girder-slicer-cli-web 1.3.0

A girder plugin for exposing slicer CLIs over the web

A Girder plugin for exposing slicer execution model CLIs over the web using docker and girder_worker.

Installation

Slicer CLI Web is both a Girder plugin and a Girder Worker plugin. It allows dockerized tasks to be run from the Girder user interface.

Linux

In linux with Python 3.6, 3.7, 3.8, 3.9, or 3.10:

Prerequisites:

• An appropriate version of Python must be installed.

• MongoDB must be installed and running.

• RabbitMQ or another broker is needed to use Girder Worker.

• Docker must be installed and the current user must be part of the docker group.

To use Girder:

pip install girder-slicer-cli-web[girder]
girder build
girder serve

To use Girder 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.

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.

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

When you visit the item page of an imported CLI, an extra Configure Task section is shown. You can set all of the inputs for the CLI and indicate where output files should be stored. Selecting Run Task will have Girder Worker execute the CLI. See the Jobs panel for progress and error messages.

Docker CLIs

Slicer CLI Web executes programs from docker images. Any docker image can be used that complies with some basic responses from its ENTRYPOINT.

Specifically, when a docker image is invoked like:

docker run <docker image tag> --list_cli

it needs to respond with with a JSON dictionary of CLIs, where the keys of this dictionary are the names of the CLIs. See cli_list.json for an example.

Each available CLI needs to report what it takes as inputs and outputs. When the docker image is invoked like:

docker run <docker image tag> <cli name> --xml

it needs to return an XML specification to stdout. See Example1.xml for an example.

The XML must conform to the Slicer Execution Schema, with a few minor additions:

• Some types (image, file, transform, geometry, table, directory, item) can have a reference property. When image, file, item, directory are used with Girder, if the reference property is _girder_id_, then value will be passed as a Girder ID string rather than converted to a Girder resource.

• The region type can have a coordinateSystem property.

• The region type has an optional shapes property that is a comma-separated list of values that can include default, rectangle, polygon, and multipolygon. In the official schema, region is a vector of six values of the form x,y,z,rx,ry,rz, defining a rectangle based on its center and radius in each of three dimensions. This is the default shape. The rectangle shape allows a vector of four values defining a rectangle of the form x,y,width,height, where x,y is the left and top of the rectangle in pixel coordinates. Many algorithms that accept this value accept -1,-1,-1,-1 as a default to specify the whole conceptual space. The polygon shape allows for a list of x,y values. Polygons must always have at least four points so that the vector of values cannot be confused with the default; repeat the first vertex at the end to specify a triangle. multipolygon allow multiple polygons (or hole definitions) are specified by separating coordinates by -1,-1 (this prohibits -1,-1 from being a coordinate within a polygon).

• Some input types (image, file, item, directory) can have defaultNameMatch, defaultPathMatch, and defaultRelativePath properties. The first two are regular expressions designed to give a UI a value to match to prepopulate default values from files or paths that match the regex. defaultNameMatch is intended to match the final path element, whereas defaultPathMatch is used on the entire path as a combined string. defaultRelativePath is used to find a value that has a path relative to some base. In the Girder UI, this might be from an item.

• Input types can have a datalist property. If this is present, when the CLI is first loaded or, possibly periodically after parameters have been changed, the CLI may be called with optional parameters. The CLI is expected to return a new-line separated list of values that can be used as recommended inputs. As an example, a string input might have a datalist of --enumerate-options; the cli would be called with the existing parameters PLUS the extra parameter specified by datalist. If the result is sensible, the input control would expose this list to the user. The datalist property is a json-encoded dictionary that overrides other parameters. This should override parameters that aren’t needed to be resolved to produce the datalist (e.g., input and output files) as that will speed up the call. The CLI should respond to the modified call with a response that contains multiple <element>some text</element> values that will be the suggested data for the control.

• There are some special string parameters that, if unspecified or blank, are autopopulated. String parameters with the names of girderApiUrl and girderToken are populated with the appropriate url and token so that a running job could use girder_client to communicate with Girder.

• Internally, the ctk_cli module is used. This has two differences from the Slicer Execution Schema that are technically bugs.

  • Enumerations have bare elements under the appropriate parent tag. That is, instead of a structure like <string-enumeration>...<enumeration><element>Value 1</element><element>Value 2</element>...</enumeration></string-enumeration>, the <enumeration> tag is omitted: <string-enumeration>...<element>Value 1</element><element>Value 2</element>...</string-enumeration>.

  • Booleans specify a true or false value after the flag or long flag. The Slicer Execution Schema states that booleans should be false by default and the presense of the flag should make them true. The ctk_cli specifies that they take a single true or false parameter. This doesn’t change the xml; it cahnges what is passed to the CLI. Instead of passing --longflag to set the flag to true, --longflag true must be passed.

–list_cli response format

The response from a docker image invoked with the --list_cli option needs to be a JSON response returning a single object. The object must contain a key for each CLI. Each key has a value used to parse or handle the CLI.

Here is a commented example:

{
  // the key is the name of the CLI
  "Example1": {
    // type is typically either "python" or "cxx".  The default program
    // either runs "python <CLI key>/<CLI key>.py" for python or
    // "<CLI key>/<CLI key>" for cxx.
    "type": "python"
  },
  "Example2": {
    "type": "python",
    // The desc-type defaults to xml but can be any of "xml", "json", or
    // "yaml".  To get the CLI command line options, the CLI is invoked via
    //   docker run <docker image tag> <cli name> --<desc-type>
    "desc-type": "json"
  },
  "AnotherName": {
    // The alias allows the CLI to be invoked as either the key or the
    // alias.  This runs Example2 when invoked as AnotherName.
    "alias": "Example2",
    "type": "python"
  },
  "Example3": {
    "type": "python",
    // docker-params is a dictionary of parameters passed to the docker API
    // when the docker container is created and run.  Not all possible tags
    // are passed through.  See the docker python module for options:
    // https://docker-py.readthedocs.io/en/stable/containers.html
    "docker-params": {
      "ipc_mode": "host"
    }
  }
}

CLI Endpoints

Each exposed CLI is added as an endpoint using the REST path of slicer_cli_web/<docker image tag and version>/<cli command>/run and also using the REST path of slicer_cli_web/<internal item id>/run, where <docker image tag and version> is the combined tag and version with slashes, colons, and at signs replaced by underscores. All command line parameters can be passed as endpoint query parameters. Input items, folders, and files are specified by their Girder ID. Input images are specified by a Girder file ID. Output files are specified by name and with an associated parameter with the same name plus a _folder suffix with a Girder folder ID.

Small Example CLI Docker

The small example CLI docker image can be built locally via docker build --force-rm -t girder/slicer_cli_web:small ., or pulled from Docker Hub.

Batch Processing

All CLIs that take any single item, image, or files as inputs can be run on a set of such resources from a single directory. For non-batch processing, the ID of the image, item, or file is passed to <param>. For batch processing, the ID of a folder is passed to <param>_folder and a regular expression is passed to <param>. All items in that folder whose name matches the regex are processed. For images, only items that contain large_images are considered. For files, the first file in each considered item is used.

If two inputs have batch specifications, there must be a one-to-one correspondence between the each of the lists of items determined by the folder ID and regular expression. All of the lists are enumerated sorted by the lower case item name.

When running a batch job, a parent job initiates ordinary (non-batch) jobs. The parent job will only start another child job when the most recent child job is no longer waiting to start. This allows non-batch jobs or multiple batch jobs’ children to naturally interleave. The parent job can be canceled which will stop it from scheduling any more child jobs.

Templated Inputs

Any CLI parameter that takes a value that isn’t a Girder resource identifer can be specified with a Jinja2-style template string.

For instance, instead of typing an explicit output file name, one can specify something like {{title}}-{{reference_base}}-{{now}}{{extension}}. If this were being run on a task called “Radial Blur” on an image called “SampleImage.tiff”, where the output image referenced the image image and had a list of file extensions starting with “.png”, this would end up being converted to the value Radial Blur-SampleImage-20210428-084321.png.

The following template values are handled identically for all parameters:

• {{title}}: the displayed CLI task title.

• {{task}}: the internal task name (this usually doesn’t have spaces in it)

• {{image}}: the tag of the Docker image used for the task

• {{now}}: the local time the job started in the form yyyymmdd-HHMMSS. You can use yyyy, mm, dd, HH, MM, SS for the four digit year, and two digit month, day, 24-hour, minute, and second.

• {{parameter_<name of cli parameter>}}: any parameter that isn’t templated can be referenced by its name. For instance, in Example1 in the small-docker cli in this repo, {{parameter_stringChoice}} would get replaced by the value passed to the stringChoice parameter.

• {{parameter_<name of cli parameter>_base}} is the same as the previous item except that if the right-most part of the parameter looks like a file extension, it is removed. This can be used to get the base name of file parameters.

There are also template values specific to individual parameters:

• {{name}}: the name of this parameter. This usually doesn’t have any spaces in it.

• {{label}}: the label of the is parameter. This is what is displayed in the user interface.

• {{description}}: the description of the parameter.

• {{index}}: the index, if any, of the parameter.

• {{default}}: the default value, if any, of the parameter.

• {{extension}}: the first entry in the fileExtension value of the parameter, if any.

• {{reference}}: if the parameter has a reference to another parameter, this returns that parameter’s value. It is equivalent to {{parameter_<reference>}}.

• {{reference_base}}: the reference value mentioned previously striped of the right-most file extension.

If the local (server) environment has any environment variables that begin with SLICER_CLI_WEB_, these are accessible in the templates as {{env_(name)}}. For instance, SLICER_CLI_WEB_DASK_SERVER would be accessible as {{env_DASK_SERVER}}.