Processes

Type of Processes

Weaver supports multiple type of processes, as listed below. Each one of them are accessible through the same API interface, but they have different implications.

Builtin

These processes come pre-packaged with Weaver. They will be available directly on startup of the application and re-updated on each boot to make sure internal database references are updated with any source code changes.

Theses processes typically correspond to utility operations. They are specifically useful when employed as step within a Workflow process that requires data-type conversion between input/output of similar, but not perfectly, compatible definitions.

For example, process weaver.processes.builtin.jsonarray2netcdf takes a single input JSON file which its content contains an array-list of NetCDF file references, and returns them directly as the corresponding list of output files. These two different file formats (single JSON to multiple NetCDF) can then be used to map two processes with these respective output and inputs.

As of the latest release, following builtin processes are available:

All builtin processes are marked with weaver.processes.constants.CWL_REQUIREMENT_APP_BUILTIN in the CWL hints* section.

WPS-1/2

This kind of process corresponds to a traditional WPS XML or JSON endpoint (depending of supported version) prior to WPS-REST specification. When the WPS-REST process is deployed in Weaver using an URL reference to an WPS-1/2 process, Weaver parses and converts the XML or JSON body of the response and registers the process locally using this definition. This allows a remote server offering limited functionalities (e.g.: no REST bindings supported) to provide them through Weaver.

A minimal Deploy request body for this kind of process could be as follows:

{
  "processDescription": {
    "process": {
      "id": "my-process-reference"
    }
  },
  "executionUnit": [
    {
      "href": "https://example.com/wps?service=WPS&request=DescribeProcess&identifier=my-process&version=1.0.0"
    }
  ]
}

This would tell Weaver to locally deploy the my-process-reference process using the WPS-1 URL reference that is expected to return a DescribeProcess XML schema. Provided that this endpoint can be resolved and parsed according to typical WPS specification, this should result into a successful process registration. The deployed process would then be accessible with DescribeProcess requests.

The above deployment procedure can be automated on startup using Weaver’s wps_processes.yml configuration file. Please refer to Configuration of WPS Processes section for more details on this matter.

Warning

Because Weaver creates a snapshot of the reference process at the moment it was deployed, the local process definition could become out-of-sync with the remote reference where the Execute request will be sent. Refer to Remote Provider section for more details to work around this issue.

See also

WPS-REST

This process type is the main component of Weaver. All other process types are converted to this one either through some parsing (e.g.: WPS-1/2) or with some requirement indicators (e.g.: Builtin, Workflow) for special handling.

When deploying one such process directly, it is expected to have a reference to a CWL Application Package. This is most of the time employed to wrap a reference docker image process. The reference package can be provided in multiple ways as presented below.

Note

When a process is deployed with any of the below supported Application Package formats, additional parsing of this CWL as well as complementary details directly within the WPS deployment body is accomplished. See Correspondance between CWL and WPS fields section for more details.

Package as Literal Unit Block

In this situation, the CWL definition is provided as is using JSON-formatted package embedded within the POST {WEAVER_URL}/processes (Deploy) request. The request payload would take the following shape:

{
  "processDescription": {
    "process": {
      "id": "my-process-reference"
    }
  },
  "executionUnit": [
    {
      "unit": {
        "cwlVersion": "v1.0",
        "class": "CommandLineTool",
        "inputs": ["<...>"],
        "outputs": ["<...>"],
        "<...>": "<...>"
      }
    }
  ]
}

ESGF-CWT

For traditional WPS-1 process type, Weaver adds default values to CWL definition. As we can see in weaver/processes/wps_package.py, the following default values for the CWL package are:

cwl_package = OrderedDict([
    ("cwlVersion", "v1.0"),
    ("class", "CommandLineTool"),
    ("hints", {
        CWL_REQUIREMENT_APP_WPS1: {
            "provider": get_url_without_query(wps_service_url),
            "process": process_id,
        }}),
])

In ESGF-CWT, ESGF-CWTRequirement hint is used instead of default WPS1Requirement, contained in the weaver.processes.constants.CWL_REQUIREMENT_APP_WPS1 variable up here. The handling of this technicality is handled in weaver/processes/wps_package.py. We can define ESGF-CWT processes using this syntax:

"cwlVersion": "v1.0",
"class": "CommandLineTool",
"hints": {
    "ESGF-CWTRequirement": {
        "provider": "https://edas.nccs.nasa.gov/wps/cwt",
        "process": "xarray.subset"
    }
}

Workflow

Processes categorized as Workflow are very similar to WPS-REST processes. From the API standpoint, they actually look exactly the same as an atomic process when calling DescribeProcess or Execute requests. The difference lies within the referenced Application Package which uses a CWL Workflow instead of typical CWL CommandLineTool, and therefore, modifies how the process is internally executed.

For Workflow processes to be deploy-able and executable, it is mandatory that Weaver is configured as EMS (see: Configuration Settings). This requirement is due to the nature of workflows that chain processes that need to be dispatched to known remote ADES servers (see: Configuration of Data Sources and Workflow Operations).

Given that a Workflow process was successfully deployed and that all process steps can be resolved, calling its Execute request will tell Weaver to parse the chain of operations and send step process execution requests to relevant ADES picked according to data sources. Each step’s job will then gradually be monitored from the remote ADES until completion, and upon successful result, the EMS will retrieve the data references to pass it down to the following step. When the complete chain succeeds, the final results of the last step will be provide as Workflow output as for atomic processes. In case of failure, the error will be indicated in the log with the appropriate step and message where the error occurred.

Note

Although chaining sub-workflow(s) within a bigger scoped workflow is technically possible, this have not yet been fully explored (tested) in Weaver. There is a chance that data-source resolution fails to identify where to dispatch the step in this situation. If this impacts you, please vote and indicate your concern on issue #171.

Remote Provider

Remote provider correspond to a remote service that provides similar interfaces as supported by Weaver (WPS-like). For example, a remote WPS-1 XML endpoint can be referenced as a provider. When an API Providers-scoped request is executed, for example to list is processes capabilities (see GetCapabilities), Weaver will send the corresponding request using the registered reference URL to access the remote server and reply with parsed response, as if they its processes were registered locally.

Since remote providers obviously require access to the remote service, Weaver will only be able to provide results if the service is accessible with respect to standard implementation features and supported specifications.

The main advantage of using Weaver’s endpoint rather than directly accessing the referenced remote provider processes is in the case of limited functionality offered by the service. For instance, WPS-1 do not always offer GetStatus feature, and there is no extensive job monitoring availability. Since Weaver wraps the original reference with its own endpoints, these features indirectly become employable. Similarly, although WPS-1 offer XML-only endpoints, the parsing operation accomplished by Weaver makes theses services available as WPS-REST JSON endpoints. On top of that, registering remote providers into Weaver allows the user to use it as a central hub to keep references to all his accessible services and dispatch jobs from a common location.

A remote provider differs from previously presented WPS-1/2 processes such that the underlying processes of the service are not registered locally. For example, if a remote service has two WPS processes, only top-level service URL will be registered locally (in Weaver’s database) and the application will have no explicit knowledge of these remote processes. When calling process-specific requests (e.g.: DescribeProcess or Execute), Weaver will re-send the corresponding request directly to the remote provider each time and return the result accordingly. On the other hand, a WPS-1/2 reference would be parsed and saved locally with the response at the time of deployment. This means that a deployed WPS-1/2 reference would act as a snapshot of the reference (which could become out-of-sync), while Remote Provider will dynamically update according to the re-fetched response from the remote service. If our example remote service was extended to have a third WPS process, it would immediately be reflected in GetCapabilities and DescribeProcess retrieved via Weaver Providers-scoped requests. This would not be the case for the WPS-1/2 reference that would need manual update (deploy the third process to register it in Weaver).

An example body of the register provider request could be as follows:

{
  "id": "my-service",
  "url": "https://example.com/wps",
  "public": true
}

Then, processes of this registered remote provider will be accessible. For example, if the referenced service by the above URL add a WPS process identified by my-process, its JSON description would be obtained with following request (DescribeProviderProcess):

GET {WEAVER_URL}/providers/my-service/processes/my-process

Note

Process my-process in the example is not registered locally. From the point of view of Weaver’s processes (i.e.: route /processes/{id}), it does NOT exist. You must absolutely use the prefixed /providers/{id} route.

Warning

API requests scoped under Providers are Weaver-specific implementation. These are not part of OGC API - Processes specification.

Managing processes included in Weaver ADES/EMS

Following steps represent the typical steps applied to deploy a process, execute it and retrieve the results.

Register a new process (Deploy)

Deployment of a new process is accomplished through the POST {WEAVER_URL}/processes POST {WEAVER_URL}/processes (Deploy) request.

The request body requires mainly two components:

  • processDescription:
    Defines the process identifier, metadata, inputs, outputs, and some execution specifications. This mostly corresponds to information that corresponds to a traditional WPS definition.
  • executionUnit:
    Defines the core details of the Application Package. This corresponds to the explicit CWL definition that indicates how to execute the given application.

Upon deploy request, Weaver will either respond with a successful result, or with the appropriate error message, whether caused by conflicting ID, invalid definitions or other parsing issues. A successful process deployment will result in this process to become available for following steps.

Warning

When a process is deployed, it is not necessarily available immediately. This is because process visibility also needs to be updated. The process must be made public to allow its discovery. For updating visibility, please refer to the PUT {WEAVER_URL}/processes/{id}/visibility (Visibility) request.

After deployment and visibility preconditions have been met, the corresponding process should become available through DescribeProcess requests and other routes that depend on an existing process.

Note that when a process is deployed using the WPS-REST interface, it also becomes available through the WPS-1/2 interface with the same identifier and definition. Because of compatibility limitations, some parameters in the WPS-1/2 might not be perfectly mapped to the equivalent or adjusted WPS-REST interface, although this concerns mostly only new features such as status monitoring. For most traditional use cases, properties are mapped between the two interfaces, but it is recommended to use the WPS-REST one because of the added features.

Access registered process(es) (GetCapabilities, DescribeProcess)

Available processes can all be listed using GET {WEAVER_URL}/processes (GetCapabilities) request. This request will return all locally registered process summaries. Other return formats and filters are also available according to provided request query parameters. Note that processes not marked with public visibility will not be listed in this result.

For more specific process details, the GET {WEAVER_URL}/processes/{id} (DescribeProcess) request should be used. This will return all information that define the process references and expected inputs/outputs.

Note

For remote processes (see: Remote Provider), Provider requests are also available for more fine-grained search of underlying processes. These processes are not necessarily listed as local processes, and will therefore sometime not yield any result if using the typical DescribeProcess endpoint.

All routes listed under Process requests should normally be applicable for remote processes by prefixing them with /providers/{id}.

Execution of a process (Execute)

Process execution (i.e.: submitting a job) is accomplished using the POST {WEAVER_URL}/processes/{id}/jobs (Execute) request. This section will first describe the basics of this request format, and after go into details for specific use cases and parametrization of various input/output combinations.

Todo

detail execute I/O (basic example)

Todo

detail returned location + example

This location can then be employed to call GetStatus monitoring request.

Process Operations

Todo

detail ‘operations’ accomplished (stage-in, exec-cwl, stage-out)

Workflow Operations

Todo

same as prev + ‘operations’ (deploy, visibility, exec-remote for each step)

File Reference Types

Most inputs can be categorized into two of the most commonly employed types, namely LiteralData and ComplexData. The former represents basic values such as integers or strings, while the other represents a file reference. Files in Weaver (and WPS in general) can be specified with any formats as MIME-type.

As for standard WPS, remote file references are usually limited to http(s) scheme, unless the process takes an input string and parses the unusual reference from the literal data to process it by itself. On the other hand, Weaver supports all following reference schemes.

  • http(s)://

  • file://

  • opensearchfile:// [experimental]

  • s3:// [experimental]

The method in which Weaver will handle such references depends on its configuration, in other words, whether it is running as ADES or EMS (see: Configuration), as well as depending on some other CWL package requirements. These use-cases are described below.

Warning

Missing schemes in URL reference are considered identical as if file:// was used. In most cases, if not always, an execution request should not employ this scheme unless the file is ensured to be at the specific location where the running Weaver application can find it. This scheme is usually only employed as byproduct of the fetch operation that Weaver uses to provide the file locally to underlying CWL application package to be executed.

When Weaver is able to figure out that the process needs to be executed locally in ADES mode, it will fetch all necessary files prior to process execution in order to make them available to the CWL package. When Weaver is in EMS configuration, it will always forward the references (regardless of scheme) exactly as provided as input of the process execution request, since it assumes it needs to dispatch the execution to another ADES remote server, and therefore only needs to verify that the file reference is reachable remotely. In this case, it becomes the responsibility of this remote instance to handle the reference appropriately. This also avoids potential problems such as if Weaver as EMS doesn’t have authorized access to a link that only the target ADES would have access to.

When CWL package defines WPS1Requirement under hints for corresponding WPS-1/2 remote processes being monitored by Weaver, it will skip fetching of http(s)-based references since that would otherwise lead to useless double downloads (one on Weaver and the other on the WPS side). It is the same in case of ESGF-CWTRequirement employed for ESGF-CWT processes. Because these processes do not normally

Note

When Weaver is fetching remote files with http(s)://, it can take advantage of additional request options to support unusual or server-specific handling of remote reference as necessary. This could be employed for instance to attribute access permissions only to some given ADES server by providing additional authorization tokens to the requests. Please refer to Configuration of Request Options for this matter.

When using S3 references, Weaver will attempt to retrieve the file using server configuration and credentials. Provided that the corresponding S3 bucket can be accessed by the running Weaver application, it will fetch the file and store it locally temporarily for CWL execution.

Note

When using S3 buckets, authorization are handled through typical AWS credentials and role permissions. This means that AWS access must be granted to the application in order to allow it fetching the file. There are also different formats of S3 reference formats handled by Weaver. Please refer to Configuration of AWS S3 Buckets for more details.

When using OpenSearch references, additional parameters are necessary to handle retrieval of specific file URL. Please refer to OpenSearch Data Source for more details.

Following table summarize the default behaviour of input file reference handling of different situations when received as input argument of process execution. For simplification, keyword <any> is used to indicate that any other value in the corresponding column can be substituted for a given row when applied with conditions of other columns, which results to same operational behaviour. Elements that behave similarly are also presented together in rows to reduce displayed combinations.

Configuration

Process Type

File Scheme

Applied Operation

<any>

<any>

opensearchfile://

Query and re-process 1

ADES

file://

Convert to http(s):// 2

http(s)://

Nothing (left unmodified)

s3://

Fetch and convert to http(s):// 4

WPS-REST (CWL) 3

file://

Nothing (file already local)

http(s)://

Fetch and convert to file://

s3://

EMS

file://

Convert to http(s):// 2

http(s)://

Nothing (left unmodified)

s3://

Footnotes

1

References defined by opensearch:// will trigger an OpenSearch query using the provided URL as well as other input additional parameters (see OpenSearch Data Source). After processing of this query, retrieved file references will be re-processed using the summarized logic in the table for the given use case.

2(1,2,3)

When a file:// (or empty scheme) maps to a local file that needs to be exposed externally for another remote process, the conversion to http(s):// scheme employs setting weaver.wps_outputs_url to form the result URL reference. The file is placed in weaver.wps_outputs_dir to expose it as HTTP(S) endpoint.

3(1,2)

When the process refers to a remote WPS-REST process (i.e.: remote WPS instance that supports REST bindings but that is not necessarily an ADES), Weaver simply wraps and monitor its remote execution, therefore files are handled just as for any other type of remote WPS-like servers. When the process contains an actual CWL Application Package that defines a CommandLineTool (including docker images), files are fetched as it will be executed locally. See CWL CommandLineTool, WPS-REST and Remote Providers for further details.

4

When an s3:// file is fetched, is gets downloaded to a temporary file:// location, which is NOT necessarily exposed as http(s)://. If execution is transferred to a remove process that is expected to not support S3 references, only then the file gets converted as in 2.

5

Workflows are only available on EMS instances. Since they chain processes, no fetch is needed as the first sub-step process will do it instead. See section about workflows as well as CWL Workflow for more details.

Todo

method to indicate explicit fetch to override these? (https://github.com/crim-ca/weaver/issues/183)

Todo

add tests that validate each combination of operation

OpenSearch Data Source

Todo

EOImage with AOI/TOI/CollectionId for OpenSearch

Multiple Inputs

Todo

repeating IDs example for WPS multi-inputs

Multiple Outputs

Although CWL allows output arrays, WPS does not support it directly, as only single values are allowed for WPS outputs according to original specification. To work around this, Metalink files can be used to provide a single output reference that embeds other references. This approach is also employed and preferred as described in PyWPS Multiple Outputs.

Todo

fix doc when Multiple Output is supported with metalink (https://github.com/crim-ca/weaver/issues/25)

Todo

add example of multi-output process definition

Todo

and how CWL maps them with WPS

Warning

This feature is being worked on (Weaver Issue #25). Direct support between

Email Notification

When submitting a job for execution, it is possible to provide the notification_email field. Doing so will tell Weaver to send an email to the specified address with successful or failure details upon job completion. The format of the email is configurable from weaver.ini.example file with email-specific settings (see: Configuration).

Monitoring of a process (GetStatus)

Todo

job status body example (success vs fail)

Obtaining output results, logs or errors

Todo

job logs/exceptions body example

Any job executed on Weaver will provide minimal log information, such as process job setup, moment when it started execution and final status. The extent of other log entries will more often than not depend on the verbosity of the underlying process being executed. When executing an Application Package, Weaver tries as best as possible to collect standard output and error steams to report them through log and exception lists.

Since Weaver can only report as much details as provided by the running application, it is recommended to provide progressive status updates when developing applications in order to help understand problematic steps in event of process execution failures. In the case of remote WPS processes monitored by Weaver, this means gradually reporting process status updates (e.g.: calling WPSResponse.update_status if you are using |pywps|_, see: Progress and Status Report), using print and/or logging operation in scripts or docker images executed through CWL CommandLineTool, etc.

Note

Job logs and exceptions are a Weaver-specific implementation. They are not part of traditional OGC API - Processes.

Special Weaver EMS use-cases

This section highlight the additional behaviour available only through an EMS-configured Weaver instance. Some other points are already described in other sections, but are briefly indicated here for conciseness.

ADES dispatching using Data Sources

Todo

add details, data-source defines where to send request of known ADES

Todo

reference config weaver.data_sources

Workflow (Chaining Step Processes)

Todo

add details, explanation done in below reference