From 52204fec6b73ff64b709798d8136f2e64dc3269a Mon Sep 17 00:00:00 2001 From: Johan Viklund Date: Tue, 28 Nov 2023 11:12:28 +0100 Subject: [PATCH 1/6] Adding s3inbox service to the aggregate mapping --- aggregate-mappings.json | 1 + 1 file changed, 1 insertion(+) diff --git a/aggregate-mappings.json b/aggregate-mappings.json index 00d7de5..85c172a 100644 --- a/aggregate-mappings.json +++ b/aggregate-mappings.json @@ -5,6 +5,7 @@ "sda/cmd/intercept/intercept.md": "docs/services/intercept.md", "sda/cmd/mapper/mapper.md": "docs/services/mapper.md", "sda/cmd/verify/verify.md": "docs/services/verify.md", + "sda/cmd/s3inbox/s3inbox.md": "docs/services/s3inbox.md", "sda/sda.md": "docs/services/sda.md" } } From 3199407b43aaa8b171bb6620641c495aee3c8612 Mon Sep 17 00:00:00 2001 From: Johan Viklund Date: Tue, 28 Nov 2023 11:16:15 +0100 Subject: [PATCH 2/6] Fix broken links --- docs/submission.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/submission.md b/docs/submission.md index adb831c..f605f12 100644 --- a/docs/submission.md +++ b/docs/submission.md @@ -131,7 +131,7 @@ Mina SSHD. > NOTE: > Sources are located at the separate repository: -> Essentially, it's a +> Essentially, it's a > Spring-based Maven project, integrated with the > [Local Message Broker](connection.md#local-message-broker). From e48218e8912b042c111b9256c6ab44af923da731 Mon Sep 17 00:00:00 2001 From: Johan Viklund Date: Tue, 28 Nov 2023 11:17:42 +0100 Subject: [PATCH 3/6] Upgrade links to https --- docs/CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index bb5fc32..e5ca5e9 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -67,7 +67,7 @@ Some tips about writing helpful commit messages: 6. Wrap the body at 72 characters. 7. Use the body to explain what and why vs. how. -For an in-depth explanation of the above points, please see [How to Write a Git Commit Message](http://chris.beams.io/posts/git-commit/). +For an in-depth explanation of the above points, please see [How to Write a Git Commit Message](https://chris.beams.io/posts/git-commit/). ### How we do code reviews From 5cece3c3f45e34b8efe2e212741702cfc433a3df Mon Sep 17 00:00:00 2001 From: Stefan Negru Date: Tue, 28 Nov 2023 13:29:35 +0200 Subject: [PATCH 4/6] fix links in sda.md when moving from sensitive-data-archive to neic-sda the links differ in sda.md fix that --- aggregate-repositories.sh | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/aggregate-repositories.sh b/aggregate-repositories.sh index 70a4096..de52a87 100755 --- a/aggregate-repositories.sh +++ b/aggregate-repositories.sh @@ -29,6 +29,11 @@ do fi done + # add special use case for sda.md links + + sed -i -E 's/cmd\/(.+)\//services\//g' docs/services/sda.md + git add docs/services/sda.md + # check if there are any changes if ! git status | grep 'nothing to commit' then From 93ec6937b58cf83263bf0713a2a80182c0da146f Mon Sep 17 00:00:00 2001 From: Stefan Negru Date: Wed, 29 Nov 2023 17:40:27 +0200 Subject: [PATCH 5/6] refined sed commnad Co-authored-by: Alex Aperis <76202622+aaperis@users.noreply.github.com> --- aggregate-repositories.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/aggregate-repositories.sh b/aggregate-repositories.sh index de52a87..cf05669 100755 --- a/aggregate-repositories.sh +++ b/aggregate-repositories.sh @@ -31,7 +31,7 @@ do # add special use case for sda.md links - sed -i -E 's/cmd\/(.+)\//services\//g' docs/services/sda.md + sed -i -E 's#cmd\/(.+)\/#''#g' docs/services/sda.md git add docs/services/sda.md # check if there are any changes From b6952ac77f3d777ae714b507a17c14e3b02ca658 Mon Sep 17 00:00:00 2001 From: Stefan Negru Date: Fri, 1 Dec 2023 11:42:59 +0200 Subject: [PATCH 6/6] fix links according to automated PR script --- docs/services/sda.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/services/sda.md b/docs/services/sda.md index e0dd00b..5304d6a 100644 --- a/docs/services/sda.md +++ b/docs/services/sda.md @@ -10,12 +10,12 @@ It can be used as part of a [Federated EGA](https://ega-archive.org/federated) o The SDA submission pipeline has four main steps: -1. [Ingest](cmd/ingest/ingest.md) splits file headers from files, moving the header to the database and the file content to the archive storage. -2. [Verify](cmd/verify/verify.md) verifies that the header is encrypted with the correct key, and that the checksums match the user-provided checksums. -3. [Finalize](cmd/finalize/finalize.md) associates a stable accessionID with each archive file and backups the file. -4. [Mapper](cmd/mapper/mapper.md) maps file accessionIDs to a datasetID. +1. [Ingest](ingest.md) splits file headers from files, moving the header to the database and the file content to the archive storage. +2. [Verify](verify.md) verifies that the header is encrypted with the correct key, and that the checksums match the user-provided checksums. +3. [Finalize](finalize.md) associates a stable accessionID with each archive file and backups the file. +4. [Mapper](mapper.md) maps file accessionIDs to a datasetID. There are also three additional support services: -1. [Intercept](cmd/intercept/intercept.md) relays messages from `CentralEGA` to the system. -2. [s3inbox](cmd/s3inbox/s3inbox.md) proxies uploads to the an S3 compatible storage backend. +1. [Intercept](intercept.md) relays messages from `CentralEGA` to the system. +2. [s3inbox](s3inbox.md) proxies uploads to the an S3 compatible storage backend.