From cbdecd527be0c13a42b8816a972d135b40592d26 Mon Sep 17 00:00:00 2001
From: Stefan Negru <stefan@blankdots.com>
Date: Mon, 13 Nov 2023 15:25:15 +0200
Subject: [PATCH] integrate pipeline from sda.md

---
 aggregate-mappings.json   |  3 ++-
 docs/services/pipeline.md | 23 --------------------
 mkdocs.yml                | 46 ++++++++++++++++++---------------------
 3 files changed, 23 insertions(+), 49 deletions(-)
 delete mode 100644 docs/services/pipeline.md

diff --git a/aggregate-mappings.json b/aggregate-mappings.json
index 88c28da..d19d2ec 100644
--- a/aggregate-mappings.json
+++ b/aggregate-mappings.json
@@ -4,6 +4,7 @@
         "sda/cmd/ingest/ingest.md": "docs/services/ingest.md",
         "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/verify/verify.md": "docs/services/verify.md",
+        "sda/cmd/sda.md": "docs/services/sda.md"
     }
 }
diff --git a/docs/services/pipeline.md b/docs/services/pipeline.md
deleted file mode 100644
index 5b4a3f2..0000000
--- a/docs/services/pipeline.md
+++ /dev/null
@@ -1,23 +0,0 @@
-sda-pipeline
-============
-
-Repository:
-[neicnordic/sda-pipeline](https://github.com/neicnordic/sda-pipeline/)
-
-`sda-pipeline` is part of [NeIC Sensitive Data Archive](https://neic-sda.readthedocs.io/en/latest/) and implements the components required for data submission.
-It can be used as part of a [Federated EGA](https://ega-archive.org/federated) or as an isolated Sensitive Data Archive.
-`sda-pipeline` was built with support for both S3 and POSIX storage.
-
-The SDA pipeline has four main steps:
-
-1. [Ingest](ingest.md) splits file headers from files, moving the header to the database and the file content to the archive storage.
-1. [Verify](verify.md) verifies that the header is encrypted with the correct key, and that the checksums match the user-provided checksums.
-1. [Finalize](finalize.md) associates a stable accessionID with each archive file.
-1. [Mapper](mapper.md) maps file accessionIDs to a datasetID.
-
-There are also three additional support services:
-
-1. [Backup](backup.md) copies data from archive storage to backup storage, optionally re-encrypting and re-attaching the headers.
-1. [Intercept](intercept.md) relays messages from Central EGA to the system.
-1. [Notify](notify.md) sends e-mail messages to users.
-
diff --git a/mkdocs.yml b/mkdocs.yml
index 9fe258f..7254dc7 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -5,29 +5,25 @@ markdown_extensions:
 plugins:
   - include-markdown
 theme:
-    name: readthedocs
+  name: readthedocs
 nav:
-  - Home: 'index.md'
-  - 'Structure':
-      - Introduction: 'structure.md'
-      - Getting started: 'setup.md'
-      - 'deploy.md'
-      - Tests: 'tests.md'
-  - 'Communication':
-      - Database setup: 'db.md'
-      - Encryption: 'encryption.md'
-      - Data Submission: 'submission.md'
-      - Interfacing with CEGA: 'connection.md'
-  - 'Services':
-      - SDA-Pipeline: 'services/pipeline.md'
-      - 'services/ingest.md'
-      - 'services/verify.md'
-      - 'services/finalize.md'
-      - 'services/backup.md'
-      - 'services/mapper.md'
-      - Data Retrieval API: 'dataout.md'
-  - 'Guides':
-      - Contributing: 'CONTRIBUTING.md'
-
-
-      
+  - Home: "index.md"
+  - "Structure":
+      - Introduction: "structure.md"
+      - Getting started: "setup.md"
+      - "deploy.md"
+      - Tests: "tests.md"
+  - "Communication":
+      - Database setup: "db.md"
+      - Encryption: "encryption.md"
+      - Data Submission: "submission.md"
+      - Interfacing with CEGA: "connection.md"
+  - "Services":
+      - SDA: "services/sda.md"
+      - "services/ingest.md"
+      - "services/verify.md"
+      - "services/finalize.md"
+      - "services/mapper.md"
+      - Data Retrieval API: "dataout.md"
+  - "Guides":
+      - Contributing: "CONTRIBUTING.md"