pyxetabase 4.0.0.dev36__tar.gz → 4.0.0.dev40__tar.gz

{pyxetabase-4.0.0.dev36 → pyxetabase-4.0.0.dev40}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev36
+Version: 4.0.0.dev40
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-4.0.0.dev36 → pyxetabase-4.0.0.dev40}/pyxetabase/rest_clients/_parent_rest_clients.py

@@ -1,6 +1,7 @@
-import json
+import os
+import requests
 
-from pyxetabase.commons import execute
+from pyxetabase.commons import execute, _create_rest_url, snake_to_camel_case
 from pyxetabase.rest_response import RestResponse
 from pyxetabase.retry import retry
 
@@ -87,18 +88,23 @@ class _ParentRestClient(object):
     def _post(self, category, resource, data=None, query_id=None, subcategory=None,
               second_query_id=None, **options):
         """Queries the REST service and returns the result"""
-        if data is not None:
-            return self._rest_retry(
-                method='post', category=category, resource=resource, query_id=query_id,
-                subcategory=subcategory, second_query_id=second_query_id,
-                data=data, **options
-            )
+        # Special treatment for the "/{apiVersion}/files/upload" endpoint
+        if category == 'files' and resource == 'upload':
+            response = self._upload(category=category, resource=resource, **options)
+            return RestResponse(response)
         else:
-            return self._rest_retry(
-                method='post', category=category, resource=resource, query_id=query_id,
-                subcategory=subcategory, second_query_id=second_query_id,
-                **options
-            )
+            if data is not None:
+                return self._rest_retry(
+                    method='post', category=category, resource=resource, query_id=query_id,
+                    subcategory=subcategory, second_query_id=second_query_id,
+                    data=data, **options
+                )
+            else:
+                return self._rest_retry(
+                    method='post', category=category, resource=resource, query_id=query_id,
+                    subcategory=subcategory, second_query_id=second_query_id,
+                    **options
+                )
 
     def _delete(self, category, resource, query_id=None, subcategory=None,
                 second_query_id=None, **options):
@@ -108,3 +114,31 @@ class _ParentRestClient(object):
             subcategory=subcategory, second_query_id=second_query_id,
             **options
         )
+
+    def _upload(self, category, resource, **options):
+        """Upload files"""
+
+        # Checking that the parameter file contains the file path to upload
+        if 'file' not in options or not isinstance(options['file'], str):
+            raise ValueError('To upload a file, please specify the file path as the "file" parameter.')
+
+        # Creating URL and headers
+        url, header = _create_rest_url(host=self._cfg.host, version=self._cfg.version, sid=self.token,
+                                       category=category, resource=resource, options=options)
+
+        # Creating data
+        data = {}
+        for k, v in options.items():
+            if k == 'file':  # Param "file" is not included in data
+                continue
+            data[snake_to_camel_case(k)] = v
+
+        # Uploading
+        fpath = os.path.realpath(os.path.expanduser(options['file']))
+        with open(fpath, "rb") as f:
+            fhand = {"file": (fpath, f, "application/octet-stream")}
+            response = requests.post(url, headers=header, files=fhand, data=data or None)
+            if response.status_code != 200:
+                raise Exception(response.content)
+
+        return response.json()

{pyxetabase-4.0.0.dev36 → pyxetabase-4.0.0.dev40}/pyxetabase/rest_clients/admin_client.py

@@ -54,16 +54,13 @@ class Admin(_ParentRestClient):
 
         return self._post(category='admin', resource='install', subcategory='catalog', data=data, **options)
 
-    def jwt_catalog(self, data=None, **options):
+    def list_organizations(self, **options):
         """
-        Change JWT secret key.
-        PATH: /{apiVersion}/admin/catalog/jwt
-
-        :param dict data: JSON containing the parameters. (REQUIRED)
-        :param str organization: Organization id.
+        List current Organizations.
+        PATH: /{apiVersion}/admin/organizations/list
         """
 
-        return self._post(category='admin', resource='jwt', subcategory='catalog', data=data, **options)
+        return self._get(category='admin', resource='list', subcategory='organizations', **options)
 
     def fetch_resource(self, data=None, **options):
         """

{pyxetabase-4.0.0.dev36 → pyxetabase-4.0.0.dev40}/pyxetabase/rest_clients/clinical_analysis_client.py

@@ -350,6 +350,32 @@ class ClinicalAnalysis(_ParentRestClient):
 
         return self._get(category='analysis', resource='info', subcategory='clinical/interpretation', second_query_id=interpretations, **options)
 
+    def run_interpreter_cancer_tiering(self, data=None, **options):
+        """
+        Run cancer tiering interpretation analysis.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/cancerTiering/run
+
+        :param dict data: Cancer tiering interpretation analysis params.
+            (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        """
+
+        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/cancerTiering', data=data, **options)
+
     def run_interpreter_exomiser(self, data=None, **options):
         """
         Run exomiser interpretation analysis.
@@ -375,31 +401,62 @@ class ClinicalAnalysis(_ParentRestClient):
 
         return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/exomiser', data=data, **options)
 
-    def query_interpreter_rd(self, **options):
+    def run_interpreter_team(self, data=None, **options):
+        """
+        Run TEAM interpretation analysis.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/team/run
+
+        :param dict data: TEAM interpretation analysis params. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID.
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
+        """
+
+        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/team', data=data, **options)
+
+    def run_interpreter_tiering(self, data=None, **options):
         """
-        RD interpretation analysis.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/rd/query
+        Run tiering interpretation analysis.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/tiering/run
 
-        :param str clinical_analysis_id: Clinical analysis ID.
-        :param str proband_id: Proband ID.
-        :param str family_id: Family ID.
-        :param str panel_ids: List of panel IDs (separated by commas).
-        :param str disorder_id: Disorder ID.
-        :param str config_file: RD interpretation configuration file
-            (otherwise the default one will be used).
+        :param dict data: Tiering interpretation analysis params. (REQUIRED)
         :param str study: Study [[organization@]project:]study where study and
             project can be either the ID or UUID.
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_description: Job description.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
         """
 
-        return self._get(category='analysis', resource='query', subcategory='clinical/interpreter/rd', **options)
+        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/tiering', data=data, **options)
 
-    def run_interpreter_rd(self, data=None, **options):
+    def run_interpreter_zetta(self, data=None, **options):
         """
-        Run clinical interpretation analysis for rare diseases.
-        PATH: /{apiVersion}/analysis/clinical/interpreter/rd/run
+        Run Zetta interpretation analysis.
+        PATH: /{apiVersion}/analysis/clinical/interpreter/zetta/run
 
-        :param dict data: Parameters to execute the rare disease
-            interpretation analysis. (REQUIRED)
+        :param dict data: Zetta interpretation analysis params. (REQUIRED)
         :param str study: Study [[organization@]project:]study where study and
             project can be either the ID or UUID.
         :param str job_id: Job ID. It must be a unique string within the
@@ -417,7 +474,7 @@ class ClinicalAnalysis(_ParentRestClient):
             execution, but the job will not actually run.
         """
 
-        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/rd', data=data, **options)
+        return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/zetta', data=data, **options)
 
     def load(self, data=None, **options):
         """

{pyxetabase-4.0.0.dev36 → pyxetabase-4.0.0.dev40}/pyxetabase/rest_clients/cohort_client.py

@@ -61,6 +61,9 @@ class Cohort(_ParentRestClient):
         :param str status: status.
         :param str internal_status: internalStatus.
         :param str annotation: Cohort annotation.
+        :param str tags: Tags. Also admits basic regular expressions using the
+            operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
+            sensitive, '~/value/i' for case insensitive search.
         :param str acl: acl.
         :param str samples: Cohort sample IDs.
         :param str num_samples: Number of samples.
@@ -137,6 +140,9 @@ class Cohort(_ParentRestClient):
         :param str uuid: Comma separated list of cohort IDs up to a maximum of
             100.
         :param str type: Cohort type.
+        :param str tags: Tags. Also admits basic regular expressions using the
+            operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
+            sensitive, '~/value/i' for case insensitive search.
         :param str creation_date: creationDate.
         :param str modification_date: modificationDate.
         :param bool deleted: deleted.
@@ -223,6 +229,9 @@ class Cohort(_ParentRestClient):
         :param str uuid: Comma separated list of cohort IDs up to a maximum of
             100.
         :param str type: Cohort type.
+        :param str tags: Tags. Also admits basic regular expressions using the
+            operator '~', i.e. '~{perl-regex}' e.g. '~value' for case
+            sensitive, '~/value/i' for case insensitive search.
         :param str creation_date: creationDate.
         :param str modification_date: modificationDate.
         :param bool deleted: deleted.
@@ -303,6 +312,8 @@ class Cohort(_ParentRestClient):
         :param str annotation_sets_action: Action to be performed if the array
             of annotationSets is being updated. Allowed values: ['ADD SET
             REMOVE']
+        :param str tags_action: Action to be performed if the array of tags is
+            being updated. Allowed values: ['ADD SET REMOVE']
         :param bool include_result: Flag indicating to include the created or
             updated document result in the response.
         :param dict data: body.

{pyxetabase-4.0.0.dev36 → pyxetabase-4.0.0.dev40}/pyxetabase/rest_clients/disease_panel_client.py

@@ -192,6 +192,19 @@ class DiseasePanel(_ParentRestClient):
 
         :param str study: Study [[organization@]project:]study where study and
             project can be either the ID or UUID.
+        :param str job_id: Job ID. It must be a unique string within the
+            study. An ID will be autogenerated automatically if not provided.
+        :param str job_depends_on: Comma separated list of existing job IDs
+            the job will depend on.
+        :param str job_description: Job description.
+        :param str job_tags: Job tags.
+        :param str job_scheduled_start_time: Time when the job is scheduled to
+            start.
+        :param str job_priority: Priority of the job.
+        :param bool job_dry_run: Flag indicating that the job will be executed
+            in dry-run mode. In this mode, OpenCGA will validate that all
+            parameters and prerequisites are correctly set for successful
+            execution, but the job will not actually run.
         :param dict data: Panel parameters.
         """
 

{pyxetabase-4.0.0.dev36 → pyxetabase-4.0.0.dev40}/pyxetabase/rest_clients/variant_operation_client.py

@@ -627,33 +627,6 @@ class VariantOperation(_ParentRestClient):
 
         return self._post(category='operation', resource='secondaryIndex', subcategory='variant', data=data, **options)
 
-    def delete_variant_secondary_index(self, **options):
-        """
-        Remove a secondary index from the search engine for a specific set of
-            samples.
-        PATH: /{apiVersion}/operation/variant/secondaryIndex/delete
-
-        :param str job_id: Job ID. It must be a unique string within the
-            study. An ID will be autogenerated automatically if not provided.
-        :param str job_description: Job description.
-        :param str job_depends_on: Comma separated list of existing job IDs
-            the job will depend on.
-        :param str job_tags: Job tags.
-        :param str job_scheduled_start_time: Time when the job is scheduled to
-            start.
-        :param str job_priority: Priority of the job.
-        :param bool job_dry_run: Flag indicating that the job will be executed
-            in dry-run mode. In this mode, OpenCGA will validate that all
-            parameters and prerequisites are correctly set for successful
-            execution, but the job will not actually run.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str samples: Samples to remove. Needs to provide all the
-            samples in the secondary index.
-        """
-
-        return self._delete(category='operation', resource='delete', subcategory='variant/secondaryIndex', **options)
-
     def setup_variant(self, data=None, **options):
         """
         Execute Variant Setup to allow using the variant engine. This setup is

{pyxetabase-4.0.0.dev36 → pyxetabase-4.0.0.dev40}/pyxetabase.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 4.0.0.dev36
+Version: 4.0.0.dev40
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-4.0.0.dev36 → pyxetabase-4.0.0.dev40}/setup.py

@@ -14,7 +14,7 @@ with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
 
 setup(
     name='pyxetabase',
-    version='4.0.0.dev36',
+    version='4.0.0.dev40',
     description='A REST client for OpenCGA enterprise REST web services',
     long_description=long_description,
     long_description_content_type='text/x-rst',