Merge branch 'develop' into TASK-6013

opencga-app/app/misc/clients/copyright.txt

@@ -0,0 +1,13 @@
+Copyright 2015-2024 OpenCB
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

opencga-app/app/misc/clients/java_client_generator.py

@@ -36,19 +36,7 @@ def get_imports(self):
 
         headers = []
         headers.append('/*')
-        headers.append('* Copyright 2015-' + str(date.today().year) + ' OpenCB')
-        headers.append('*')
-        headers.append('* Licensed under the Apache License, Version 2.0 (the "License");')
-        headers.append('* you may not use this file except in compliance with the License.')
-        headers.append('* You may obtain a copy of the License at')
-        headers.append('*')
-        headers.append('*     http://www.apache.org/licenses/LICENSE-2.0')
-        headers.append('*')
-        headers.append('* Unless required by applicable law or agreed to in writing, software')
-        headers.append('* distributed under the License is distributed on an "AS IS" BASIS,')
-        headers.append('* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.')
-        headers.append('* See the License for the specific language governing permissions and')
-        headers.append('* limitations under the License.')
+        headers.append(self.get_copyright_message(prefix='* '))
         headers.append('*/')
         headers.append('')
         # We need to calculate the Java package and no use: headers.append('package org.opencb.opencga.client.rest.clients;')
@@ -99,7 +87,6 @@ def get_class_definition(self, category):
         text.append('/**')
         text.append(' * This class contains methods for the {} webservices.'.format(
             self.categories[self.get_category_name(category)]))
-        text.append(' *{}Client version: {}'.format(' ' * 4, self.version))
         text.append(' *{}PATH: {}'.format(' ' * 4, self.get_category_path(category)))
         text.append(' */')
         text.append('public class {}Client extends {} {{'.format(self.categories[self.get_category_name(category)], parentClientClass))

opencga-app/app/misc/clients/javascript_client_generator.py

@@ -28,18 +28,10 @@ def __init__(self, server_url, output_dir):
         }
 
     def get_imports(self):
+        copyright = self.get_copyright_message(prefix=' * ')
         auto_msg = "\n * ".join(self.get_autogenerated_message())
         return (f'/**\n'
-                f' * Copyright 2015-2020 OpenCB\n'
-                f' * Licensed under the Apache License, Version 2.0 (the "License");\n'
-                f' * you may not use this file except in compliance with the License.\n'
-                f' * You may obtain a copy of the License at\n'
-                f' * http://www.apache.org/licenses/LICENSE-2.0\n'
-                f' * Unless required by applicable law or agreed to in writing, software\n'
-                f' * distributed under the License is distributed on an "AS IS" BASIS,\n'
-                f' * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n'
-                f' * See the License for the specific language governing permissions and\n'
-                f' * limitations under the License.\n'
+                f'{copyright}\n'
                 f' * {auto_msg}'
                 f' \n *\n**/\n\n'
                 f'import OpenCGAParentClass from "./../opencga-parent-class.js";\n\n')

opencga-app/app/misc/clients/python_client_generator.py

@@ -70,7 +70,6 @@ def get_class_definition(self, category):
         text.append('{}"""'.format(' ' * 4))
         text.append('{}This class contains methods for the \'{}\' webservices'.format(' ' * 4,
                                                                                       self.get_category_name(category)))
-        text.append('{}Client version: {}'.format(' ' * 4, self.version))
         text.append('{}PATH: {}'.format(' ' * 4, category['path']))
         text.append('{}"""'.format(' ' * 4))
         text.append('')

opencga-app/app/misc/clients/r_client_generator.py

@@ -75,6 +75,7 @@ def get_class_definition(self, category):
                                                        myEndpoint['path'],
                                                        ", ".join(endpoint_params)))
         path_params = set(class_path_params)
+        path_params = sorted(list(path_params))
         text.append("#'\n#' @md")
         text.append("#' @seealso \\url{http://docs.opencb.org/display/opencga/Using+OpenCGA} and the RESTful API documentation")
         text.append("#' \\url{http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/}")

opencga-app/app/misc/clients/rest_client_generator.py

@@ -56,14 +56,39 @@ def __init__(self, rest_api_file, output_dir):
             'Admin': 'Admin'
         }
 
+    @staticmethod
+    def get_copyright_message(prefix=""):
+        # copyright = [
+        #     'Copyright 2015-2024 OpenCB',
+        #     '',
+        #     'Licensed under the Apache License, Version 2.0 (the "License");',
+        #     'you may not use this file except in compliance with the License.',
+        #     'You may obtain a copy of the License at',
+        #     '',
+        #     '    http://www.apache.org/licenses/LICENSE-2.0',
+        #     '',
+        #     'Unless required by applicable law or agreed to in writing, software',
+        #     'distributed under the License is distributed on an "AS IS" BASIS,',
+        #     'WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.',
+        #     'See the License for the specific language governing permissions and',
+        #     'limitations under the License.'
+        # ]
+        copyright_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'copyright.txt')
+        print("Reading from file: ", copyright_file)
+        with open(copyright_file, 'r') as file:
+            copyright = file.read().splitlines()
+        ## Add prefix to each line
+        if prefix:
+            for line in range(len(copyright)):
+                copyright[line] = (prefix + copyright[line]).rstrip()
+        return "\n".join(copyright)
+
     @staticmethod
     def get_autogenerated_message():
-        date_ = datetime.now().strftime("%Y-%m-%d")
         return [
             'WARNING: AUTOGENERATED CODE',
             '',
             'This code was generated by a tool.',
-            'Autogenerated on: ' + date_,
             '',
             'Manual changes to this file may cause unexpected behavior in your application.',
             'Manual changes to this file will be overwritten if the code is regenerated.'

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java

@@ -1,19 +1,3 @@
-/*
-* Copyright 2015-2024-05-24 OpenCB
-*
-* Licensed under the Apache License, Version 2.0 (the "License");
-* you may not use this file except in compliance with the License.
-* You may obtain a copy of the License at
-*
-*     http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing, software
-* distributed under the License is distributed on an "AS IS" BASIS,
-* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-* See the License for the specific language governing permissions and
-* limitations under the License.
-*/
-
 package org.opencb.opencga.app.cli.main;
 
 import org.jline.reader.Candidate;

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java

@@ -1,19 +1,3 @@
-/*
-* Copyright 2015-2024-05-24 OpenCB
-*
-* Licensed under the Apache License, Version 2.0 (the "License");
-* you may not use this file except in compliance with the License.
-* You may obtain a copy of the License at
-*
-*     http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing, software
-* distributed under the License is distributed on an "AS IS" BASIS,
-* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-* See the License for the specific language governing permissions and
-* limitations under the License.
-*/
-
 package org.opencb.opencga.app.cli.main;
 
 import com.beust.jcommander.JCommander;

opencga-client/src/main/R/R/Admin-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Alignment-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/AllGenerics.R

@@ -1,26 +1,26 @@
 # ##############################################################################
 ## OrganizationClient
-setGeneric("organizationClient", function(OpencgaR, id, user, organization, endpointName, params=NULL, ...)
+setGeneric("organizationClient", function(OpencgaR, id, organization, user, endpointName, params=NULL, ...)
     standardGeneric("organizationClient"))
 
 # ##############################################################################
 ## UserClient
-setGeneric("userClient", function(OpencgaR, users, user, filterId, endpointName, params=NULL, ...)
+setGeneric("userClient", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...)
     standardGeneric("userClient"))
 
 # ##############################################################################
 ## ProjectClient
-setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...)
+setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...)
     standardGeneric("projectClient"))
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, id, studies, members, study, variableSet, group, templateId, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, group, id, members, studies, study, templateId, variableSet, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, annotationSet, members, folder, file, files, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, annotationSet, file, files, folder, members, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
@@ -30,12 +30,12 @@ setGeneric("jobClient", function(OpencgaR, job, jobs, members, endpointName, par
 
 # ##############################################################################
 ## SampleClient
-setGeneric("sampleClient", function(OpencgaR, annotationSet, samples, members, sample, endpointName, params=NULL, ...)
+setGeneric("sampleClient", function(OpencgaR, annotationSet, members, sample, samples, endpointName, params=NULL, ...)
     standardGeneric("sampleClient"))
 
 # ##############################################################################
 ## IndividualClient
-setGeneric("individualClient", function(OpencgaR, annotationSet, individuals, individual, members, endpointName, params=NULL, ...)
+setGeneric("individualClient", function(OpencgaR, annotationSet, individual, individuals, members, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
@@ -45,12 +45,12 @@ setGeneric("familyClient", function(OpencgaR, annotationSet, families, family, m
 
 # ##############################################################################
 ## CohortClient
-setGeneric("cohortClient", function(OpencgaR, cohorts, annotationSet, cohort, members, endpointName, params=NULL, ...)
+setGeneric("cohortClient", function(OpencgaR, annotationSet, cohort, cohorts, members, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
 ## PanelClient
-setGeneric("panelClient", function(OpencgaR, panels, members, endpointName, params=NULL, ...)
+setGeneric("panelClient", function(OpencgaR, members, panels, endpointName, params=NULL, ...)
     standardGeneric("panelClient"))
 
 # ##############################################################################
@@ -65,7 +65,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, interpretation, interpretations, annotationSet, members, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, annotationSet, clinicalAnalyses, clinicalAnalysis, interpretation, interpretations, members, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################

opencga-client/src/main/R/R/Clinical-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -62,7 +61,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretation, interpretations, annotationSet, members, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) {
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, annotationSet, clinicalAnalyses, clinicalAnalysis, interpretation, interpretations, members, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:

opencga-client/src/main/R/R/Cohort-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -38,7 +37,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohorts, annotationSet, cohort, members, endpointName, params=NULL, ...) {
+setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohort, cohorts, members, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update:

opencga-client/src/main/R/R/Family-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/File-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -54,7 +53,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, members, folder, file, files, endpointName, params=NULL, ...) {
+setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, file, files, folder, members, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/files/acl/{members}/update:

opencga-client/src/main/R/R/GA4GH-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Individual-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -38,7 +37,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("individualClient", "OpencgaR", function(OpencgaR, annotationSet, individuals, individual, members, endpointName, params=NULL, ...) {
+setMethod("individualClient", "OpencgaR", function(OpencgaR, annotationSet, individual, individuals, members, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update:

opencga-client/src/main/R/R/Job-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Meta-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Operation-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Organization-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -36,7 +35,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("organizationClient", "OpencgaR", function(OpencgaR, id, user, organization, endpointName, params=NULL, ...) {
+setMethod("organizationClient", "OpencgaR", function(OpencgaR, id, organization, user, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/organizations/create:

opencga-client/src/main/R/R/Panel-methods.R

@@ -2,7 +2,6 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2024-05-24
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -36,7 +35,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("panelClient", "OpencgaR", function(OpencgaR, panels, members, endpointName, params=NULL, ...) {
+setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/panels/acl/{members}/update: