From c3a47a61945fa915d4bdfb00ddc41f35e4193786 Mon Sep 17 00:00:00 2001 From: Toby Hodges Date: Tue, 28 Nov 2017 17:21:00 +0100 Subject: [PATCH 1/6] reworded advice on license specification --- _extras/recommended-practices.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_extras/recommended-practices.md b/_extras/recommended-practices.md index 3a5cc4d0..3396403d 100644 --- a/_extras/recommended-practices.md +++ b/_extras/recommended-practices.md @@ -8,7 +8,7 @@ Below are a set of recommended good practices to keep in mind when writing a Com ☐ No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate. -☐ Include a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]. [Example of license inclusion][license-example]. +☐ Include a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]. If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. For non-standard licenses without an SPDX identifier, provide a URL. [Example of license inclusion][license-example]. ☐ Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]. From 0a96c9e3ddf8b96056c35a4b427cb78f45b80b40 Mon Sep 17 00:00:00 2001 From: Toby Hodges Date: Wed, 29 Nov 2017 10:03:58 +0100 Subject: [PATCH 2/6] added example of SPDX ID usage --- _extras/recommended-practices.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/_extras/recommended-practices.md b/_extras/recommended-practices.md index 3396403d..96d27ec6 100644 --- a/_extras/recommended-practices.md +++ b/_extras/recommended-practices.md @@ -8,7 +8,16 @@ Below are a set of recommended good practices to keep in mind when writing a Com ☐ No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate. -☐ Include a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]. If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. For non-standard licenses without an SPDX identifier, provide a URL. [Example of license inclusion][license-example]. +☐ Include a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]. If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the licence by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is the taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license. + +_Example of metadata field for license with SPDX identifier:_ +~~~ +$namespaces: + s: http://schema.org/ +s:license: https://spdx.org/licenses/Apache-2.0 +# other s: declarations +~~~ +{: .source} ☐ Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]. From 0135021be7abb06c7ff61936b2ae1594870d3572 Mon Sep 17 00:00:00 2001 From: Toby Hodges Date: Wed, 29 Nov 2017 10:05:39 +0100 Subject: [PATCH 3/6] replaced license URLs with SPDX links --- _includes/cwl/metadata_example2.cwl | 2 +- _includes/cwl/metadata_example3.cwl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/_includes/cwl/metadata_example2.cwl b/_includes/cwl/metadata_example2.cwl index 0f04f738..f29f1c5f 100644 --- a/_includes/cwl/metadata_example2.cwl +++ b/_includes/cwl/metadata_example2.cwl @@ -38,7 +38,7 @@ s:contributor: s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2 s:codeRepository: https://github.com/common-workflow-language/common-workflow-language s:dateCreated: "2016-12-13" -s:license: https://www.apache.org/licenses/LICENSE-2.0 +s:license: https://spdx.org/licenses/Apache-2.0 $namespaces: s: https://schema.org/ diff --git a/_includes/cwl/metadata_example3.cwl b/_includes/cwl/metadata_example3.cwl index 155492bc..65c01c95 100644 --- a/_includes/cwl/metadata_example3.cwl +++ b/_includes/cwl/metadata_example3.cwl @@ -42,7 +42,7 @@ s:contributor: s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2 s:codeRepository: https://github.com/common-workflow-language/common-workflow-language s:dateCreated: "2016-12-13" -s:license: https://www.apache.org/licenses/LICENSE-2.0 +s:license: https://spdx.org/licenses/Apache-2.0 s:keywords: edam:topic_0091 , edam:topic_0622 s:programmingLanguage: C From 8cae1d3bd0f02bb306639f45d346cbd5c87f9b70 Mon Sep 17 00:00:00 2001 From: Toby Hodges Date: Wed, 29 Nov 2017 10:09:13 +0100 Subject: [PATCH 4/6] tried to link to metadata lesson --- _extras/recommended-practices.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/_extras/recommended-practices.md b/_extras/recommended-practices.md index 96d27ec6..1a652a3f 100644 --- a/_extras/recommended-practices.md +++ b/_extras/recommended-practices.md @@ -8,7 +8,7 @@ Below are a set of recommended good practices to keep in mind when writing a Com ☐ No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate. -☐ Include a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]. If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the licence by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is the taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license. +☐ Include a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]. If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the licence by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is the taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license. _Example of metadata field for license with SPDX identifier:_ ~~~ @@ -19,6 +19,8 @@ s:license: https://spdx.org/licenses/Apache-2.0 ~~~ {: .source} +For more examples of providing metadata within CWL descriptions, see the [Metadata and Authorship section][metadata-lesson] of this User Guide. + ☐ Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]. ☐ In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`. @@ -57,3 +59,4 @@ s:license: https://spdx.org/licenses/Apache-2.0 [file-prop]: http://www.commonwl.org/v1.0/CommandLineTool.html#File [orcid]: https://orcid.org [subworkflow]: http://www.commonwl.org/v1.0/Workflow.html#SubworkflowFeatureRequirement +[metadata-lesson]: /17-metadata/ From e02a86242660e0c70b5c103db12f3bb6d9aca5e0 Mon Sep 17 00:00:00 2001 From: Toby Hodges Date: Wed, 29 Nov 2017 10:11:41 +0100 Subject: [PATCH 5/6] fix metadata lesson link? --- _extras/recommended-practices.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_extras/recommended-practices.md b/_extras/recommended-practices.md index 1a652a3f..262e4592 100644 --- a/_extras/recommended-practices.md +++ b/_extras/recommended-practices.md @@ -59,4 +59,4 @@ For more examples of providing metadata within CWL descriptions, see the [Metada [file-prop]: http://www.commonwl.org/v1.0/CommandLineTool.html#File [orcid]: https://orcid.org [subworkflow]: http://www.commonwl.org/v1.0/Workflow.html#SubworkflowFeatureRequirement -[metadata-lesson]: /17-metadata/ +[metadata-lesson]: /user_guide/17-metadata/ From fe6800e0fc070bf8aab99f712f65df3d7af11887 Mon Sep 17 00:00:00 2001 From: Toby Hodges Date: Wed, 29 Nov 2017 10:17:11 +0100 Subject: [PATCH 6/6] changes Apache 2.0 license link to point to SPDX --- _extras/recommended-practices.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_extras/recommended-practices.md b/_extras/recommended-practices.md index 262e4592..81aa7f6b 100644 --- a/_extras/recommended-practices.md +++ b/_extras/recommended-practices.md @@ -51,7 +51,7 @@ For more examples of providing metadata within CWL descriptions, see the [Metada ☐ CWL implementations which also implement [`SubworkflowFeatureRequirement`][subworkflow] can support nesting workflows as a step within others. Complex workflows with individual components which can be abstracted should utilise this to make their workflow modular and allow sections of them to be easily reused. -[apache-license]: https://www.apache.org/licenses/LICENSE-2.0#apply +[apache-license]: https://spdx.org/licenses/Apache-2.0.html [license-example]: https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl/blob/master/workflows/emg-assembly.cwl#L200 [scicrunch-issue]: https://github.com/common-workflow-language/common-workflow-language/issues/scicrunch.org [edam-example]: http://edamontology.org/format_1915