.route('/evaluate', methods=['POST'])
-class EvaluateModel(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-            data, project_path = resolve_request_data(request)
-            vame.evaluate_model(
-                **data,
-                save_logs=True
-            )
-            return dict(result=get_evaluation_images(project_path))
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-@api.route('/segment', methods=['POST'])
-class Segment(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-            data, project_path = resolve_request_data(request)
-            result = vame.pose_segmentation(
-                **data,
-                save_logs=True
-            )
-            return dict(result=result)
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-@api.route('/motif_videos', methods=['POST'])
-class MotifVideos(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-            data, project_path = resolve_request_data(request)
-            result = vame.motif_videos(
-                **data,
-                save_logs=True
-            )
-            return dict(result=result)
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-@api.route('/community', methods=['POST'])
-class Community(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-            data, project_path = resolve_request_data(request)
-            result = vame.community(
-                **data,
-                save_logs=True
-            )
-            return dict(result=result)
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-@api.route('/community_videos', methods=['POST'])
-class CommunityVideos(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-            data, project_path = resolve_request_data(request)
-            result = vame.community_videos(
-                **data,
-                save_logs=True
-            )
-            return dict(result=result)
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-@api.route('/visualization', methods=['POST'])
-class Visualization(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-            data, project_path = resolve_request_data(request)
-            vame.visualization(
-                **data,
-                save_logs=True
-            )
-            return dict(result=get_visualization_images(project_path))
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-@api.route('/generative_model', methods=['POST'])
-class GenerativeModel(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-            data, project_path = resolve_request_data(request)
-            result = vame.generative_model(**data)
-            return dict(result=result)
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-@api.route('/gif', methods=['POST'])
-class CreateGif(Resource):
-    @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    def post(self):
-        import vame
-        try:
-            data, project_path = resolve_request_data(request)
-            result = vame.gif(**data)
-            return dict(result=result)
-        except Exception as exception:
-            if notBadRequestException(exception):
-                api.abort(500, str(exception))
-
-def signal_handler(sig, frame):
-    print('Received SIGTERM, shutting down...')
-    os._exit(0)
-
-signal.signal(signal.SIGTERM, signal_handler)
-
-if __name__ == "__main__":
-    env_port = os.getenv('PORT')
-    PORT = int(env_port) if env_port else 8641
-    HOST = os.getenv('HOST') or 'localhost'
-
-    VAME_PROJECTS_DIRECTORY.mkdir(exist_ok=True, parents=True) # Create the VAME_PROJECTS_DIRECTORY if it doesn't exist
-    VAME_LOG_DIRECTORY.mkdir(exist_ok=True, parents=True)  # Create the VAME_LOG_DIRECTORY if it doesn't exist
-
-    # Create the global files if they don't exist
-    global_files = [GLOBAL_STATES_FILE, GLOBAL_SETTINGS_FILE]
-    for file in global_files:
-        if not file.exists():
-            with open(file, "w") as f:
-                json.dump({}, f)
-
-    # Run the app
-    try:
-        print(f"Flask server started at {HOST}:{PORT}")
-        app.run(host=HOST, port = PORT)
-
-    except Exception as e:
-        print(f"An error occurred that closed the server: {e}")
-        raise e
diff --git a/src/services/vameApi/app/routes/vame.py b/src/services/vameApi/app/routes/vame.py
index 81a8aef..8f9c940 100644
--- a/src/services/vameApi/app/routes/vame.py
+++ b/src/services/vameApi/app/routes/vame.py
@@ -11,6 +11,8 @@ class Align(Resource):
     @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         import vame
+        import matplotlib
+        matplotlib.use('agg')
         try:
 
             data, project_path = resolve_request_data(request)
@@ -45,6 +47,8 @@ class CreateTrainset(Resource):
     @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         import vame
+        import matplotlib
+        matplotlib.use('agg')
         try:
             data, project_path = resolve_request_data(request)
 
@@ -63,6 +67,8 @@ class TrainModel(Resource):
     @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         import vame
+        import matplotlib
+        matplotlib.use('agg')
         try:
             data, project_path = resolve_request_data(request)
 
@@ -99,6 +105,8 @@ class Segment(Resource):
     @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         import vame
+        import matplotlib
+        matplotlib.use('agg')
         try:
             data, project_path = resolve_request_data(request)
             result = vame.pose_segmentation(
@@ -115,6 +123,8 @@ class MotifVideos(Resource):
     @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         import vame
+        import matplotlib
+        matplotlib.use('agg')
         try:
             data, project_path = resolve_request_data(request)
             result = vame.motif_videos(
@@ -131,6 +141,8 @@ class Community(Resource):
     @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         import vame
+        import matplotlib
+        matplotlib.use('agg')
         try:
             data, project_path = resolve_request_data(request)
             result = vame.community(
@@ -147,6 +159,8 @@ class CommunityVideos(Resource):
     @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         import vame
+        import matplotlib
+        matplotlib.use('agg')
         try:
             data, project_path = resolve_request_data(request)
             result = vame.community_videos(
@@ -163,6 +177,8 @@ class Visualization(Resource):
     @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         import vame
+        import matplotlib
+        matplotlib.use('agg')
         try:
             data, project_path = resolve_request_data(request)
             vame.visualization(
@@ -179,6 +195,8 @@ class GenerativeModel(Resource):
     @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         import vame
+        import matplotlib
+        matplotlib.use('agg')
         try:
             data, project_path = resolve_request_data(request)
             result = vame.generative_model(**data)
@@ -192,6 +210,8 @@ class CreateGif(Resource):
     @api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         import vame
+        import matplotlib
+        matplotlib.use('agg')
         try:
             data, project_path = resolve_request_data(request)
             result = vame.gif(**data)
diff --git a/src/services/vameApi/app/services/project_service.py b/src/services/vameApi/app/services/project_service.py
index 0b4e538..483f605 100644
--- a/src/services/vameApi/app/services/project_service.py
+++ b/src/services/vameApi/app/services/project_service.py
@@ -157,17 +157,26 @@ def load_project(project_path: Path):
     original_videos = list(map(lambda file: str(file), get_files(original_videos_location)))
     original_csvs = list(map(lambda file: str(file), get_files(original_csvs_location)))
 
+    motif_videos_created_hmm=all(map(lambda videos: len(videos) > 0, videos["motif"]["hmm"].values()))
+    motif_videos_created_kmeans=all(map(lambda videos: len(videos) > 0, videos["motif"]["kmeans"].values()))
+
+    community_videos_created_hmm = all(map(lambda videos: len(videos) > 0, videos["community"]["kmeans"].values()))
+    community_videos_created_kmeans = all(map(lambda videos: len(videos) > 0, videos["community"]["hmm"].values()))
+
+    umaps_created_hmm = any(map(lambda videos: len(videos) > 0, images["visualization"]["hmm"].values()))
+
+    umaps_created_kmeans = any(map(lambda videos: len(videos) > 0, images["visualization"]["kmeans"].values()))
+
     # Provide project workflow status
     workflow = dict(
         organized = (project_path / 'data' / 'train').exists(),
         pose_ref_index_description=get_pose_ref_index_description(original_csvs[0]),
         modeled = len(images["evaluation"]) > 0,
         segmented = has_latent_vector_files,
-        motif_videos_created_hmm = all(map(lambda videos: len(videos) > 0, videos["motif"]["hmm"].values())),
-        motif_videos_created_kmeans = all(map(lambda videos: len(videos) > 0, videos["motif"]["kmeans"].values())),
-        communities_created = has_communities,
-        community_videos_created = all(map(lambda videos: len(videos) > 0, videos["community"].values())),
-        umaps_created = any(map(lambda videos: len(videos) > 0, images["visualization"].values())),
+        motif_videos_created=(lambda: motif_videos_created_hmm or motif_videos_created_kmeans)(),
+        communities_created=has_communities,
+        community_videos_created = (lambda: community_videos_created_hmm or community_videos_created_kmeans)(),
+        umaps_created = (lambda: umaps_created_hmm or umaps_created_kmeans)(),
     )
 
     return dict(