Add review comment option

Author: tmorrell

CITATION.cff

@@ -15,4 +15,4 @@ keywords:
   - metadata
   - software
   - Invenio
-date-released: 2023-05-17
+date-released: 2023-05-25

caltechdata_api/caltechdata_write.py

@@ -101,7 +101,10 @@ def add_file_links(
     return metadata
 
 
-def send_to_community(review_link, data, headers, publish, community):
+def send_to_community(review_link, data, headers, publish, community, message=None):
+
+    if not message:
+        message = "This record is submitted automatically with the CaltechDATA API"
 
     data = {
         "receiver": {"community": community},
@@ -113,7 +116,7 @@ def send_to_community(review_link, data, headers, publish, community):
     submit_link = result.json()["links"]["actions"]["submit"]
     data = comment = {
         "payload": {
-            "content": "This record is submitted automatically with the CaltechDATA API",
+            "content": message,
             "format": "html",
         }
     }
@@ -148,6 +151,7 @@ def caltechdata_write(
     file_descriptions=[],
     s3_link=None,
     default_preview=None,
+    review_message=None,
 ):
     """
     File links are links to files existing in external systems that will
@@ -218,7 +222,8 @@ def caltechdata_write(
                     "provider": "external",
                 }
 
-    metadata["pids"] = pids
+    if "pids" not in metadata:
+        metadata["pids"] = pids
 
     if authors == False:
         data = customize_schema.customize_schema(metadata, schema=schema)
@@ -247,8 +252,6 @@ def caltechdata_write(
     elif default_preview:
         data["files"] = {"enabled": True, "default_preview": default_preview}
 
-    print(data)
-
     # Make draft and publish
     result = requests.post(url + "/api/records", headers=headers, json=data)
     if result.status_code != 201:
@@ -262,7 +265,9 @@ def caltechdata_write(
 
     if community:
         review_link = result.json()["links"]["review"]
-        send_to_community(review_link, data, headers, publish, community)
+        send_to_community(
+            review_link, data, headers, publish, community, review_message
+        )
 
     else:
         if publish:

codemeta.json

@@ -6,7 +6,7 @@
   "codeRepository": "https://github.com/caltechlibrary/caltechdata_api",
   "issueTracker": "https://github.com/caltechlibrary/caltechdata_api/issues",
   "license": "https://data.caltech.edu/license",
-  "version": "1.4.0",
+  "version": "1.4.1",
   "author": [
     {
       "@type": "Person",
@@ -21,13 +21,24 @@
     }],
   "developmentStatus": "active",
   "downloadUrl":
-  "https://github.com/caltechlibrary/caltechdata_api/archive/1.4.0.zip",
+  "https://github.com/caltechlibrary/caltechdata_api/archive/1.4.1.zip",
   "keywords": [
     "GitHub",
     "metadata",
     "software",
     "Invenio"
   ],
-  "maintainer": "https://orcid.org/0000-0001-9266-5146",
+  "maintainer": [
+    {
+      "@type": "Person",
+      "givenName": "Thomas E",
+      "familyName": "Morrell",
+      "affiliation": {
+                "@type": "Organization",
+                "name": "Caltech Library"
+            },
+      "email": "[email protected]",
+      "@id": "https://orcid.org/0000-0001-9266-5146"
+    }],
   "programmingLanguage": "Python"
 }

process_tomograms.py

@@ -66,13 +66,15 @@ def create_detailed_description(information, annotation):
         species = information["species/Specimen"][0]
         if "name" in species:
             sp = species["name"]
-            description += f"{s}Species / Specimen:{e} {sp}{sep}"
-            keywords.append(sp)
+            if sp != 'Unspecified':
+                description += f"{s}Species / Specimen:{e} {sp}{sep}"
+                keywords.append(sp)
         if "strain" in species:
             st = species["strain"]
-            description += f"{s}Strain:{e} {st}{sep}"
-            if st not in keywords:
-                keywords.append(st)
+            if st != "None":
+                description += f"{s}Strain:{e} {st}{sep}"
+                if st not in keywords:
+                    keywords.append(st)
     if "tiltSeriesCollection" in information:
         settings = ""
         info = information["tiltSeriesCollection"][0]
@@ -99,8 +101,9 @@ def create_detailed_description(information, annotation):
         description += f"{s}Tilt Series Settings:{e} {settings}{sep}"
         if "Microscope" in info:
             if info["Microscope"] != "":
-                description += f'{s}Microscope:{e} {info["Microscope"]}{sep}'
-                keywords.append(info["Microscope"])
+                if info["Microscope"] != "None":
+                    description += f'{s}Microscope:{e} {info["Microscope"]}{sep}'
+                    keywords.append(info["Microscope"])
         if "acquisitionSoftware" in info:
             description += (
                 f'{s}Acquisition Software:{e} {info["acquisitionSoftware"]}{sep}'
@@ -238,9 +241,11 @@ def process_record(source, edit=None):
         embargoed = True
     metadata["identifiers"] = [{"identifier": idv, "identifierType": "tiltid"}]
     if "collaboratorsAndRoles" in annotation:
-        metadata["contributors"] = parse_collaborators(
-            annotation["collaboratorsAndRoles"]
-        )
+        with open("collab_not_completed.txt", "a") as myfile:
+            myfile.write(f"{idv}\n")
+        #metadata["contributors"] = parse_collaborators(
+        #    annotation["collaboratorsAndRoles"]
+        #)
     creators = []
     for name in information["dataTakenBy"]:
         creator = {

tomogram_ids.json

@@ -22,7 +22,7 @@
 production = False
 publish = True
 authors = True
-community = "5ab46cf6-8210-4ade-89ca-1e06d82a0de6"
+community = "70768bd5-918b-441b-bd45-12a3f296447c"
 
 response = caltechdata_write(
     metadata,