Clients: use script to autogenerate

[julie-sullivan]

I'd like to use the opencga script to autogenerate the clients for CellBase.

Can we use the same script, or do we need to modify the current one?

[julie-sullivan]

Here are the changes I made so far:

# java_client_generator.py
+            'Admin': 'Admin',
+            'Clinical': 'Clinical',
+            'Gene': 'Gene',
+            'Chromosome': 'Genome Sequence',
+            'Protein': 'Protein',
+            'Region': 'Region',
+            'Regulation': 'Regulation',
+            'Species': 'Species',
+            'TFBS': 'TF',
+            'Transcript': 'Transcript',
+            'Variant': 'Variant',
+            'Xref': 'Id'

The version number is hardcoded:

# rest_client_generator.py

-            server_url + '/webservices/rest/v2/meta/about'
+            server_url + '/webservices/rest/v5/meta/about'

-        for category in requests.get(self.server_url + '/webservices/rest/v2/meta/api').json()['responses'][0]['results'][0]:
+        for category in requests.get(self.server_url + '/webservices/rest/v5/meta/api').json()['responses'][0]['results'][0]:

Also CellBase uses version instead of apiVersion

-        return category['path'].replace('/{apiVersion}/', '')
+        return category['path'].replace('/{apiVersion}/', '').replace('/{version}/', '')

-        return endpoint['path'].replace('/{apiVersion}/', '')
+        return endpoint['path'].replace('/{apiVersion}/', '').replace('/{version}/', '')

[julie-sullivan]

The error I am working on now is that CellBase has /{species} prepended to most end points, OpenCGA does not have this.

~/git/opencga/opencga-app/app/misc/clients (develop) $ python3 java_client_generator.py http://127.0.1.1:9090/cellbase /tmp
Processing {species}/clinical/variant/search
Traceback (most recent call last):
  File "java_client_generator.py", line 307, in <module>
    sys.exit(main())
  File "java_client_generator.py", line 304, in main
    client_generator.create_rest_clients()
  File "/home/julie/git/opencga/opencga-app/app/misc/clients/rest_client_generator.py", line 199, in create_rest_clients
    text.append(self.get_method_definition(category, endpoint))
  File "java_client_generator.py", line 126, in get_method_definition
    typed_parameters.append(self.get_parameter_type(parameter) + ' ' + parameter)
  File "java_client_generator.py", line 206, in get_parameter_type
    param_type = super().get_parameter_type(parameter)
  File "/home/julie/git/opencga/opencga-app/app/misc/clients/rest_client_generator.py", line 83, in get_parameter_type
    return self.parameters[parameter]['type']
KeyError: 'species'

[julie-sullivan]

I've added the scripts to CellBase (with the changes I listed above):

https://github.com/opencb/cellbase/tree/develop/cellbase-app/app/clients

• species is in each path, and is needed by each method. How should this be handled?

[imedina]

Just worth mentioning the clients to be generated include Java, Python, R and Javascript, is this right?

[julie-sullivan]

Yes! That is correct.