Merge branch 'master' of https://github.com/girder/slicer_cli_web into slicer-cli-web-singularity

Author: willdunklin

example-average-color/Dockerfile

@@ -1,8 +1,9 @@
 FROM python:3.11-slim
 LABEL maintainer="Kitware, Inc. <kitware@kitware.com>"
 
-RUN pip install --find-links https://girder.github.io/large_image_wheels large_image[sources]
-RUN pip install girder-slicer-cli-web
+RUN pip install --no-cache-dir --find-links https://girder.github.io/large_image_wheels large_image[sources]
+
+RUN pip install --no-cache-dir girder-slicer-cli-web
 
 COPY . /
 ENTRYPOINT ["python", "./cli_list.py"]

example-girder-requests/Dockerfile

@@ -1,9 +1,9 @@
 FROM python:3.11-slim
 MAINTAINER David Manthey <david.manthey@kitware.com>
 
-RUN pip install --find-links https://girder.github.io/large_image_wheels large_image[sources]
-RUN pip install girder-slicer-cli-web
-RUN pip install girder-client
+RUN pip install --no-cache--dir --find-links https://girder.github.io/large_image_wheels large_image[sources]
+RUN pip install --no-cache--dir girder-slicer-cli-web
+RUN pip install --no-cache--dir girder-client
 
 COPY . $PWD
 ENTRYPOINT ["python", "./cli_list.py"]

slicer_cli_web/image_job.py

@@ -18,6 +18,7 @@
 
 import json
 import os
+import time
 
 import docker
 from girder import logger
@@ -213,7 +214,7 @@ def jobPullAndLoad(job):
                 switch_to_sif_image_folder()
                 pull_image_and_convert_to_sif(pullList)
             else:
-                pullDockerImage(docker_client, pullList)
+                pullDockerImage(docker_client, pullList, job)
         except DockerImageNotFoundError as err:
             errorState = True
             notExistSet = set(err.imageName)
@@ -389,19 +390,57 @@ def getCliData(name, client, job):
         raise DockerImageError('Error getting %s cli data from image ' % (name) + str(err))
 
 
-def pullDockerImage(client, names):
+def pullDockerImage(client, names, job=None):
     """
     Attempt to pull the docker images listed in names. Failure results in a
     DockerImageNotFoundError being raised
 
-    :params client: The docker python client
-    :params names: A list of docker images to be pulled from the Dockerhub
+    :param client: The docker python client
+    :param names: A list of docker images to be pulled from the Dockerhub
+    :param job: A job to update with status.
     """
     imgNotExistList = []
     for name in names:
         try:
             logger.info('Pulling %s image', name)
-            client.images.pull(name)
+            lastlog = time.time()
+            stats = {}
+            for line in client.api.pull(name, stream=True, decode=True):
+                try:
+                    line.update(line.get('progressDetail', {}))
+                    if 'id' not in line or ('total' not in line and line['id'] not in stats):
+                        continue
+                    stats.setdefault(line['id'], line).update(line)
+                    if time.time() - lastlog >= 10:
+                        total = sum(record['total'] for record in stats.values())
+                        downloaded = sum(
+                            record['total'] for record in stats.values()
+                            if record['status'] != 'Downloading')
+                        downloaded += sum(
+                            record['current'] for record in stats.values()
+                            if record['status'] == 'Downloading')
+                        extracted = sum(
+                            record['total'] for record in stats.values()
+                            if record['status'] == 'Pull complete')
+                        extracted += sum(
+                            record['current'] for record in stats.values()
+                            if record['status'] == 'Extracting')
+                        if total:
+                            msg = f'Pulling {name} image: '
+                            if downloaded < total:
+                                val = downloaded
+                                msg += 'downloaded '
+                            else:
+                                val = extracted
+                                msg += 'extracted '
+                            msg += f'{val}/{total} ({val * 100 / total:4.2f}%)'
+                            logger.info(msg)
+                            if job:
+                                job = Job().updateJob(job, log=msg + '\n')
+                        lastlog = time.time()
+                except Exception:
+                    # Don't fail if the log code has an issue
+                    pass
             # some invalid image names will not be pulled but the pull method
             # will not throw an exception so the only way to confirm if a pull
             # succeeded is to attempt a docker inspect on the image

slicer_cli_web/prepare_task.py

@@ -189,7 +189,8 @@ def _add_optional_output_param(param, args, user, result_hooks, reference, templ
     ref = reference.copy()
     ref['identifier'] = param.identifier()
     result_hooks.append(GirderUploadVolumePathToFolder(
-        path, folder, upload_kwargs={'reference': json.dumps(ref)}))
+        path, folder, must_exist=False,
+        upload_kwargs={'reference': json.dumps(ref)}))
 
     return container_args
 

slicer_cli_web/web_client/views/ItemSelectorWidget.js

@@ -69,7 +69,7 @@ const ItemSelectorWidget = BrowserWidget.extend({
                 settings.input = {
                     label: 'Item name',
                     validate: (val) => {
-                        if (val && val.trim()) {
+                        if ((val && val.trim()) || (!val && !this.model.required)) {
                             return $.Deferred().resolve().promise();
                         }
                         return $.Deferred().reject('Specify an item name').promise();
@@ -264,14 +264,22 @@ const ItemSelectorWidget = BrowserWidget.extend({
                 });
                 break;
             case 'new-file':
-                this.model.set({
-                    path: this._path(),
-                    parent: model,
-                    value: new ItemModel({
-                        name: fileName,
-                        folderId: model.id
-                    })
-                });
+                if (!fileName) {
+                    this.model.set({
+                        path: this._path(),
+                        parent: model,
+                        value: null
+                    });
+                } else {
+                    this.model.set({
+                        path: this._path(),
+                        parent: model,
+                        value: new ItemModel({
+                            name: fileName,
+                            folderId: model.id
+                        })
+                    });
+                }
                 break;
             case 'multi':
                 if (fileName.trim() === '') {

small-docker/Dockerfile

@@ -14,7 +14,7 @@ RUN chmod a+x /usr/local/bin/groupadd
 RUN touch /usr/local/bin/useradd
 RUN chmod a+x /usr/local/bin/useradd
 
-RUN pip install girder-slicer-cli-web
+RUN pip install --no-cache-dir girder-slicer-cli-web
 COPY . $PWD
 
 ENTRYPOINT ["python", "./cli_list.py"]