Merge pull request #8 from emdb-empiar/feature/idr_references

Schema update - now we accept references to IDR

empiar_depositor/empiar_deposition.schema.json

@@ -44,10 +44,13 @@
         3,
         4,
         5,
-        6
+        6,
+        7,
+        8,
+        9
       ],
       "default": 3,
-      "description": "Type of the EMPIAR entry: 1 - image data collected using soft x-ray tomography, 2 - simulated data, for instance, created using InSilicoTEM (note: we only accept simulated data in special circumstances such as test/training sets for validation challenges: you need to ask for and be granted permission PRIOR to deposition otherwise the dataset will be rejected), 3 - raw image data relating to structures deposited to the Electron Microscopy Data Bank, 4 - image data collected using serial block-face scanning electron microscopy (like the Gatan 3View system), 5 - image data collected using focused ion beam scanning electron microscopy, 6 - integrative hybrid modelling data.",
+      "description": "Type of the EMPIAR entry: 1 - image data collected using soft x-ray tomography, 2 - simulated data, for instance, created using InSilicoTEM (note: we only accept simulated data in special circumstances such as test/training sets for validation challenges: you need to ask for and be granted permission PRIOR to deposition otherwise the dataset will be rejected), 3 - raw image data relating to structures deposited to the Electron Microscopy Data Bank, 4 - image data collected using serial block-face scanning electron microscopy (like the Gatan 3View system), 5 - image data collected using focused ion beam scanning electron microscopy, 6 - integrative hybrid modelling data, 7 - correlative light-electron microscopy, 8 - correlative light X-ray microscopy, 9 - microcrystal electron diffraction",
       "examples": [
         3
       ]
@@ -94,6 +97,27 @@
       "default": [],
       "description": "Array of references to BioStudies"
     },
+    "idr_references": {
+      "$id": "/properties/idr_references",
+      "type": "array",
+      "items": {
+        "$id": "/properties/idr_references/items",
+        "type": "object",
+        "properties": {
+          "name": {
+            "$id": "/properties/idr_references/items/properties/name",
+            "type": "string",
+            "pattern": "^idr.*$",
+            "title": "The Name Schema ",
+            "examples": [
+              "idr1040"
+            ]
+          }
+        }
+      },
+      "default": [],
+      "description": "Array of references to IDR"
+    },
     "authors": {
       "$id": "/properties/authors",
       "type": "array",

empiar_depositor/empiar_depositor.py

@@ -19,6 +19,7 @@
 under the License.
 
 Version history
+1.6b20, 20200429, Andrii Iudin: Schema update - now we accept references to IDR.
 1.6b19, 20200302, Andrii Iudin: It is now possible to upload Big Data Viewer HDF5 files.
 1.6b18, 20200220, Andrii Iudin: Moved Scipion workflow outside of image sets.
 1.6b17, 20200218, Andrii Iudin: Added Scipion workflow to the schema and the example JSON.
@@ -423,7 +424,7 @@ 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 = "1.6b19"
+        version = "1.6b20"
 
         parser = argparse.ArgumentParser(prog=prog, usage=usage, add_help=False,
                                          formatter_class=argparse.RawTextHelpFormatter)

setup.py

@@ -11,7 +11,7 @@
 
 setup(
     name='empiar-depositor',
-    version='1.6b19',
+    version='1.6b20',
     packages=find_packages(),
     author="Andrii Iudin",
     author_email="andrii@ebi.ac.uk, andrii.iudin@gmail.com",