pyxetabase 3.1.0.dev2__tar.gz → 4.0.0.dev30__tar.gz

{pyxetabase-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 3.1.0.dev2
+Version: 4.0.0.dev30
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/pyxetabase/commons.py

@@ -145,22 +145,22 @@ def _fetch(config, sid, category, resource, method, subcategory=None, query_id=N
         # Getting REST response
         if method == 'get':
             try:
-                r = requests.get(url, headers=header, cookies=config.cookies)
+                r = requests.get(url, headers=header, cookies=config.cookies, verify=not config.tlsAllowInvalidCertificates)
             except requests.exceptions.ConnectionError:
                 sleep(1)
-                r = requests.get(url, headers=header, cookies=config.cookies)
+                r = requests.get(url, headers=header, cookies=config.cookies, verify=not config.tlsAllowInvalidCertificates)
         elif method == 'post':
             try:
-                r = requests.post(url, json=data, headers=header, cookies=config.cookies)
+                r = requests.post(url, json=data, headers=header, cookies=config.cookies, verify=not config.tlsAllowInvalidCertificates)
             except requests.exceptions.ConnectionError:
                 sleep(1)
-                r = requests.post(url, json=data, headers=header, cookies=config.cookies)
+                r = requests.post(url, json=data, headers=header, cookies=config.cookies, verify=not config.tlsAllowInvalidCertificates)
         elif method == 'delete':
             try:
-                r = requests.delete(url, headers=header, cookies=config.cookies)
+                r = requests.delete(url, headers=header, cookies=config.cookies, verify=not config.tlsAllowInvalidCertificates)
             except requests.exceptions.ConnectionError:
                 sleep(1)
-                r = requests.delete(url, headers=header, cookies=config.cookies)
+                r = requests.delete(url, headers=header, cookies=config.cookies, verify=not config.tlsAllowInvalidCertificates)
         else:
             raise NotImplementedError('method: ' + method + ' not implemented.')
 

{pyxetabase-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/pyxetabase/opencga_config.py

@@ -37,12 +37,21 @@ class ClientConfiguration(object):
         return config_dict
 
     def get_sso_login_info(self):
+        # Checking if SSO login is specified
         if (('sso_login' in self._config and self._config['sso_login']) or
                 ('cookies' in self._config and self._config['cookies'])):
-            python_session_fhand = open(os.path.expanduser("~/.opencga/session.json"), 'r')
+
+            # Getting session file name
+            if 'name' in self._config['rest'] and self._config['rest']['name']:
+                host_name = self._config['rest']['name']
+            else:
+                host_name = 'opencga'
+            python_session_fhand = open(os.path.expanduser("~/.opencga/{}_session.json".format(host_name)), 'r')
+
+            # Loading info from session file
             session_info = json.loads(python_session_fhand.read())
             self._config['sso_login'] = True
-            self._config['cookies'] = session_info['cookies']
+            self._config['cookies'] = session_info['attributes']['cookies']
             self._config['token'] = session_info['token']
 
     def _validate_configuration(self):
@@ -55,16 +64,46 @@ class ClientConfiguration(object):
         if 'host' not in self._config['rest'] or not self._config['rest']['host']:
             raise ValueError('Missing configuration field "host".')
 
-        self._validate_host(self._config['rest']['host'])
+        self._validate_host()
 
-    @staticmethod
-    def _validate_host(host):
+    def _validate_host(self):
         try:
-            r = requests.head(host, timeout=2)
+            r = requests.head(self.host, timeout=2, verify=not self.tlsAllowInvalidCertificates)
             if r.status_code == 302:
                 return
+        except requests.exceptions.SSLError:
+            raise Exception('Invalid SSL certificate from "{}"'.format(self.host))
         except requests.ConnectionError:
-            raise Exception('Unreachable host "{}"'.format(host))
+            raise Exception('Unreachable host "{}"'.format(self.host))
+
+    @property
+    def host(self):
+        return self._config['rest']['host']
+
+    @host.setter
+    def host(self, new_host):
+        self._config['rest']['host'] = new_host
+
+    @property
+    def tlsAllowInvalidCertificates(self):
+        if ('tlsAllowInvalidCertificates' in self._config['rest']
+                and self._config['rest']['tlsAllowInvalidCertificates'] is not None):
+            return self._config['rest']['tlsAllowInvalidCertificates']
+        else:
+            return False
+
+    @property
+    def version(self):
+        return self._config['version'] if 'version' in self._config else 'v2'
+
+    @property
+    def cookies(self):
+        if 'cookies' in self._config and self._config['cookies']:
+            python_session_fhand = open(os.path.expanduser("~/.opencga/python_session.json"), 'r')
+            session_info = json.loads(python_session_fhand.read())
+            return session_info['cookies']
+        else:
+            return None
 
     @property
     def configuration(self):
@@ -77,7 +116,19 @@ class ClientConfiguration(object):
     @host.setter
     def host(self, host):
         self._config['rest']['host'] = host
-        self._validate_host(host)
+        self._validate_host()
+
+    @property
+    def tlsAllowInvalidCertificates(self):
+        if ('tlsAllowInvalidCertificates' in self._config['rest'] and
+                self._config['rest']['tlsAllowInvalidCertificates'] is not None):
+            return self._config['rest']['tlsAllowInvalidCertificates']
+        else:
+            return False
+
+    @tlsAllowInvalidCertificates.setter
+    def tlsAllowInvalidCertificates(self, tlsAllowInvalidCertificates):
+        self._config['rest']['tlsAllowInvalidCertificates'] = tlsAllowInvalidCertificates
 
     @property
     def version(self):

{pyxetabase-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/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-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/pyxetabase/rest_clients/admin_client.py

@@ -147,8 +147,7 @@ class Admin(_ParentRestClient):
 
     def sync_users(self, data=None, **options):
         """
-        Synchronise a group of users from an authentication origin with a
-            group in a study from catalog.
+        [DEPRECATED] Moved to /users/sync.
         PATH: /{apiVersion}/admin/users/sync
 
         :param dict data: JSON containing the parameters. (REQUIRED)

{pyxetabase-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/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-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/pyxetabase/rest_clients/file_client.py

@@ -420,7 +420,7 @@ class File(_ParentRestClient):
             MICROARRAY_EXPRESSION_TWOCHANNELS_GENEPIX DATAMATRIX_EXPRESSION
             IDLIST IDLIST_RANKED ANNOTATION_GENEVSANNOTATION OTHER_NEWICK
             OTHER_BLAST OTHER_INTERACTION OTHER_GENOTYPE OTHER_PLINK OTHER_VCF
-            OTHER_PED VCF4 VARIANT ALIGNMENT COVERAGE SEQUENCE PEDIGREE
+            OTHER_PED VCF4 CVDB VARIANT ALIGNMENT COVERAGE SEQUENCE PEDIGREE
             REFERENCE_GENOME NONE UNKNOWN']
         :param str checksum: Expected MD5 file checksum.
         :param bool resource: Boolean field indicating whether the file is a

{pyxetabase-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/pyxetabase/rest_clients/meta_client.py

@@ -55,15 +55,16 @@ class Meta(_ParentRestClient):
 
         return self._get(category='meta', resource='model', **options)
 
-    def openapi(self, **options):
+    def openapi(self, url, **options):
         """
         Opencga openapi json.
         PATH: /{apiVersion}/meta/openapi
 
-        :param str environment: Environment of the app.
-        :param str host: Opencga host without environment.
+        :param str url: Opencga host with environment. (REQUIRED)
+        :param str study: Opencga study to be default in queries.
         """
 
+        options['url'] = url
         return self._get(category='meta', resource='openapi', **options)
 
     def ping(self, **options):

{pyxetabase-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/pyxetabase/rest_clients/study_client.py

@@ -166,6 +166,19 @@ class Study(_ParentRestClient):
 
         return self._get(category='studies', resource='groups', query_id=study, **options)
 
+    def sync_groups(self, study, data=None, **options):
+        """
+        Associate a remote group from an authentication origin with a local
+            group in a study.
+        PATH: /{apiVersion}/studies/{study}/groups/sync
+
+        :param dict data: JSON containing the parameters. (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        """
+
+        return self._post(category='studies', resource='sync', query_id=study, subcategory='groups', data=data, **options)
+
     def update_groups(self, study, data=None, **options):
         """
         Add or remove a group.
@@ -386,6 +399,21 @@ class Study(_ParentRestClient):
 
         return self._post(category='studies', resource='update', query_id=study, data=data, **options)
 
+    def sync_users(self, study, authentication_origin_id, **options):
+        """
+        Synchronize all users from the remote groups of a given authentication
+            origin.
+        PATH: /{apiVersion}/studies/{study}/users/sync
+
+        :param str authentication_origin_id: Authentication origin ID.
+            (REQUIRED)
+        :param str study: Study [[organization@]project:]study where study and
+            project can be either the ID or UUID. (REQUIRED)
+        """
+
+        options['authenticationOriginId'] = authentication_origin_id
+        return self._post(category='studies', resource='sync', query_id=study, subcategory='users', **options)
+
     def variable_sets(self, study, **options):
         """
         Fetch variableSets from a study.

{pyxetabase-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/pyxetabase/rest_clients/variant_operation_client.py

@@ -86,6 +86,32 @@ class VariantOperation(_ParentRestClient):
 
         return self._delete(category='operation', resource='delete', subcategory='variant/annotation', **options)
 
+    def variant_annotation_extension_configure(self, data=None, **options):
+        """
+        Install a variant annotation extension and configure the project to
+            use it.
+        PATH: /{apiVersion}/operation/variant/annotation/extension/configure
+
+        :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 project: project.
+        :param dict data: Parameters to configure a variant annotation
+            extension.
+        """
+
+        return self._post(category='operation', resource='configure', subcategory='variant/annotation/extension', data=data, **options)
+
     def index_variant_annotation(self, data=None, **options):
         """
         Create and load variant annotations into the database.
@@ -601,33 +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-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/pyxetabase.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyxetabase
-Version: 3.1.0.dev2
+Version: 4.0.0.dev30
 Summary: A REST client for OpenCGA enterprise REST web services
 Author: Daniel Perez-Gil
 Author-email: daniel.perez@zettagenomics.com

{pyxetabase-3.1.0.dev2 → pyxetabase-4.0.0.dev30}/setup.py

@@ -14,7 +14,7 @@ with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
 
 setup(
     name='pyxetabase',
-    version='3.1.0.dev2',
+    version='4.0.0.dev30',
     description='A REST client for OpenCGA enterprise REST web services',
     long_description=long_description,
     long_description_content_type='text/x-rst',