Merge pull request #109 from EGA-archive/md5-contains

Moving the "contains" to its right place
EGA-archive · Jun 15, 2020 · 2b9ca74 · 2b9ca74
2 parents e4eaadc + 2ef2bc0
commit 2b9ca74
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Showing 6 changed files with 23 additions and 22 deletions.
diff --git a/docs/amqp.rst b/docs/amqp.rst
@@ -80,16 +80,17 @@ Message interface (API) CEGA |connect| LEGA
 It is necessary to agree on the format of the messages exchanged
 between Central EGA and any Local EGAs. All messages are
 JSON-formatted. The `JSON schemas to described the message formats
-<https://github.com/EGA-archive/LocalEGA/tree/docs/ingestion/schemas>`_
+<https://github.com/EGA-archive/LocalEGA/tree/master/ingestion/schemas>`_
 can be found in the repository.
 
 When the brokers exchange messages, the message headers have the following properties:
 
 - a content type: ``application/json``
 - delivery mode: 2 (for persistence)
-- and a **required** correlation id.
-
-The correlation id is a uuid of 37 characters, generated by `uuid_generate <https://linux.die.net/man/3/uuid_generate>`_.
+- and a **required** correlation id, i.e. a `36-characters string
+  <https://en.wikipedia.org/wiki/Universally_unique_identifier#Format>`_
+  (as generated by `uuid_generate
+  <https://linux.die.net/man/3/uuid_generate>`_).
 
 
 Central EGA |cegatolega| Local EGA

diff --git a/docs/encryption.rst b/docs/encryption.rst
@@ -18,9 +18,9 @@ part is called the Crypt4GH header.
    :target: https://crypt4gh.readthedocs.io/en/latest/_images/encryption.png
    :alt: Encryption
 
-There are `several advantages for using the Crypt4GH format
-<https://crypt4gh.readthedocs.io/en/latest/encryption.html>`_. The
-main ones are:
+There are several advantages for using `the Crypt4GH format
+<http://samtools.github.io/hts-specs/crypt4gh.pdf>`_. The main ones
+are:
 
 * No re-encryption upon ingestion (only decryption).
 * Minimal re-encryption for data distribution.

diff --git a/docs/ingestion-save.html b/docs/ingestion-save.html
@@ -9,13 +9,16 @@
   <tbody>
     <tr>
       <td>db</td>
-      <td>A Postgres database</td>
-      <td><i class="fa fa-battery-full lega-stable"></i></td>
+      <td>A Postgres database. See
+      the <a href="https://github.com/EGA-archive/LocalEGA/blob/master/ingestion/db/archive-db.sql">long-term
+      database schema</a>, for an example.
+      </td>
+      <td><i class="fa fa-battery-full lega-stable" title="For illustration only"></i></td>
     </tr>
     <tr>
       <td>storage</td>
       <td>A POSIX file system or an S3-backed disk</td>
-      <td><i class="fa fa-battery-full lega-stable"></i></td>
+      <td><i class="fa fa-battery-full lega-stable" title="For illustration only"></i></td>
     </tr>
     <tr>
       <td>save2db</td>

diff --git a/docs/ingestion.rst b/docs/ingestion.rst
@@ -17,9 +17,9 @@ architecture with the following components:
    :target: ./_static/ingestion.png
    :alt: Ingestion Architecture and Connected Components
 
-The reference implementation implements the ingestion using a
-microservice architecture with an internal database, a staging area
-and a local broker.
+The reference implementation uses a microservice architecture with an
+internal database, a staging area and a local broker, for the
+ingestion pipeline.
 
 .. raw:: html
    :file: ingestion.html
@@ -50,7 +50,7 @@ POSIX compliant file system. In order to use an S3-backed storage, the
 Local EGA system administrator can use `s3fs-fuse
 <https://github.com/s3fs-fuse/s3fs-fuse>`_, or update the code (`as it
 was once done
-<https://github.com/EGA-archive/LocalEGA/blob/v0.3.0/lega/utils/storage.py>`_
+<https://github.com/EGA-archive/LocalEGA/blob/v0.4.0/lega/utils/storage.py>`_
 and is now offload to our swedish and finnish partners).
 
 If any of the above steps generates an error, we exit the workflow and
@@ -70,9 +70,6 @@ regularly.
 .. raw:: html
    :file: ingestion-save.html
 
-See the `long-term database schema
-<https://github.com/EGA-archive/LocalEGA/blob/master/ingestion/db/archive-db.sql>`_,
-for an example.
 
 
 

diff --git a/ingestion/schemas/ingestion-accession.json b/ingestion/schemas/ingestion-accession.json
@@ -130,11 +130,6 @@
                 [ { "type": "sha256", "value": "82E4e60e7beb3db2e06A00a079788F7d71f75b61a4b75f28c4c942703dabb6d6" },
                   { "type": "md5"   , "value": "7Ac236b1a8dce2dac89e7cf45d2b48BD" }]
             ],
-	    "contains": {
-                "type": "object",
-                "properties": { "type": { "const": "md5" } },
-                "required": ["type"],
-            },
             "additionalItems": false,
             "items": {
 		"anyOf": [ { "$ref": "#/definitions/checksum-sha256" },

diff --git a/ingestion/schemas/ingestion-to-cega.json b/ingestion/schemas/ingestion-to-cega.json
@@ -121,6 +121,11 @@
                 [ { "type": "sha256", "value": "82E4e60e7beb3db2e06A00a079788F7d71f75b61a4b75f28c4c942703dabb6d6" },
                   { "type": "md5"   , "value": "7Ac236b1a8dce2dac89e7cf45d2b48BD" }]
             ],
+	    "contains": {
+                "type": "object",
+                "properties": { "type": { "const": "md5" } },
+                "required": [ "type" ],
+            },
             "additionalItems": false,
             "items": {
 		"anyOf": [ { "$ref": "#/definitions/checksum-sha256" },