Merge pull request #208 from hubmapconsortium/entity-api-schema-template

Entity api schema template

Author: yuanzhou

.gitignore

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

entity-api-spec.yaml

@@ -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."
@@ -445,7 +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
@@ -941,7 +941,7 @@ 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:
@@ -1329,7 +1329,7 @@ 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
@@ -1421,5 +1421,4 @@ 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_templating/README.md

@@ -0,0 +1,19 @@
+# Schema Templating
+
+A collection of files and scripts used to modifying Openapi specification files in yaml format.
+
+## How to run
+
+Run build-schema.sh in this directory with 1 argument: a file path to a yaml schema "template" file.
+The directory example-yaml-templates has a number of yaml files that have tags of the pattern "X-replace-..."
+When build-schema.sh is run with the path to the desired file, general_schema_template_transformer.py will be executed
+The X-replace tags have under them url's or direct file paths to the location of yaml files where desired information is located.
+If that yaml file also has X-replace tags, this process will repeat until all replacements are made. The final result
+is output as a new yaml file called my-spec.yaml. If build-schema.sh does not receive precisely 1 argument, an error is thrown.
+If the file given as an argument does not exist, an error is also thrown.
+
+### Usage
+
+````
+./build-schema.sh example-yaml-templates/search-api-spec-TEMPLATE.yaml
+````

src/schema_templating/build-schema.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+FILE="$1"
+SCRIPTDIRECTORY=$(dirname ${BASH_SOURCE[0]})
+if (( $# == 1)); then
+  if test -f "$FILE"; then
+    ${SCRIPTDIRECTORY}/general_schema_template_transformer.py $FILE > ${SCRIPTDIRECTORY}/my-spec.yaml
+    var=$( cat ${SCRIPTDIRECTORY}/my-spec.yaml)
+  else
+    echo "$FILE does not exist"
+  fi
+else
+  echo "$# arguments were passed. Please pass exactly 1 argument that is the name of an existing file"
+fi
+if test -f "./my-spec.yaml"; then
+  if test -z "$var"; then
+    rm $SCRIPTDIRECTORY/my-spec.yaml
+  fi
+fi

src/schema_templating/example-yaml-templates/api-template-test/antibody-TEMPLATE.yaml

@@ -0,0 +1,115 @@
+x-ref-openapi: 3.0.0
+x-ref-info:
+  x-ref-description: 'The HuBMAP Antibody API is a standard RESTful web service with create operations.<br><br>'
+  x-ref-version: 1.0.0
+  x-ref-title: HuBMAP Antibody API
+  x-ref-contact:
+    x-ref-name: HuBMAP Help Desk
+    x-ref-email: [email protected]
+  x-ref-license:
+   x-ref-name: MIT License
+    x-ref-url: 'https://github.com/hubmapconsortium/antibody-api/blob/master/license.txt'
+x-ref-servers:
+  - x-ref-url: 'https://antibody.api.hubmapconsortium.org'
+x-ref-components:
+  x-ref-securitySchemes:
+    x-ref-bearerAuth:
+      x-ref-type: http
+      x-ref-scheme: bearer
+  x-ref-schemas:
+    x-ref-Antibody:
+      x-ref-type: object
+      x-ref-properties:
+        avr_url:
+          type: string
+          description: "The URL of the AVR PDF."
+        protocols_io_doi:
+          type: string
+          description: "The protocols.io doi pointing the protocol under wich the sample was obtained and/or prepared."
+        x-ref-uniprot_accession_number:
+          x-ref-type: string
+        target_name:
+          type: string
+          description: "The name of the antibody's target."
+        rrid:
+          type: string
+        x-ref-antibody_name:
+          x-ref-type: string
+          x-ref-description: "The antibody's name."
+        host_organism:
+          type: string
+          description: "The antibody's host organism."
+        clonality:
+          type: string
+          enum:
+            - monoclonal
+            - polyclonal
+          description: "One of the values: monoclonal, polyclonal."
+        vendor:
+          type: string
+          description: "The antibody's vendor."
+        catalog_number:
+          type: string
+        x-ref-lot_number:
+          x-ref-type: string
+        recombinant:
+          type: boolean
+          description: "True if the antibody is recombinant."
+        organ_or_tissue:
+          type: string
+          description: "Organ or tissue affected."
+        hubmap_platform:
+          type: string
+          description: "The assay employed for the antibody."
+        submitter_orciid:
+          type: string
+          description: "The ORCID iD of the submitter."
+        created_by_user_displayname:
+          type: string
+          description: "The name of the person or process authenticated when creating the object"
+        created_by_user_email:
+          type: string
+          description: "The email address of the person or process authenticated when creating the object."
+        created_by_user_sub:
+          type: string
+          description: "The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object."
+        group_uuid:
+          type: string
+          description: "The uuid of globus group which the user who created this antibody is a member of."
+x-ref-security:
+  - x-ref-bearerAuth: []
+x-ref-paths:
+  '/antibodies':
+    post:
+      summary: Create an antibody
+      parameters:
+      requestBody:
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                antibody:
+                  $ref: '#/components/schemas/Antibody'
+                  description: "The Antibody to be created."
+      responses:
+        '200':
+          description: The antibody was successfully created and the new ID is returned
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  id:
+                    type: integer
+                    description: "The ID of the Antibody just created."
+        '400':
+          description: No JSON body supplied
+        '401':
+          description: The user's token has expired or the user did not supply a valid token
+        '403':
+          description: The user is not authorized to create the entity
+        '406':
+          description: The antibody data submitted did not pass validation
+        '500':
+          description: Internal error