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devel:workflow_specification_syntax [2013/09/09 15:23] – epujadas | beewm:devel:workflow_specification_syntax [2016/05/20 12:11] (current) – admin | ||
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<code xml> | <code xml> | ||
- | < | + | < |
< | < | ||
< | < | ||
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< | < | ||
< | < | ||
- | <dataset name=" | + | <dataset name=" |
.... | .... | ||
</ | </ | ||
</ | </ | ||
< | < | ||
- | <module name=" | + | <module name=" |
<params (optional)> | <params (optional)> | ||
<param name=" | <param name=" | ||
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< | < | ||
< | < | ||
- | <dataset name=" | + | <dataset name=" |
<files (considered and required only for datasets to store) in_dir=" | <files (considered and required only for datasets to store) in_dir=" | ||
</ | </ | ||
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< | < | ||
<dataset name=" | <dataset name=" | ||
- | <dataset name=" | + | <dataset name=" |
<dataset name=" | <dataset name=" | ||
</ | </ | ||
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==== < | ==== < | ||
Name of the workflow. | Name of the workflow. | ||
+ | Workflow | ||
==== < | ==== < | ||
Author of the workflow. | Author of the workflow. | ||
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When a process is started by submitting a particular workflow together with one or several input datasets, it will be checked that: | When a process is started by submitting a particular workflow together with one or several input datasets, it will be checked that: | ||
* the input dataset(s) identified by its storage ID exist in storage | * the input dataset(s) identified by its storage ID exist in storage | ||
- | * the input dataset(s) in storage have the same type as specified in the ''< | + | * the input dataset(s) in storage have the same type as specified in the ''< |
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==== <dataset type=" | ==== <dataset type=" | ||
- | Required. Corresponds to the dataset type provided by the storage. It is used for validation purposes. | + | Optional. Corresponds to the dataset type provided by the storage. It is used for validation purposes. |
==== <dataset stage=" | ==== <dataset stage=" | ||
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:!: This feature is not implemented. The application behaves as this value would be set to true. To be discussed if it is needed, since the directory of a dataset could be specified as metadata or as variable. | :!: This feature is not implemented. The application behaves as this value would be set to true. To be discussed if it is needed, since the directory of a dataset could be specified as metadata or as variable. | ||
+ | |||
+ | |||
+ | ==== <files in_dir=" | ||
+ | With this element, the files and/or directories to stage are selected. All the ''" | ||
+ | * located in the ''" | ||
+ | * matching the regex expression specified in the ''" | ||
===== <module name=" | ===== <module name=" | ||
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====== Resolving Workflow Templates ====== | ====== Resolving Workflow Templates ====== | ||
- | The workflow template should be resolved by substituting the variable values with the effectively used values to provide traceability. | ||
- | The resolved workflow should be stored together with the stored results (as it is in the current iBrain2).\\ | ||
- | Variables are specified with the following terminology: | ||
- | ===== Example ===== | + | |
- | The template snippet: | + | Bee supports the use of variables in its workflow description file.\\ |
- | <code xml> | + | Variables are specified with the following terminology: |
- | ... | + | Please check **[[:beewm:devel: |
- | < | + | |
- | <module name=" | + | |
- | < | + | |
- | < | + | |
- | ... | + | |
- | </ | + | |
- | would be resolved into: | + | |
- | <code xml> | + | |
- | ... | + | |
- | < | + | |
- | <module name=" | + | |
- | < | + | |
- | < | + | |
- | ... | + | |
- | </ | + |