Merge pull request #209 from hubmapconsortium/test-release

v2.0.14 release

Author: yuanzhou

.gitignore

@@ -28,3 +28,11 @@ src/VERSION
 #ignore eclipse files
 .project
 .pydevproject
+
+#ignore PyCharm files
+.idea/
+../.idea/
+venv
+
+#ignore test venv
+**/testenv/

VERSION

@@ -1 +1 @@
-2.0.13
+2.0.14

entity-api-spec.yaml

@@ -1,7 +1,7 @@
 openapi: 3.0.0
 info:
   description: 'The HuBMAP Entity API is a standard RESTful web service with create, update and read operations for the standard HuBMAP provenance graph entities.<br><br>'
-  version: 2.0.11
+  version: 2.0.14
   title: HuBMAP Entity API
   contact:
     name: HuBMAP Help Desk
@@ -43,7 +43,7 @@ components:
           description: "The name of the antibody."
         channel_id:
           type: string
-          description: "The assay specific identifier for the channel corresponding to the antibody." 
+          description: "The assay specific identifier for the channel corresponding to the antibody."
         conjugated_cat_number:
           type: string
           description: "An antibody may be conjugated to a fluorescent tag or a metal tag for detection. Conjugated antibodies may be purchased from commercial providers. Blank if not applicable."
@@ -191,7 +191,7 @@ components:
           description: "The name of the file."
         description:
           type: string
-          description: "A description of the file."
+          description: "A description of the file. The Dataset.thumbnail_file does not have this file description."
         file_uuid:
           type: string
           description: "The HuBMAP unique identifier for the file."
@@ -238,7 +238,6 @@ components:
           type: string
           readOnly: true
           description: "The name of the person or process which authenticated when the object was last modified."
-        ###### All other shared properties ######
         entity_type:
           type: string
           readOnly: true
@@ -281,14 +280,14 @@ components:
           type: array
           items:
             type: string
-            format: file_id
+            format: temp_file_id
           description: 'List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {"files": [{"temp_file_id":"dzevgd6xjs4d5grmcp4n","description":"This is image file one"},{"temp_file_id":"yrahjadfhadf","description":"This is image file two"}]}'
         image_files_to_remove:
           writeOnly: true
           type: array
           items:
             type: string
-            format: file_id
+            format: file_uuid
           description: 'List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"]'
         metadata:
           type: object
@@ -367,7 +366,6 @@ components:
           type: string
           readOnly: true
           description: "The name of the person or process which authenticated when the object was last modified."
-        ###### All other shared properties ######
         entity_type:
           type: string
           readOnly: true
@@ -447,7 +445,7 @@ components:
             - snatacseq
             - snrnaseq
             - tissue_lysate
-            - wgs    
+            - wgs
           description: "A code representing the type of specimen.  Must be one of the codes specified in: [tissue sample types](https://github.com/hubmapconsortium/search-api/blob/master/src/search-schema/data/definitions/enums/tissue_sample_types.yaml)"
         specimen_type_other:
           type: string
@@ -534,14 +532,14 @@ components:
           type: array
           items:
             type: string
-            format: file_id
+            format: temp_file_id
           description: 'List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {"files": [{"temp_file_id":"dzevgd6xjs4d5grmcp4n","description":"This is image file one"},{"temp_file_id":"yrahjadfhadf","description":"This is image file two"}]}'
         image_files_to_remove:
           writeOnly: true
           type: array
           items:
             type: string
-            format: file_id
+            format: file_uuid
           description: 'List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"]'
         metadata_files:
           readOnly: true
@@ -553,13 +551,13 @@ components:
           type: array
           items:
             type: string
-            format: file_id
+            format: temp_file_id
           description: 'List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {"files": [{"temp_file_id":"dzevgd6xjs4d5grmcp4n","description":"This is image file one"},{"temp_file_id":"yrahjadfhadf","description":"This is image file two"}]}'
         metadata_files_to_remove:
           type: array
           items:
             type: string
-            format: file_id
+            format: file_uuid
           description: 'List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"]'
     Dataset:
       type: object
@@ -604,7 +602,6 @@ components:
           type: string
           readOnly: true
           description: "The name of the person or process which authenticated when the object was last modified."
-        ###### All other shared properties ######
         entity_type:
           type: string
           readOnly: true
@@ -770,6 +767,19 @@ components:
           type: string
           readOnly: true
           description: "The uuid of next revision dataset"
+        thumbnail_file:
+          readOnly: true
+          description: 'The dataset thumbnail file detail. Stored in db as a stringfied json, e.g., {"filename": "thumbnail.jpg", "file_uuid": "c35002f9c3d49f8b77e1e2cd4a01803d"}'
+        thumbnail_file_to_add:
+          writeOnly: true
+          type: string
+          format: temp_file_id
+          description: 'Just a temporary file id. Provide as a json object with an temp_file_id like {"temp_file_id":"dzevgd6xjs4d5grmcp4n"}'
+        thumbnail_file_to_remove:
+          writeOnly: true
+          type: string
+          format: file_uuid
+          description: 'The thumbnail image file previously uploaded to delete. Provide as a string of the file_uuid like: "c35002f9c3d49f8b77e1e2cd4a01803d"'
     Upload:
       type: object
       properties:
@@ -897,7 +907,6 @@ components:
           type: string
           readOnly: true
           description: "The name of the person or process which authenticated when the object was last modified."
-        ###### All other shared properties ######
         entity_type:
           type: string
           readOnly: true
@@ -934,7 +943,7 @@ security:
 paths:
   '/entities/{id}':
     get:
-      summary: Retrieve a provenance entity by id.  Entity types of Donor, Sample and Datasets. 
+      summary: Retrieve a provenance entity by id.  Entity types of Donor, Sample and Datasets.
       security:
         - bearerAuth: []
       parameters:
@@ -1322,7 +1331,7 @@ paths:
           description: Internal error
   '/doi/redirect/{id}':
     get:
-      summary: Redirect a request from a doi service  
+      summary: Redirect a request from a doi service
       parameters:
         - name: id
           in: path
@@ -1414,5 +1423,4 @@ paths:
         '404':
           description: The target dataset could not be found
         '500':
-          description: Internal error
-         
+          description: Internal error

src/requirements.txt

@@ -4,10 +4,16 @@ neo4j==4.2.1
 prov==2.0.0
 Werkzeug==1.0.1
 
+# For schema templating
+nested-lookup==0.2.22
+
 # The commons package requires requests>=2.22.0 and PyYAML>=5.3.1
 requests==2.25.1
 PyYAML==5.4.1
 
 # The branch name of commons to be used during image build
 # Default is master branch specified in docker-compose.yml if not set
 git+git://github.com/hubmapconsortium/commons.git@${COMMONS_BRANCH}#egg=hubmap-commons
+
+# For unit test
+nose2==0.10.0

src/schema/provenance_schema.yaml

@@ -342,7 +342,37 @@ ENTITIES:
         immutable: true
         description: "The uuid of next revision dataset"
         on_read_trigger: get_next_revision_uuid
-
+      # No like image and metadata files handling for Donor/Sample
+      # Dataset has only one thumbnail file
+      thumbnail_file:
+        generated: true
+        type: json_string
+        description: "The dataset thumbnail file detail. Stored in db as a stringfied json, e.g., {'filename': 'thumbnail.jpg', 'file_uuid': 'dadasdasdadda'}"
+        # The updated_peripherally tag is a temporary measure to correctly handle any attributes
+        # which are potentially updated by multiple triggers
+        updated_peripherally: true
+      thumbnail_file_to_add:
+        type: json_string 
+        transient: true
+        exposed: false
+        description: 'Just a temporary file id. Provide as a json object with an temp_file_id like {"temp_file_id":"dzevgd6xjs4d5grmcp4n"}'
+        before_create_trigger: commit_thumbnail_file
+        # This before_update_trigger with the same commit process can be used by ingest-api to update the dataset via PUT call
+        before_update_trigger: commit_thumbnail_file
+        # The updated_peripherally tag is a temporary measure to correctly handle any attributes
+        # which are potentially updated by multiple triggers
+        updated_peripherally: true
+      thumbnail_file_to_remove:
+        # This is only valid on update via a PUT request
+        type: string 
+        transient: true
+        exposed: false
+        description: 'The thumbnail image file previously uploaded to delete. Provide as a string of the file_uuid like: "232934234234234234234270c0ea6c51d604a850558ef2247d0b4"'
+        before_update_trigger: delete_thumbnail_file
+        # The updated_peripherally tag is a temporary measure to correctly handle any attributes
+        # which are potentially updated by multiple triggers
+        updated_peripherally: true
+        
 
   ############################################# Donor #############################################
   Donor: