From d6c6265ec98043d6aae6747431593fa3ddde7d9f Mon Sep 17 00:00:00 2001 From: bogdang989 Date: Mon, 13 Jan 2020 14:58:50 +0100 Subject: [PATCH 1/4] Fix secondaryFiles DSL example title --- salad/schema_salad/metaschema/sfdsl_res.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/salad/schema_salad/metaschema/sfdsl_res.yml b/salad/schema_salad/metaschema/sfdsl_res.yml index f619495..871b8e0 100644 --- a/salad/schema_salad/metaschema/sfdsl_res.yml +++ b/salad/schema_salad/metaschema/sfdsl_res.yml @@ -10,7 +10,7 @@ stripped off and the value of the field `required` is set to `False` * The remaining value is assigned to the field `pattern` - ### Type DSL example + ### Secondary files DSL example Given the following schema: From 944d5aac888610fcd54997c887e94edef8d75f78 Mon Sep 17 00:00:00 2001 From: bogdang989 Date: Mon, 13 Jan 2020 15:11:38 +0100 Subject: [PATCH 2/4] Add doc for SecondaryFileSchema --- Process.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/Process.yml b/Process.yml index ec1d1ba..61cc2db 100644 --- a/Process.yml +++ b/Process.yml @@ -939,6 +939,11 @@ $graph: set to `false` and the expected secondary file does not exist. Default value for `required` field is `true` for secondary files on input and `false` for secondary files on output. + doc: | + Secondary files are specified using a mini DSL for secondary files. For + implementation details and examples, please see + [this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files) + in the Schema Salad specification. - name: LoadListingRequirement type: record From c157f7e90369ad0e19287b22cbb6a55e4f50cca2 Mon Sep 17 00:00:00 2001 From: bogdang989 Date: Mon, 13 Jan 2020 15:12:02 +0100 Subject: [PATCH 3/4] Fix broken links --- Workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Workflow.yml b/Workflow.yml index f6c58e6..7e8217e 100644 --- a/Workflow.yml +++ b/Workflow.yml @@ -103,8 +103,8 @@ $graph: contain either a non-string value accepted by the field type, or a valid expression which returns a value having one of the the other types defined for that field. - * [WorkflowStepInput](WorkflowStepInput) now has a `loadContents` field. - * [WorkflowStepInput.id](WorkflowStepInput) field value does not have to match an + * [WorkflowStepInput](#WorkflowStepInput) now has a `loadContents` field. + * [WorkflowStepInput.id](#WorkflowStepInput) field value does not have to match an `input.id` value from the process specified in the `run` field. See also the [CWL Command Line Tool Description, v1.1 changelog](CommandLineTool.html#Changelog). From e21b6a0ef1a4fe070bc46c08ed102f1d8f7ce652 Mon Sep 17 00:00:00 2001 From: bogdang989 Date: Mon, 13 Jan 2020 15:52:52 +0100 Subject: [PATCH 4/4] Update doc for SecondaryFileSchema --- Process.yml | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/Process.yml b/Process.yml index 61cc2db..54bda65 100644 --- a/Process.yml +++ b/Process.yml @@ -940,8 +940,17 @@ $graph: Default value for `required` field is `true` for secondary files on input and `false` for secondary files on output. doc: | - Secondary files are specified using a mini DSL for secondary files. For - implementation details and examples, please see + Secondary files are specified using the following micro-DSL for secondary files: + + * If the value is a string, it is transformed to an object with two fields + `pattern` and `required` + * By default, the value of `required` is `null` + (this indicates default behavior, which may be based on the context) + * If the value ends with a question mark `?` the question mark is + stripped off and the value of the field `required` is set to `False` + * The remaining value is assigned to the field `pattern` + + For implementation details and examples, please see [this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files) in the Schema Salad specification.