Girder 5

README.rst

@@ -33,7 +33,7 @@ To use Girder Worker:
 
 .. code-block:: bash
 
-  pip install girder-slicer-cli-web[worker]
+  pip install 'girder-slicer-cli-web[worker]'
   GW_DIRECT_PATHS=true girder_worker -l info -Ofair --prefetch-multiplier=1
 
 The first time you start Girder, you'll need to configure it with at least one user and one assetstore (see the Girder_ documentation).  Additionally, it is recommended that you install some dockerized tasks, such as the HistomicsTK_ algorithms.  This can be done going to the Admin Console, Plugins, Slicer CLI Web settings.  Set a default task upload folder, then import the ``dsarchive/histomicstk:latest`` docker image.
@@ -44,9 +44,24 @@ Girder Plugin
 Importing Docker Images
 =======================
 
-When installed in Girder, an admin user can go to the Admin Console -> Plugins -> Slicer CLI Web to add Docker images.  Select a Docker image and an existing folder and then select Import Image.  Slicer CLI Web will pull the Docker image if it is not available on the Girder machine.
+Once a docker image has been created and pushed to Docker Hub, you can register the image's CLI as a set of tasks on the server. To do so,
+use the client upload script bundled with this tool. To install it, run:
+
+.. code-block:: bash
+
+  pip install 'girder-slicer-cli-web[client]'
+
+Create an API key with the "Manage Slicer CLI tasks" scope, and set it in your environment and run a command like this example:
+
+.. code-block:: bash
+
+  GIRDER_API_KEY=my_key_vale upload-slicer-cli-task https://my-girder-host.com/api/v1 641b8578cdcf8f129805524b my-slicer-cli-image:latest
+
+The first argument of this command is the API URL of the server, the second is a Girder folder ID where the tasks will live, and the
+last argument is the docker image identifier. (If the image does not exist locally it will be pulled.) If you just want to create a
+single CLI task rather than all tasks from ``--list_cli``, you can pass ``--cli=CliName``. If you wish to replace the existing tasks
+with the latest specifications, also pass the ``--replace`` flag to the command.
 
-For each docker image that is imported, a folder is created with the image tag.  Within this folder, a subfolder is created with the image version.  The subfolder will have one item per CLI that the Docker image reports.  These items can be moved after they have been imported, just like standard Girder items.
 
 Running CLIs
 ============

setup.py

@@ -63,14 +63,19 @@ def prerelease_local_scheme(version):
     ],
     extras_require={
         'girder': [
-            'docker>=2.6.0',
-            'girder>=3.0.4',
-            'girder-jobs>=3.0.3',
-            'girder-worker[girder]>=0.6.0',
+            'girder>=5.0.0a2',
+            'girder-jobs>=5.0.0a2',
+            # TODO restore this when girder-worker is released
+            #'girder-worker[girder]>=5',
         ],
         'worker': [
             'docker>=2.6.0',
-            'girder-worker[worker]>=0.6.0',
+            # TODO restore this when girder-worker is released
+            #'girder-worker[worker]>=5',
+        ],
+        'client': [
+            'click',
+            'girder-client',
         ]
     },
     entry_points={
@@ -79,6 +84,9 @@ def prerelease_local_scheme(version):
         ],
         'girder_worker_plugins': [
             'slicer_cli_web = slicer_cli_web.girder_worker_plugin:SlicerCLIWebWorkerPlugin'
+        ],
+        'console_scripts': [
+            'upload-slicer-cli-task = slicer_cli_web.upload_slicer_cli_task:upload_slicer_cli_task'
         ]
     },
     python_requires='>=3.8',

slicer_cli_web/__init__.py

@@ -34,5 +34,6 @@
     # package is not installed
     pass
 
-
 __license__ = 'Apache 2.0'
+
+TOKEN_SCOPE_MANAGE_TASKS = 'slicer_cli_web.manage_tasks'

slicer_cli_web/cli_list_entrypoint.py

@@ -1,14 +1,12 @@
 import argparse
 import json
+import logging
 import os
 import subprocess
 import sys
 import textwrap as _textwrap
 
-try:
-    from girder import logger
-except ImportError:
-    import logging as logger
+logger = logging.getLogger(__name__)
 
 
 class _MultilineHelpFormatter(argparse.HelpFormatter):

slicer_cli_web/docker_resource.py

@@ -14,27 +14,32 @@
 #  limitations under the License.
 #############################################################################
 
-
+import copy
 import json
 import os
 import re
+import time
+from base64 import b64decode
 
 import pymongo
 from girder.api import access
 from girder.api.describe import Description, autoDescribeRoute, describeRoute
-from girder.api.rest import setRawResponse, setResponseHeader
+from girder.api.rest import filtermodel, setRawResponse, setResponseHeader
 from girder.api.v1.resource import Resource, RestException
 from girder.constants import AccessType, SortDir
 from girder.exceptions import AccessException
+from girder.models.folder import Folder
 from girder.models.item import Item
+from girder.models.token import Token
 from girder.utility import path as path_util
 from girder.utility.model_importer import ModelImporter
 from girder_jobs.constants import JobStatus
 from girder_jobs.models.job import Job
 
+from . import TOKEN_SCOPE_MANAGE_TASKS, rest_slicer_cli
+from .cli_utils import as_model, get_cli_parameters
 from .config import PluginSettings
-from .models import CLIItem, DockerImageItem, DockerImageNotFoundError
-from .rest_slicer_cli import genRESTEndPointsForSlicerCLIsForItem
+from .models import CLIItem, DockerImageItem, DockerImageNotFoundError, parser
 
 
 class DockerResource(Resource):
@@ -51,6 +56,7 @@ def __init__(self, name):
         self.resourceName = name
         self.jobType = 'slicer_cli_web_job'
         self.route('PUT', ('docker_image',), self.setImages)
+        self.route('POST', ('cli',), self.createOrReplaceCli)
         self.route('DELETE', ('docker_image',), self.deleteImage)
         self.route('GET', ('docker_image',), self.getDockerImages)
 
@@ -62,7 +68,60 @@ def __init__(self, name):
 
         self.route('GET', ('path_match', ), self.getMatchingResource)
 
-        self._generateAllItemEndPoints()
+        self.route('POST', ('cli', ':id', 'run'), self.runCli)
+        self.route('POST', ('cli', ':id', 'rerun'), self.rerunCli)
+        self.route('POST', ('cli', ':id', 'datalist', ':key'), self.datalistHandler)
+
+    @access.user
+    @autoDescribeRoute(
+        Description('Run a Slicer CLI job.')
+        .modelParam('id', 'The slicer CLI task item', Item, level=AccessType.READ)
+    )
+    def runCli(self, item, params):
+        user = self.getCurrentUser()
+        token = Token().createToken(user=user)
+        return cliSubHandler(CLIItem(item), params, user, token).job
+
+    @access.user
+    @autoDescribeRoute(
+        Description('Re-run a Slicer CLI job.')
+        .modelParam('id', 'The slicer CLI item task', Item, level=AccessType.READ)
+        .modelParam('jobId', 'The job to re-run', Job, level=AccessType.READ)
+    )
+    def rerunCli(self, item, job, params):
+        user = self.getCurrentUser()
+        newParams = job.get('_original_params', {})
+        newParams.update(params)
+
+        token = Token().createToken(user=user)
+        return cliSubHandler(CLIItem(item), newParams, user, token).job
+
+    @access.user
+    @describeRoute(
+        Description('Lookup a datalist parameter on a CLI task')
+        .modelParam('id', 'The slicer CLI item task', Item, level=AccessType.READ)
+        .param('key', 'The parameter name to look up')
+        .deprecated()
+    )
+    def datalistHandler(self, item, key, params):
+        # TODO we should change any client that is using this to instead poll the job rather than
+        #   waiting for it to finish in the request thread.
+        user = self.getCurrentUser()
+
+        currentItem = CLIItem(item)
+        token = Token().createToken(user=user)
+        job = cliSubHandler(currentItem, params, user, token, key).job
+        delay = 0.01
+        while job['status'] not in {JobStatus.SUCCESS, JobStatus.ERROR, JobStatus.CANCELED}:
+            time.sleep(delay)
+            delay = min(delay * 1.5, 1.0)
+            job = Job().load(id=job['_id'], force=True, includeLog=True)
+        result = ''.join(job['log']) if 'log' in job else ''
+        if '<element' in result:
+            result = result[result.index('<element'):]
+        if '</element>' in result:
+            result = result[:result.rindex('</element>') + 10]
+        return result
 
     @access.public
     @describeRoute(
@@ -183,7 +242,7 @@ def parseImageNameList(self, param):
                 raise RestException('Image %s does not have a tag or digest' % img)
         return nameList
 
-    @access.admin
+    @access.admin(scope=TOKEN_SCOPE_MANAGE_TASKS)
     @describeRoute(
         Description('Add one or a list of images')
         .notes('Must be a system administrator to call this.')
@@ -210,6 +269,37 @@ def setImages(self, params):
             raise RestException('no upload folder given or defined by default')
         return self._createPutImageJob(nameList, folder, params.get('pull', None))
 
+    @access.admin(scope=TOKEN_SCOPE_MANAGE_TASKS)
+    @filtermodel(Item)
+    @autoDescribeRoute(
+        Description('Add or replace an item task.')
+        .notes('Must be a system administrator to call this.')
+        .modelParam('folder', 'The folder ID to upload the task to.', paramType='formData',
+                    model=Folder, level=AccessType.WRITE)
+        .param('image', 'The docker image identifier.')
+        .param('name', 'The name of the item to create or replace.')
+        .param('replace', 'Whether to replace an existing item with this name.', dataType='boolean')
+        .param('spec', 'Base64-encoded XML spec of the CLI.')
+        .errorResponse('You are not a system administrator.', 403)
+    )
+    def createOrReplaceCli(self, folder: dict, image: str, name: str, replace: bool, spec: str):
+        try:
+            spec = b64decode(spec).decode()
+        except ValueError:
+            raise RestException('The CLI spec must be base64-encoded UTF-8.')
+
+        item = Item().createItem(
+            name, creator=self.getCurrentUser(), folder=folder, reuseExisting=replace
+        )
+        metadata = dict(
+            slicerCLIType='task',
+            type='Unknown',  # TODO does "type" matter behaviorally? If so get it from the client
+            digest=None,  # TODO should we support this?
+            image=image,
+            **parser._parse_xml_desc(item, self.getCurrentUser(), spec)
+        )
+        return Item().setMetadata(item, metadata)
+
     def _createPutImageJob(self, nameList, baseFolder, pull=False):
         job = Job().createLocalJob(
             module='slicer_cli_web.image_job',
@@ -261,7 +351,9 @@ def _generateAllItemEndPoints(self):
         seen = set()
         for item in items:
             # default if not seen yet
-            genRESTEndPointsForSlicerCLIsForItem(self, item, item.restPath not in seen)
+            rest_slicer_cli.genRESTEndPointsForSlicerCLIsForItem(
+                self, item, item.restPath not in seen
+            )
             seen.add(item.restPath)
 
     def addRestEndpoints(self, event):
@@ -390,3 +482,101 @@ def getMatchingResource(self, name, path, type, relative_path, base_id, base_typ
         except pymongo.errors.ExecutionTimeout:
             return None
         return None
+
+
+def cliSubHandler(cliItem, params, user, token, datalistKey=None):
+    """
+    Create a job for a Slicer CLI item and schedule it.
+
+    :param currentItem: a CLIItem model.
+    :param params: parameter dictionary passed to the endpoint.
+    :param user: user model for the current user.
+    :param token: allocated token for the job.
+    :param datalistKey: if not None, a param name for this CLI that has a datalist.
+    """
+    from .girder_worker_plugin.direct_docker_run import run
+
+    clim = as_model(cliItem.xml)
+    cliTitle = clim.title
+
+    original_params = copy.deepcopy(params)
+    index_params, opt_params, simple_out_params = get_cli_parameters(clim)
+
+    datalistSpec = {
+        param.name: json.loads(param.datalist)
+        for param in index_params + opt_params
+        if param.channel != 'output' and param.datalist
+    }
+
+    container_args = [cliItem.name]
+    reference = {'slicer_cli_web': {
+        'title': cliTitle,
+        'image': cliItem.image,
+        'name': cliItem.name,
+    }}
+    now = time.localtime()
+    templateParams = {
+        'title': cliTitle,  # e.g., "Detects Nuclei"
+        'task': cliItem.name,  # e.g., "NucleiDetection"
+        'image': cliItem.image,  # e.g., "dsarchive/histomicstk:latest"
+        'now': time.strftime('%Y%m%d-%H%M%S', now),
+        'yyyy': time.strftime('%Y', now),
+        'mm': time.strftime('%m', now),
+        'dd': time.strftime('%d', now),
+        'HH': time.strftime('%H', now),
+        'MM': time.strftime('%M', now),
+        'SS': time.strftime('%S', now),
+    }
+
+    has_simple_return_file = bool(simple_out_params)
+    sub_index_params, sub_opt_params = index_params, opt_params
+
+    if datalistKey:
+        datalist = datalistSpec[datalistKey]
+        params = params.copy()
+        params.update(datalist)
+        sub_index_params = [
+            param if param.name not in datalist or not rest_slicer_cli.is_on_girder(param)
+            else rest_slicer_cli.stringifyParam(param)
+            for param in index_params
+            if (param.name not in datalist or datalist.get(param.name) is not None) and
+            param.name not in {k + rest_slicer_cli.FOLDER_SUFFIX for k in datalist}
+        ]
+        sub_opt_params = [
+            param if param.name not in datalist or not rest_slicer_cli.is_on_girder(param)
+            else rest_slicer_cli.stringifyParam(param)
+            for param in opt_params
+            if param.channel != 'output' and (
+                param.name not in datalist or datalist.get(param.name) is not None) and
+            param.name not in {k + rest_slicer_cli.FOLDER_SUFFIX for k in datalist}
+        ]
+
+    args, result_hooks, primary_input_name = rest_slicer_cli.prepare_task(
+        params, user, token, sub_index_params, sub_opt_params,
+        has_simple_return_file, reference, templateParams=templateParams)
+    container_args.extend(args)
+
+    jobType = '%s#%s' % (cliItem.image, cliItem.name)
+
+    if primary_input_name:
+        jobTitle = '%s on %s' % (cliTitle, primary_input_name)
+    else:
+        jobTitle = cliTitle
+
+    job_kwargs = cliItem.item.get('meta', {}).get('docker-params', {})
+    job = run.delay(
+        girder_user=user,
+        girder_job_type=jobType,
+        girder_job_title=jobTitle,
+        girder_result_hooks=result_hooks,
+        image=cliItem.digest,
+        pull_image='if-not-present',
+        container_args=container_args,
+        **job_kwargs
+    )
+    jobRecord = Job().load(job.job['_id'], force=True)
+    job.job['_original_params'] = jobRecord['_original_params'] = original_params
+    job.job['_original_name'] = jobRecord['_original_name'] = cliItem.name
+    job.job['_original_path'] = jobRecord['_original_path'] = cliItem.restBasePath
+    Job().save(jobRecord)
+    return job