Merge 91b07cd into 1ebf541

emdb-empiar · Dec 7, 2021 · 701ccdf · 701ccdf
2 parents 1ebf541 + 91b07cd
commit 701ccdf
Show file tree

Hide file tree

Showing 4 changed files with 62 additions and 8 deletions.
diff --git a/empiar_depositor/empiar_deposition.schema.json b/empiar_depositor/empiar_deposition.schema.json
@@ -2,10 +2,6 @@
   "$id": "https://empiar.org/empiar_deposition.schema.json#",
   "type": "object",
   "definitions": {},
-  "self": {
-    "format": "jsonschema",
-    "version": "1-0-0"
-  },
   "$schema": "http://json-schema.org/schema#",
   "properties": {
     "title": {
@@ -118,6 +114,57 @@
       "default": [],
       "description": "Array of references to IDR"
     },
+    "empiar_references": {
+      "$id": "/properties/empiar_references",
+      "type": "array",
+      "items": {
+        "$id": "/properties/empiar_references/items",
+        "type": "object",
+        "properties": {
+          "name": {
+            "$id": "/properties/empiar_references/items/properties/name",
+            "type": "string",
+            "pattern": "^EMPIAR-\\d+$",
+            "title": "The Name Schema ",
+            "examples": [
+              "EMPIAR-10002"
+            ]
+          }
+        }
+      },
+      "default": [],
+      "description": "Array of references to EMPIAR"
+    },
+    "workflows": {
+      "$id": "/properties/workflows",
+      "type": "array",
+      "items": {
+        "$id": "/properties/workflows/items",
+        "type": "object",
+        "properties": {
+          "url": {
+            "$id": "/properties/workflows/items/properties/url",
+            "type": "string",
+            "pattern": "^https:\/\/.+$",
+            "title": "The Url Schema ",
+            "examples": [
+              "https://doi.org/10.48546/workflowhub.workflow.201.1"
+            ]
+          },
+          "type": {
+            "$id": "properties/workflows/items/properties/type",
+            "type": "integer",
+            "title": "The Type Schema ",
+            "description": "Currently supported value: 1 - WorkflowHub.",
+            "enum": [
+              1
+            ]
+          }
+        }
+      },
+      "default": [],
+      "description": "Array of workflows"
+    },
     "authors": {
       "$id": "/properties/authors",
       "type": "array",
@@ -589,7 +636,7 @@
       "type": "array",
       "minItems": 1,
       "items": {
-        "$id": "/properties/corresponding_author",
+        "$id": "/properties/corresponding_authors",
         "type": "object",
         "properties": {
           "author_orcid": {
@@ -1755,7 +1802,7 @@
               "string"
             ],
             "title": "The Details Schema ",
-            "maxlength": 65535,
+            "maxLength": 65535,
             "default": null,
             "examples": [
               "Three-dimensional in situ structure of a T4bP machine in its piliated and non-piliated states constructed from its tilt series."

diff --git a/empiar_depositor/empiar_depositor.py b/empiar_depositor/empiar_depositor.py
@@ -19,6 +19,7 @@
 under the License.
 
 Version history
+1.6b25, 20211015, Andrii Iudin: Added an option to specify workflows, JSON schema updated to the latest draft
 1.6b24, 20210729, Andrii Iudin: Switched to top url
 1.6b23, 20210113, Andrii Iudin: It is now possible to get entry id and directory as an output on successful deposition
 without submitting the entry
@@ -542,7 +543,7 @@ def main(args=None):
     empiar-depositor -r 10 ABC123 -e ~/Downloads/dep_thumb.png 0123456789 -g 01234567-89a-bcde-fghi-jklmnopqrstu ~/Docu\
 ments/empiar_deposition_1.json ~/Downloads/micrographs
                 """
-        version = "1.6b24"
+        version = "1.6b25"
 
         possible_rights_help_text = "Rights can be 1 - Owner, 2 - View only, 3 - View and Edit, 4 - View, Edit and " \
                                     "Submit. There can be only one deposition owner."

diff --git a/empiar_depositor/tests/deposition_json/working_example.json b/empiar_depositor/tests/deposition_json/working_example.json
@@ -7,6 +7,12 @@
       "name": "EMD-8000"
     }
   ],
+  "workflows": [
+    {
+      "url": "https://doi.org/10.48546/workflowhub.workflow.201.1",
+      "type": 1
+    }
+  ],
   "authors": [
     {
       "name": "('Smith', 'JW')",

diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 
 setup(
     name='empiar-depositor',
-    version='1.6b24',
+    version='1.6b25',
     packages=find_packages(),
     author="Andrii Iudin",
     author_email="andrii@ebi.ac.uk, andrii.iudin@gmail.com",