https://github.com/buchanae/cwl
common workflow language library and runtime
https://github.com/buchanae/cwl
cwl
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common workflow language library and runtime
- Host: GitHub
- URL: https://github.com/buchanae/cwl
- Owner: buchanae
- License: mit
- Created: 2017-10-24T17:36:12.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-12-19T18:58:53.000Z (over 6 years ago)
- Last Synced: 2024-11-14T21:15:39.429Z (5 months ago)
- Topics: cwl
- Language: Go
- Homepage:
- Size: 274 KB
- Stars: 7
- Watchers: 6
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: readme.md
- License: LICENSE
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README
[](https://opensource.org/licenses/MIT)
[](http://godoc.org/github.com/buchanae/cwl)
This is a Go library and command line tool for working with the [common workflow language (CWL)](http://commonwl.org).
The core library includes the data type
present in the CWL spec (CommandLineTool, Workflow, etc.), with a few extra utilities for loading and working with CWL documents.
For details, see the [reference docs](https://godoc.org/github.com/buchanae/cwl).
## Subpackages
The [process](./process) library contains experimental, unfinished code for processing CWL documents in order to execute commands and workflows.
The [expr](./expr) library contains utilities for parsing CWL expressions out of strings. This parser is not yet robust (see the known issues below).
## Alpha quality
At the time of this writing, this library is only a couple weeks old. I feel that the core CWL document loading library is fairly stable, but I can't promise that there aren't plenty of bugs lurking.
The command line tool is far from stable, and needs work before becoming useful.
The [process](./process) library is highly experimental. Processing CWL tools and workflows in a robust manner is not a trivial task.
## CLI
The `cwl` command line tool includes a few commands for loading, inspecting, and experimental support for running commands. See the [releases](https://github.com/buchanae/cwl/releases) page to download the command line tool binary.
## Usage (CLI)
The command line tool is still young and therefore fairly useless. Still:
```
cwl dump https://raw.githubusercontent.com/buchanae/cwl/master/examples/array-inputs.cwl
// ...outputs the normalized document in JSON.
```
`cwl run` exists and is experimental. This command will run a CWL document, similar `cwltool`.
## Usage (library)
```go
package main
import (
"log"
"github.com/buchanae/cwl"
)
func main() {
// Load a CWL CommandLineTool document.
path := "https://raw.githubusercontent.com/buchanae/cwl/master/examples/array-inputs.cwl"
doc, err := cwl.Load(path)
if err != nil {
log.Fatal(err)
}
tool := doc.(*cwl.Tool)
// Print the ID of all the input fields
for _, input := range tool.Inputs {
log.Println(input.ID)
}
}
```
```
go run main.go
2018/03/12 18:16:22 filesA
2018/03/12 18:16:22 filesB
2018/03/12 18:16:22 filesC
```
## Normalization
The CWL spec allows multiple different types for some fields, e.g. `CommandLineTool.inputs` may be a string, a list of strings, a map of string to string, a map of string to object, and so on. This is rather difficult to program against, especially in a statically typed language without generics or union types (i.e. Go).
This library normalizes all fields to a single type, often prefering a list where a string and map might be allowed. In the example above, [`CommandLineTool.inputs`](https://godoc.org/github.com/buchanae/cwl#Tool) is a list.
Similarly, many fields might be a [CWL expression](http://www.commonwl.org/v1.0/CommandLineTool.html#Expressions). In this library, any field which *might* be an expression has the type [`Expression`](https://godoc.org/github.com/buchanae/cwl#Expression).
## Notable changes and known issues
I've taken some liberties with the CWL spec:
- `CommandLineTool` is named `Tool` instead, for brevity.
- [Schema Salad](http://www.commonwl.org/v1.0/SchemaSalad.html) is not implemented and likely won't be implemented.
- `$include` and `$import` statements are not yet implemented, but will be.
- The CWL expression parser is not robust and will not correctly parse complex expressions, especially those containing `$()` and escaping.
- documentation and examples are still sparse, more on the way soon.