resource_id -> resource_path

.github/scripts/s3_client.py

@@ -128,23 +128,23 @@ def load_file(self, path) -> str:
         # response = requests.get(url)
         # return response.content
 
-    def check_versions(self, resource_id: str) -> Iterator[VersionStatus]:
+    def check_versions(self, resource_path: str) -> Iterator[VersionStatus]:
         """
         Check model repository for version of model-name.
 
         Returns dictionary of version-status pairs.
         """
-        logger.debug("Checking versions for {}", resource_id)
-        version_folders = self.ls(f"{resource_id}/", only_folders=True)
+        logger.debug("Checking versions for {}", resource_path)
+        version_folders = self.ls(f"{resource_path}/", only_folders=True)
 
         # For each folder get the contents of status.json
         for version in version_folders:
 
-            yield self.get_version_status(resource_id, version)
+            yield self.get_version_status(resource_path, version)
 
-    def get_unpublished_version(self, resource_id: str) -> str:
+    def get_unpublished_version(self, resource_path: str) -> str:
         """Get the unpublisted version"""
-        versions = list(self.check_versions(resource_id))
+        versions = list(self.check_versions(resource_path))
         if len(versions) == 0:
             return "1"
         unpublished = [version for version in versions if version.status == "staging"]
@@ -155,49 +155,51 @@ def get_unpublished_version(self, resource_id: str) -> str:
             raise ValueError("Opps! We seem to have > 1 staging versions!!")
         return unpublished[0].version
 
-    def get_version_status(self, resource_id: str, version: str) -> VersionStatus:
-        status = self.get_status(resource_id, version)
+    def get_version_status(self, resource_path: str, version: str) -> VersionStatus:
+        status = self.get_status(resource_path, version)
         status_str = status.get("status", "status-field-unset")
-        version_path = f"{resource_id}/{version}"
+        version_path = f"{resource_path}/{version}"
         return VersionStatus(version, status_str, version_path)
 
-    def get_status(self, resource_id: str, version: str) -> dict:
-        version_path = f"{resource_id}/{version}"
-        logger.debug("resource_id: {}, version: {}", resource_id, version)
+    def get_status(self, resource_path: str, version: str) -> dict:
+        version_path = f"{resource_path}/{version}"
+        logger.debug("resource_path: {}, version: {}", resource_path, version)
         status_path = f"{version_path}/status.json"
         logger.debug("Getting status using path {}", status_path)
         status = self.load_file(status_path)
         status = json.loads(status)
         return status
 
-    def put_status(self, resource_id: str, version: str, status: dict):
-        logger.debug("Updating status for {}-{}, with {}", resource_id, version, status)
+    def put_status(self, resource_path: str, version: str, status: dict):
+        logger.debug(
+            "Updating status for {}-{}, with {}", resource_path, version, status
+        )
         contents = json.dumps(status).encode()
         file_object = io.BytesIO(contents)
 
         self.put(
-            f"{resource_id}/{version}/status.json",
+            f"{resource_path}/{version}/status.json",
             file_object,
             length=len(contents),
             content_type="application/json",
         )
 
-    def get_log(self, resource_id: str, version: str) -> dict:
-        version_path = f"{resource_id}/{version}"
-        logger.debug("resource_id: {}, version: {}", resource_id, version)
+    def get_log(self, resource_path: str, version: str) -> dict:
+        version_path = f"{resource_path}/{version}"
+        logger.debug("resource_path: {}, version: {}", resource_path, version)
         path = f"{version_path}/log.json"
         logger.debug("Getting log using path {}", path)
         log = self.load_file(path)
         log = json.loads(log)
         return log
 
-    def put_log(self, resource_id: str, version: str, log: dict):
-        logger.debug("Updating log for {}-{}, with {}", resource_id, version, log)
+    def put_log(self, resource_path: str, version: str, log: dict):
+        logger.debug("Updating log for {}-{}, with {}", resource_path, version, log)
         contents = json.dumps(log).encode()
         file_object = io.BytesIO(contents)
 
         self.put(
-            f"{resource_id}/{version}/log.json",
+            f"{resource_path}/{version}/log.json",
             file_object,
             length=len(contents),
             content_type="application/json",

.github/scripts/update_status.sh

@@ -5,15 +5,15 @@
 # S3_FOLDER
 # S3_ACCESS_KEY_ID
 # S3_SECRET_ACCESS_KEY
-# First arg is now resource_id
+# First arg is now resource_path
 
 FILENAME=status.json
 
-RESOURCE_ID=$1
+resource_path=$1
 STATUS=$2
 
-if [ -z "$RESOURCE_ID" ]; then
-    printf '%s\n' "RESOURCE_ID is unset or empty" >&2;
+if [ -z "$resource_path" ]; then
+    printf '%s\n' "resource_path is unset or empty" >&2;
     exit 1
 fi
 if [ -z "$S3_HOST" ]; then
@@ -40,7 +40,7 @@ fi
 
 #curl -X PUT -H 'Content-Type: application/json' -d '{"status": "'"$2"'"}' "$1"
 
-RESOURCE="/${S3_BUCKET}/${S3_FOLDER}/${RESOURCE_ID}/${FILENAME}"
+RESOURCE="/${S3_BUCKET}/${S3_FOLDER}/${resource_path}/${FILENAME}"
 CONTENT_TYPE="application/json"
 DATE=`date -R`
 _SIGNATURE="PUT\n\n${CONTENT_TYPE}\n${DATE}\n${RESOURCE}"

.github/workflows/ci_runner.yaml

@@ -3,8 +3,8 @@ name: CI Runner
 on:
     workflow_dispatch:
         inputs:
-            resource_id:
-                description: 'Bioimageio ID - to be used to access the resource on S3'
+            resource_path:
+                description: 'Bioimageio wide, version specific resource identifier "resource_path/version"'
                 required: true
                 type: string
             package_url:
@@ -38,19 +38,19 @@ jobs:
                 python -m pip install "minio==7.2.3" "ruamel.yaml==0.18.5" "bioimageio.spec==0.4.9.post5" "typer"
           - name: Unzip model file
             run: |
-                python .github/scripts/update_status.py    "${{ inputs.resource_id }}" "Unzipping package" "1"
-                python .github/scripts/unzip_model.py "${{inputs.resource_id}}" "${{inputs.package_url}}"
+                python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Unzipping package" "1"
+                python .github/scripts/unzip_model.py "${{inputs.resource_path}}" "${{inputs.package_url}}"
 
           - name: Validate format
             id: validate
             run: |
-                python .github/scripts/update_status.py    "${{ inputs.resource_id }}" "Starting validation" "2"
-                python .github/scripts/validate_format.py    "${{ inputs.resource_id }}" "${{inputs.package_url}}"
+                python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Starting validation" "2"
+                python .github/scripts/validate_format.py    "${{ inputs.resource_path }}" "${{inputs.package_url}}"
           - run: |
-              python .github/scripts/update_status.py    "${{ inputs.resource_id }}" "Starting additional tests" "3"
+              python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Starting additional tests" "3"
             if: steps.validate.outputs.has_dynamic_test_cases == 'yes'
           - run: |
-                python .github/scripts/update_status.py    "${{ inputs.resource_id }}" "Validation done" "3"
+                python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Validation done" "3"
             if: steps.validate.outputs.has_dynamic_test_cases == 'no'
 
 
@@ -90,4 +90,4 @@ jobs:
         steps:
           - uses: actions/checkout@v4
           - run: |
-                python .github/scripts/update_status.py    "${{ inputs.resource_id }}" "Awaiting review" "4"
+                python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Awaiting review" "4"

.github/workflows/publish.yaml

@@ -3,7 +3,7 @@ name: publish
 on:
     workflow_dispatch:
         inputs:
-            resource_id:
+            resource_path:
                 description: 'Bioimageio ID of the resource - to be used to access the resource on S3'
                 required: true
                 type: string
@@ -33,6 +33,6 @@ jobs:
                 python -m pip install "minio==7.2.3" "loguru==0.7.2" "packaging==23.2" "spdx-license-list==3.22" "ruamel.yaml==0.18.5" "typer"
           - name: Publish to Zenodo
             run: |
-                python .github/scripts/update_status.py "${{ inputs.resource_id }}" "Publishing to Zenodo" "5"
-                python .github/scripts/upload_model_to_zenodo.py --resource_id "${{inputs.resource_id}}"
-                python .github/scripts/update_status.py "${{ inputs.resource_id }}" "Publishing complete" "6"
+                python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Publishing to Zenodo" "5"
+                python .github/scripts/upload_model_to_zenodo.py --resource_path "${{inputs.resource_path}}"
+                python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Publishing complete" "6"

functions/create_status.js

@@ -19,7 +19,7 @@ export default async (event, context) => {
     //'ref': 'main',
     //'inputs':{
     //'status_url': data.status_url,
-    //'resource_id': data.resource_id,
+    //'resource_path': data.resource_path,
     //}
     //})
     //};

functions/notify_ci.js

@@ -12,8 +12,8 @@ const headers = {
 
 export default async (event, context) => {
     const data = await event.json();
-    if (!data.resource_id) {
-        const error_message = "Failed: resource_id not found in request json";
+    if (!data.resource_path) {
+        const error_message = "Failed: resource_path not found in request json";
         console.error()
         const res = Response.json({ 'message': error_message, 'status': 500 });
         res.headers.set("Access-Control-Allow-Origin", "*");
@@ -38,7 +38,7 @@ export default async (event, context) => {
         body: JSON.stringify({
             'ref': GITHUB_BRANCH,
             'inputs': {
-                'resource_id': data.resource_id,
+                'resource_path': data.resource_path,
                 'package_url': data.package_url,
             }
         })

src/components/Uploader/Review.svelte

@@ -7,7 +7,7 @@
 
     import JSONTree from 'svelte-json-tree';
     let model_name_message = "";
-    let resource_id = uploader.resource_id;
+    let resource_path = uploader.resource_path;
     let rdf = uploader.rdf;
     let ready_to_publish = uploader.ready_to_publish();
 
@@ -24,14 +24,14 @@
 
     async function regenerate_nickname(){
         await uploader.regenerate_nickname();
-        resource_id = uploader.resource_id;
+        resource_path = uploader.resource_path;
         ready_to_publish = uploader.ready_to_publish();
         console.log("Ready to publish?", ready_to_publish);
         rdf = uploader.rdf;
         //rerender = !rerender;
     }
 
-    if(!resource_id) regenerate_nickname();
+    if(!resource_path) regenerate_nickname();
 
 </script>
 
@@ -44,9 +44,9 @@
 <!--{#key rerender}-->
 <p class="level">
     {#if model_name_message }({model_name_message}){/if}
-    {#if resource_id}
+    {#if resource_path}
         Your model nickname is:
-        <code style="min-width:10em;">{resource_id.name} {resource_id.icon}&nbsp;</code>
+        <code style="min-width:10em;">{resource_path.name} {resource_path.icon}&nbsp;</code>
     {/if}
     <button on:click={regenerate_nickname}>Regenerate nickname</button>
 </p>

src/components/Uploader/UploadStatus.svelte

@@ -11,7 +11,7 @@
     let error_element: Object;
     let last_error_object: Error;
     let step: UploaderStep = uploader.status.step;
-    let model_name = uploader.resource_id.name;
+    let model_name = uploader.resource_path.name;
     const dispatch = createEventDispatcher();
 
     function copy_error_to_clipboard(text: string){
@@ -76,7 +76,7 @@
     <h4>Almost there,</h4>
 
     <p><b>There's nothing you need to do right now. Your model is uploaded and the CI-bots have started their work!</b><p>
-    <p>You can check the status of the CI at any point from <a href="#/status/{uploader.resource_id.name}">here</a></p>
+    <p>You can check the status of the CI at any point from <a href="#/status/{uploader.resource_path.name}">here</a></p>
 
 
     <button on:click={restart}>Upload another model</button>

src/components/Uploader/index.svelte

@@ -70,7 +70,7 @@
 {:else if step == "uploading"}
     <UploadStatus {uploader} on:done={()=>{step="add"}} />
 <!--{:else if step == "done"}-->
-    <!--<a href="/status/{uploader.resource_id.name}">Go to status page</a>-->
+    <!--<a href="/status/{uploader.resource_path.name}">Go to status page</a>-->
 {:else}
     <Notification>
         Opps! something went wrong 😬

src/lib/uploader.ts

@@ -62,7 +62,7 @@ export class Uploader {
     error_object: Error | null = null;
     files: File[] = [];
     login_url: string | null = null;
-    resource_id: ResourceId | null = null;
+    resource_path: ResourceId | null = null;
     package_url: string | null = null;
     rdf: any = null;
     render_callbacks: (() => void)[] = [];
@@ -92,7 +92,7 @@ export class Uploader {
     }
 
     reset() {
-        this.resource_id = null;
+        this.resource_path = null;
         this.rdf = null;
         this.status.reset();
     }
@@ -251,7 +251,7 @@ export class Uploader {
 
     ready_to_publish() {
         if (!this.ready_for_review()) return false;
-        if (!this.resource_id) return false;
+        if (!this.resource_path) return false;
         return true;
     }
 
@@ -266,7 +266,7 @@ export class Uploader {
             const model_name = Object.assign(new ResourceId, await (await fetch(generate_name_url)).json());
             console.log("Generated name:", model_name);
             const error = "";
-            this.resource_id = model_name;
+            this.resource_path = model_name;
             this.rdf.nickname = model_name.name;
             return { model_name, error };
         } catch (err) {
@@ -278,13 +278,13 @@ export class Uploader {
     }
 
     async upload_file(file: File, progress_callback: null | ((val: string, tot: string) => null)) {
-        if (!this.resource_id) {
-            throw new Error("Unable to upload, resource_id not set");
+        if (!this.resource_path) {
+            throw new Error("Unable to upload, resource_path not set");
         };
         this.status.message = "Uploading";
         this.status.step = UploaderStep.UPLOADING;
         this.render();
-        const filename = `${this.resource_id.id}/${file.name}`;
+        const filename = `${this.resource_path.id}/${file.name}`;
         const url_put = await this.storage.generate_presigned_url(
             this.storage_info.bucket,
             this.storage_info.prefix + filename,
@@ -422,7 +422,7 @@ export class Uploader {
             const resp = await fetch(notify_ci_url, {
                 method: 'POST',
                 headers: { "Content-Type": "application/json" },
-                body: JSON.stringify({ 'resource_id': this.resource_id!.id, 'package_url': this.zip_urls!.get })
+                body: JSON.stringify({ 'resource_path': this.resource_path!.id, 'package_url': this.zip_urls!.get })
             });
             if (resp.status === 200) {
                 const ci_resp = (await resp.json());