PyPI - seqslab-cli - Versions diffs - 3.3.0__tar.gz → 3.3.1__tar.gz - Mend

@@ -240,6 +240,11 @@ class BaseJobs:
                           "names. For example, ~{Sample_Name}_S~{Sample_ID} matches `NA12878_S1.fastq.gz` with "
                           "Sample_Name as `NA12878` and Sample_ID as `1` (optional, defaulting to ~{Sample_ID}).",
               aliases=["fq_sig"])
+    @argument("token_lifetime",
+              type=int,
+              positional=False,
+              description="Specify the duration, in hours, for the SeqsLab API token lifespan for this run (optional, "
+                          "default = 2).")
     def request_runsheet(self,
                          working_dir: str,
                          run_sheet: str,
@@ -247,7 +252,8 @@ class BaseJobs:
                          integrity: bool = False,
                          trust: bool = False,
                          kernel_version: str = '',
-                         fastq_signature: str = '~{Sample_ID}'
+                         fastq_signature: str = '~{Sample_ID}',
+                         token_lifetime: int = 2
                          ):
         """
         Parse run_sheet.csv and create a request.json file for each WES run.
@@ -269,13 +275,14 @@ class BaseJobs:
                                trust=trust, is_runsheet_template=True,
                                is_single_end=run_sheet.SampleSheet.is_single_end,
                                kernel_version=kernel_version,
-                               fq_signature=fastq_signature)
+                               fq_signature=fastq_signature,
+                               token_lifetime=token_lifetime)
         return 0
     def _runs_routine(self, run: Run, working_dir: str, workspace: str, execs: str = None,
                       integrity: bool = False, trust: bool = False, kernel_version: str = '',
                       is_runsheet_template: bool = False,
-                      is_single_end: bool = False, fq_signature: str = '~{Sample_ID}', ):
+                      is_single_end: bool = False, fq_signature: str = '~{Sample_ID}', token_lifetime: int = 2):
         def label_field_validation(label):
             message = f'label Name ({label}) can only contain alphanumeric characters ' \
@@ -314,7 +321,8 @@ class BaseJobs:
             "name": run.run_name,
             'workflow_params': params,
             'workflow_backend_params': parameters.workflow_backend_params(execs_path, workspace, run.runtimes,
-                                                                          integrity, trust, kernel_version),
+                                                                          integrity, trust, kernel_version,
+                                                                          token_lifetime),
             'workflow_url': run.workflow_url,
             "workflow_type_version": wf_info[0],
             'workflow_type': wf_info[1],
@@ -345,8 +353,8 @@ class BaseJobs:
               type=str,
               description="Key:value pairs indicating the workflow name -> SeqsLab supported runtime_options names. "
                           "Multiple configuration pairs can be provided using ':' as separator, "
-                          "e.g. main=acu-m8:subworkflow=acu-m4 "
-                          "(optional, default = None, which indicates running the whole workflow.wdl using acu-m16 for "
+                          "e.g. main=m4-cluster:subworkflow=m4-8xcluster "
+                          "(optional, default = None, which indicates running the whole workflow.wdl using m4-cluster for "
                           "a single node cluster on the Azure backend).")
     @argument("integrity",
               type=bool,
@@ -362,9 +370,14 @@ class BaseJobs:
     @argument("kernel_version",
               type=str,
               description="Specify the SeqsLab kernel version (optional, default = None).")
+    @argument("token_lifetime",
+              type=int,
+              positional=False,
+              description="Specify the duration, in hours, for the SeqsLab API token lifespan for this run (optional, "
+                          "default = 2).")
     def request(self, run_name: str, working_dir: str, workflow_url: str, workspace: str,
                 execs=None, runtimes=None, integrity=False,
-                trust=False, kernel_version=''):
+                trust=False, kernel_version='', token_lifetime=2):
         """
         Create WES run request.
         """
@@ -378,7 +391,8 @@ class BaseJobs:
             cprint(e, "red")
             return -1
         self._runs_routine(run=single_run, working_dir=working_dir, workspace=workspace, execs=execs,
-                           integrity=integrity, trust=trust, kernel_version=kernel_version)
+                           integrity=integrity, trust=trust, kernel_version=kernel_version,
+                           token_lifetime=token_lifetime)
         return 0
     @command

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seqslab-cli
-Version: 3.3.0
+Version: 3.3.1
 Summary: Atgenomix SeqsLab Command Line Tool
 Home-page: https://github.com/AnomeGAP/seqslab-cli
 Author: Allen Chang

@@ -23,7 +23,7 @@ __all__ = [
 ]
-__version__ = "3.3.0"
+__version__ = "3.3.1"
 LOGGING = {
     "DIR_PATH": "/var/log/seqslab"

@@ -153,6 +153,7 @@ def workflow_backend_params(execs_json: str,
                             integrity: bool = False,
                             trust: bool = False,
                             kernel_version: str = '',
+                            token_lifetime: int = 2
                             ) -> dict:
     """
     Create workflow_backend_params.json.
@@ -180,7 +181,7 @@ def workflow_backend_params(execs_json: str,
     rt_dict = {}
     if not runtimes:
-        rt_dict = {primary_workflow_name: 'acu-m16'}
+        rt_dict = {primary_workflow_name: 'm4-cluster'}
     else:
         rtcs = runtimes.split(':')
         for rtc in rtcs:
@@ -202,6 +203,7 @@ def workflow_backend_params(execs_json: str,
         workspace=workspace,
         integrity=integrity,
         trust=trust,
+        token_lifetime=token_lifetime
     )
     return bk_template

@@ -85,12 +85,15 @@ class WorkflowParamsTemplate:
         return inputs_connection
-def WorkflowBackendParamsTemplate(graph: str, clusters: list, workspace: str, integrity: bool, trust: bool) -> dict:
+def WorkflowBackendParamsTemplate(graph: str, clusters: list, workspace: str, integrity: bool, trust: bool,
+                                  token_lifetime: int) -> dict:
     ret = {
             "clusters": clusters,
             "workspace": workspace,
             "integrity": integrity,
-            "content_trust": trust
+            "content_trust": trust,
+            "token_lifetime": token_lifetime,
+            "debug_mode": False,
     }
     if graph:
         ret.update({'graph': graph})

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seqslab-cli
-Version: 3.3.0
+Version: 3.3.1
 Summary: Atgenomix SeqsLab Command Line Tool
 Home-page: https://github.com/AnomeGAP/seqslab-cli
 Author: Allen Chang

@@ -21,7 +21,7 @@ requests-toolbelt==1.0.0
 PyJWT==2.8.0
 django-environ==0.11.2
 validators==0.22.0
-pydot==1.4.2
+pydot==2.0.0
 orjson==3.9.10
 pydantic~=2.5.3
 aiohttp_retry==2.8.3

seqslab-cli 3.3.0__tar.gz → 3.3.1__tar.gz

seqslab-cli 3.3.0tar.gz → 3.3.1tar.gz