cloudos-cli 2.42.0__tar.gz → 2.44.0__tar.gz

{cloudos_cli-2.42.0 → cloudos_cli-2.44.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.42.0
+Version: 2.44.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro

cloudos_cli-2.44.0/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.44.0'

{cloudos_cli-2.42.0 → cloudos_cli-2.44.0}/cloudos_cli/clos.py

@@ -589,14 +589,10 @@ class Cloudos:
         wt : string ['nextflow'|'wdl']
             The workflow type detected
         """
-        my_workflows_r = self.get_workflow_list(workspace_id, verify=verify)
-        my_workflows = self.process_workflow_list(my_workflows_r)
-        wt_all = my_workflows.loc[
-            (my_workflows['name'] == workflow_name) & (my_workflows['archived.status'] == False),
-            'workflowType']
-        if len(wt_all) == 0:
-            raise ValueError(f'No workflow found with name: {workflow_name}')
-        wt = wt_all.unique()
+        # get list with workflow types
+        wt_all = self.workflow_content_query(workspace_id, workflow_name, verify=verify, query="workflowType")
+        # make unique
+        wt = list(dict.fromkeys(wt_all))
         if len(wt) > 1:
             raise ValueError(f'More than one workflow type detected for {workflow_name}: {wt}')
         return str(wt[0])
@@ -623,15 +619,9 @@ class Cloudos:
         bool
             True, if the workflow is a system module, false otherwise.
         """
-        my_workflows_r = self.get_workflow_list(workspace_id, verify=verify)
-        my_workflows = self.process_workflow_list(my_workflows_r)
-        group = my_workflows.loc[
-            (my_workflows['name'] == workflow_name) & (my_workflows['archived.status'] == False),
-            'group']
-        if len(group) == 0:
-            raise ValueError(f'No workflow found with name: {workflow_name}')
-        if len(group) > 1:
-            raise ValueError(f'More than one workflow found with name: {workflow_name}')
+        # get a list of all groups
+        group = self.workflow_content_query(workspace_id, workflow_name, verify=verify, query="group")
+
         module_groups = ['system-tools',
                          'data-factory-data-connection-etl',
                          'data-factory',
@@ -640,7 +630,7 @@ class Cloudos:
                          'data-factory-omics-insights',
                          'intermediate'
                          ]
-        if group.values[0] in module_groups:
+        if group[0] in module_groups:
             return True
         else:
             return False
@@ -883,3 +873,95 @@ class Cloudos:
         if r.status_code >= 400:
             raise BadRequestException(r)
         return r
+
+    def get_project_id_from_name(self, workspace_id, project_name, verify=True):
+        """Retrieve the project ID from its name.
+
+        Parameters
+        ----------
+        workspace_id : str
+            The CloudOS workspace ID to search for the project.
+        project_name : str
+            The name of the project to search for.
+        verify : [bool | str], optional
+            Whether to use SSL verification or not. Alternatively, if
+            a string is passed, it will be interpreted as the path to
+            the SSL certificate file. Default is True.
+
+        Returns
+        -------
+        dict
+            The server response containing project details.
+
+        Raises
+        ------
+        BadRequestException
+            If the request to retrieve the project fails with a status code
+            indicating an error.
+        """
+        headers = {
+            "Content-type": "application/json",
+            "apikey": self.apikey
+        }
+        url = f"{self.cloudos_url}/api/v2/projects?teamId={workspace_id}&search={project_name}"
+        response = retry_requests_get(url, headers=headers, verify=verify)
+        if response.status_code >= 400:
+            raise BadRequestException(response)
+        content = json.loads(response.content)
+
+        project_id = next((p.get("_id") for p in content.get("projects", []) if p.get("name") == project_name), None)
+        if project_id is None:
+            raise ValueError(f"[Error] Project '{project_name}' was not found in workspace '{workspace_id}'")
+
+        return project_id
+
+    def get_workflow_content(self, workspace_id, workflow_name, verify=True):
+        """Retrieve the workflow content from API.
+
+        Parameters
+        ----------
+        workspace_id : str
+            The CloudOS workspace ID to search for the workflow.
+        workflow_name : str
+            The name of the workflow to search for.
+        verify : [bool | str], optional
+            Whether to use SSL verification or not. Alternatively, if
+            a string is passed, it will be interpreted as the path to
+            the SSL certificate file. Default is True.
+
+        Returns
+        -------
+        dict
+            The server response containing workflow details.
+
+        Raises
+        ------
+        BadRequestException
+            If the request to retrieve the project fails with a status code
+            indicating an error.
+        """
+        headers = {
+            "Content-type": "application/json",
+            "apikey": self.apikey
+        }
+        url = f"{self.cloudos_url}/api/v3/workflows?teamId={workspace_id}&search={workflow_name}"
+        response = retry_requests_get(url, headers=headers, verify=verify)
+        if response.status_code >= 400:
+            raise BadRequestException(response)
+        content = json.loads(response.content)
+        return content
+
+    def workflow_content_query(self, workspace_id, workflow_name, verify=True, query="workflowType"):
+
+        content = self.get_workflow_content(workspace_id, workflow_name, verify=verify)
+
+        # check for duplicates
+        wf = [wf.get("name") for wf in content.get("workflows", []) if wf.get("name") == workflow_name]
+
+        if len(wf) == 0:
+            raise ValueError(f'No workflow found with name: {workflow_name}')
+        if len(wf) > 1:
+            raise ValueError(f'More than one workflow found with name: {workflow_name}')
+
+        # use 'query' to look in the content
+        return [wf.get(query) for wf in content.get("workflows", []) if wf.get("name") == workflow_name]

{cloudos_cli-2.42.0 → cloudos_cli-2.44.0}/cloudos_cli/datasets/datasets.py

@@ -43,10 +43,7 @@ class Datasets(Cloudos):
     def project_id(self, v) -> None:
         if isinstance(v, property):
             # Fetch the value as not defined by user.
-            self._project_id = self.fetch_cloudos_id(
-                self.apikey,
-                self.cloudos_url,
-                'projects',
+            self._project_id = self.fetch_project_id(
                 self.workspace_id,
                 self.project_name,
                 verify=self.verify)
@@ -54,39 +51,18 @@ class Datasets(Cloudos):
             # Let the user define the value.
             self._project_id = v
 
-    def fetch_cloudos_id(self,
-                         apikey,
-                         cloudos_url,
-                         resource,
+    def fetch_project_id(self,
                          workspace_id,
-                         name,
-                         mainfile=None,
-                         importsfile=None,
-                         repository_platform='github',
+                         project_name,
                          verify=True):
-        """Fetch the cloudos id for a given name.
+        """Fetch the project id for a given name.
 
         Parameters
         ----------
-        apikey : string
-            Your CloudOS API key
-        cloudos_url : string
-            The CloudOS service url.
-        resource : string
-            The resource you want to fetch from. E.g.: projects.
         workspace_id : string
             The specific Cloudos workspace id.
-        name : string
-            The name of a CloudOS resource element.
-        mainfile : string
-            The name of the mainFile used by the workflow. Only used when resource == 'workflows'.
-            Required for WDL pipelines as different mainFiles could be loaded for a single
-            pipeline.
-        importsfile : string
-            The name of the importsFile used by the workflow. Optional and only used for WDL pipelines
-            as different importsFiles could be loaded for a single pipeline.
-        repository_platform : string
-            The name of the repository platform of the workflow resides.
+        project_name : string
+            The name of a CloudOS project element.
         verify: [bool|string]
             Whether to use SSL verification or not. Alternatively, if
             a string is passed, it will be interpreted as the path to
@@ -97,38 +73,7 @@ class Datasets(Cloudos):
         project_id : string
             The CloudOS project id for a given project name.
         """
-        allowed_resources = ['projects', 'workflows']
-        if resource not in allowed_resources:
-            raise ValueError('Your specified resource is not supported. ' +
-                             f'Use one of the following: {allowed_resources}')
-        if resource == 'workflows':
-            content = self.get_workflow_list(workspace_id, verify=verify)
-            for element in content:
-                if (element["name"] == name and element["workflowType"] == "docker" and
-                        not element["archived"]["status"]):
-                    return element["_id"]  # no mainfile or importsfile
-                if (element["name"] == name and
-                        element["repository"]["platform"] == repository_platform and
-                        not element["archived"]["status"]):
-                    if mainfile is None:
-                        return element["_id"]
-                    elif element["mainFile"] == mainfile:
-                        if importsfile is None and "importsFile" not in element.keys():
-                            return element["_id"]
-                        elif "importsFile" in element.keys() and element["importsFile"] == importsfile:
-                            return element["_id"]
-        elif resource == 'projects':
-            content = self.get_project_list(workspace_id, verify=verify)
-            # New API projects endpoint spec
-            for element in content:
-                if element["name"] == name:
-                    return element["_id"]
-        if mainfile is not None:
-            raise ValueError(f'[ERROR] A workflow named \'{name}\' with a mainFile \'{mainfile}\'' +
-                             f' and an importsFile \'{importsfile}\' was not found')
-        else:
-            raise ValueError(f'[ERROR] No {name} element in {resource} was found')
-        
+        return self.get_project_id_from_name(workspace_id, project_name, verify=verify)
 
     def list_project_content(self):
         """

{cloudos_cli-2.42.0 → cloudos_cli-2.44.0}/cloudos_cli/jobs/job.py

@@ -148,8 +148,8 @@ class Job(Cloudos):
             raise ValueError('Your specified resource is not supported. ' +
                              f'Use one of the following: {allowed_resources}')
         if resource == 'workflows':
-            content = self.get_workflow_list(workspace_id, verify=verify)
-            for element in content:
+            content = self.get_workflow_content(workspace_id, name, verify=verify)
+            for element in content["workflows"]:
                 if (element["name"] == name and element["workflowType"] == "docker" and
                         not element["archived"]["status"]):
                     return element["_id"]  # no mainfile or importsfile
@@ -164,11 +164,7 @@ class Job(Cloudos):
                         elif "importsFile" in element.keys() and element["importsFile"] == importsfile:
                             return element["_id"]
         elif resource == 'projects':
-            content = self.get_project_list(workspace_id, verify=verify)
-            # New API projects endpoint spec
-            for element in content:
-                if element["name"] == name:
-                    return element["_id"]
+            return self.get_project_id_from_name(workspace_id, self.project_name, verify=verify)
         if mainfile is not None:
             raise ValueError(f'[ERROR] A workflow named \'{name}\' with a mainFile \'{mainfile}\'' +
                              f' and an importsFile \'{importsfile}\' was not found')

{cloudos_cli-2.42.0 → cloudos_cli-2.44.0}/cloudos_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.42.0
+Version: 2.44.0
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro

cloudos_cli-2.42.0/cloudos_cli/_version.py

@@ -1 +0,0 @@
-__version__ = '2.42.0'