seqslab-cli 3.3.3__tar.gz → 3.3.4__tar.gz

{seqslab-cli-3.3.3/python/seqslab_cli.egg-info → seqslab-cli-3.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seqslab-cli
-Version: 3.3.3
+Version: 3.3.4
 Summary: Atgenomix SeqsLab Command Line Tool
 Home-page: https://github.com/AnomeGAP/seqslab-cli
 Author: Allen Chang

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/python/seqslab/__init__.py

@@ -21,6 +21,6 @@ name = "seqslab"
 __all__ = []
 
 
-__version__ = "3.3.3"
+__version__ = "3.3.4"
 
 LOGGING = {"DIR_PATH": "/var/log/seqslab"}

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/python/seqslab/auth/azuread.py

@@ -72,14 +72,14 @@ class ClientApp(AuthBaseModel):
     public_app: msal.ClientApplication = None
     confidential_app: msal.ClientApplication = None
 
-    def load_client(self, credential: str = None) -> Client:
+    def load_client(self, credential: str = None, tenant: str = None) -> Client:
         proxies = context.get_context().args.proxy
         if credential:
             if not self.confidential_app:
                 self.confidential_app = msal.ConfidentialClientApplication(
                     SOCIAL_AUTH_AZURE_KEY,
                     client_credential=credential,
-                    authority=f"https://login.microsoftonline.com/{SOCIAL_AUTH_AZURE_TENANT_ID}",
+                    authority=f"https://login.microsoftonline.com/{tenant}",
                     app_name=seqslab.name,
                     app_version=seqslab.__version__,
                     proxies=proxies,

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/python/seqslab/auth/commands.py

@@ -60,7 +60,9 @@ class BaseAuth:
         proxy: str = None,
     ) -> dict:
         scopes = azuread.SOCIAL_AUTH_AZURE_SCOPE_APP.get(scope)
-        client = aad_app.load_client(credential=credential)
+        client = aad_app.load_client(
+            credential=credential, tenant=self._decode(assertion)["tid"]
+        )
         result = client.acquire_token_silent(scopes, account=None)
         if not result:
             logging.info(
@@ -92,7 +94,7 @@ class BaseAuth:
         result = None
         token_uri = self.ACCESS_TOKEN_URL.format(backend=backend)
         scopes = azuread.SOCIAL_AUTH_AZURE_SCOPE
-        client = aad_app.load_client()
+        client = aad_app.load_client(tenant=azuread.SOCIAL_AUTH_AZURE_TENANT_ID)
         accounts = client.get_accounts()
         if accounts:
             logging.info(

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/python/seqslab/trs/template/base.py

@@ -22,7 +22,7 @@ class TrsCreateTemplate:
             primary_descriptor=primary_descriptor, zip_file=zip_file
         )
         workflow = self.desc_template(parameter)
-        calls = self.workflow_call_template(parameter)
+        calls = self.call_template(parameter)
         inputs_connections = self.inputs_connections(
             parameter=parameter, inputs_json=inputs_json
         )
@@ -41,7 +41,6 @@ class TrsCreateTemplate:
     @staticmethod
     def dot_cleaning(gs: str) -> str:
         # Standard Library
-        import re
 
         rx = r';[\w;="]+'
         return re.sub(rx, "", gs)
@@ -59,32 +58,6 @@ class TrsCreateTemplate:
                     calls.add(node.get_name().replace("CALL_", ""))
         return calls
 
-    def workflow_call_template(self, parameter: dict) -> list:
-        # adding main workflow
-        runtime_cell_select = [
-            pydot.graph_from_dot_data(
-                TrsCreateTemplate.dot_cleaning(parameter["graph"])
-            )[0].get_name()
-        ]
-
-        # parsing workflow>call information from graph string
-        graphRex = re.compile(r'graph\s\w+|}|label="call\s\w+', re.IGNORECASE)
-        wnames = []
-        matches = graphRex.findall(parameter.get("graph"))
-        if matches:
-            for e in matches:
-                if e.startswith("graph "):
-                    wnames.append(e.split(" ")[1].replace("cluster_", ""))
-                elif e.startswith("}"):
-                    wnames.pop()
-                elif e.startswith("label="):
-                    call = e.replace('label="', "").strip('"')
-                    if call.lower().startswith("call"):
-                        runtime_cell_select.append(
-                            "" + wnames[-1] + ">" + call.replace("call ", "")
-                        )
-        return runtime_cell_select
-
     def call_template(self, parameter: dict) -> list:
         calls = [
             pydot.graph_from_dot_data(

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/python/seqslab/wes/commands.py

@@ -11,6 +11,7 @@ from datetime import datetime
 from functools import lru_cache
 from typing import List
 
+import pytz
 import requests
 from nubia import argument, command, context
 from requests_toolbelt.multipart.encoder import MultipartEncoder
@@ -22,8 +23,9 @@ from seqslab.wes import API_HOSTNAME, __version__
 from seqslab.wes.internal import parameters
 from tenacity import retry, stop_after_attempt, wait_fixed
 from termcolor import cprint
+from tzlocal import get_localzone
 
-from .internal.common import get_factory
+from .resource.common import get_factory
 
 """
 Copyright (C) 2022, Atgenomix Incorporated.
@@ -186,40 +188,122 @@ class BaseJobs:
 
     @command
     @argument(
-        "run_request_id",
+        "request_path",
         type=str,
         positional=False,
-        description="Specify a previously scheduled run request ID (required). ",
+        description="Specify the request.json file to run (required).",
     )
     @argument(
-        "schedule_tag",
+        "workspace",
+        type=str,
+        description="Specify the workspace based on the signed in account (required).",
+    )
+    @argument(
+        "date",
         type=str,
         positional=False,
-        description="Specify a tag marked on previously uploaded samples for a scheduled WES run (required).",
+        aliases=["d"],
+        description="Specify the schedule date, in the format of YYYY-MM-DD (required).",
     )
     @argument(
-        "workspace",
+        "time",
         type=str,
-        description="Specify the workspace based on the signed in account (required).",
+        positional=False,
+        aliases=["t"],
+        description="Specify the schedule time, in the format of HH-MM (required).",
+    )
+    @argument(
+        "time_zone",
+        type=str,
+        choices=["UTC", "LOCAL"],
+        positional=False,
+        aliases=["z"],
+        description="Specify the time zone for the provided date and time. If 'LOCAL' is selected, the date and time "
+        "will be interpreted according to the operating system's time zone. (optional, default = UTC).",
+    )
+    @argument(
+        "recurrence",
+        type=str,
+        positional=False,
+        aliases=["r"],
+        choices=["Once", "Hourly", "Daily", "Weekly", "Monthly"],
+        description="Specify the schedule recurrence (optional, default = Once).",
     )
-    def schedule(self, run_request_id: str, schedule_tag: str, workspace: str) -> int:
+    def schedule(
+        self,
+        request_path: str,
+        workspace: str,
+        date: str,
+        time: str,
+        time_zone: str = "UTC",
+        recurrence: str = "Once",
+    ) -> int:
         """
-        Run a WES run based on a previously registered run request. Typically, the run request
-        is designed for a scheduled WES run, where the FQN-DRS connection of sequencing samples
-        are left blank for future runtime sample-resolving. Thus, by specifying a sample-resolving rule,
-        the run request can be used to serve a scheduled WES run use case.
+        Schedule a WES run with given date, time, and recurrence.
         """
-        mp = MultipartEncoder(fields={})
+        if not os.path.isfile(request_path):
+            cprint("request_path is not a file", "red")
+            return errno.EINVAL
+        else:
+            try:
+                with open(request_path, "r") as f:
+                    req = json.load(f)
+            except json.decoder.JSONDecodeError as e:
+                cprint(f"given request not in json format - {e}", "red")
+                return errno.EINVAL
+
+        if not self._is_valid_time(date, "%Y-%m-%d"):
+            cprint(f"date {date} not in YYYY-MM-DD format", "red")
+            return errno.EINVAL
+
+        if not self._is_valid_time(time, "%H:%M"):
+            cprint(f"time {time} not in HH-MM format", "red")
+            return errno.EINVAL
+
+        time_f = f"{date} {time}"
+
+        if time_zone == "LOCAL":
+            time_f, msg = self._to_utc(time_f)
+            if not time_f:
+                cprint(f"timezone transform failed {msg}", "red")
+                return errno.EINVAL
+
+        payloads = {
+            "schedule": {"schedule_type": recurrence[0], "next_run": time_f},
+            "request": req,
+        }
+
         resource = get_factory().load_resource(workspace)
-        ret = resource.sync_run_jobs(
-            data=mp,
-            headers={"Content-Type": mp.content_type},
-            run_request_id=run_request_id,
-            run_name=schedule_tag,
+        ret = resource.schedule_run(
+            data=payloads,
+        ).json()
+        cprint(
+            f"wes_schedule_id: {ret['id']}; schedule_details: {str(ret['schedule'])}",
+            "yellow",
         )
-        cprint(f"{ret.content.decode('utf-8')}", "yellow")
         return 0
 
+    @staticmethod
+    def _is_valid_time(time_str: str, time_format: str):
+        try:
+            datetime.strptime(time_str, time_format)
+            return True
+        except ValueError:
+            return False
+
+    @staticmethod
+    def _to_utc(local_t: str):
+        try:
+            local_timezone = pytz.timezone(get_localzone().key)
+            utc_t = (
+                local_timezone.localize(datetime.strptime(local_t, "%Y-%m-%d %H:%M"))
+                .astimezone(pytz.utc)
+                .strftime("%Y-%m-%d %H:%M")
+            )
+            return utc_t, None
+        except Exception as e:
+            return None, str(e)
+
     @command(aliases=["state"])
     @argument(
         "run_id",
@@ -400,8 +484,21 @@ class BaseJobs:
         else:
             execs_path = f"{working_dir}/{execs}"
 
+        resource = get_factory().load_resource(workspace)
+        ops = resource.list_operator_pipelines(page=1, page_size=1000)["results"]
+        opp_w_args = [
+            op["id"]
+            for op in ops
+            for operator in op["operators"]
+            if isinstance(operator, dict) and operator.get("arguments")
+        ]
         params = parameters.workflow_params(
-            execs_path, run, is_runsheet_template, is_single_end, fq_signature
+            execs_path,
+            run,
+            is_runsheet_template,
+            is_single_end,
+            fq_signature,
+            opp_w_args,
         )
         if not isinstance(params, dict):
             raise Exception(
@@ -620,10 +717,9 @@ class BaseJobs:
         try:
             result = get_factory().load_resource(workspace).cancel_run(run_id)
             cprint(json.dumps(result, indent=4), "yellow")
-        except requests.HTTPError:
-            cprint(f"given run_id {run_id} is not valid.", "red")
+        except requests.HTTPError as e:
+            cprint(f"Fail to cancel Job {run_id} - '{str(e)}'.", "red")
             return -1
-
         return 0
 
     @command
@@ -725,7 +821,7 @@ class BaseJobs:
         List registered operator pipelines.
         """
         resource = get_factory().load_resource(workspace)
-        r = resource.list_runtime_options(page=page, page_size=page_size)
+        r = resource.list_operator_pipelines(page=page, page_size=page_size)
 
         if isinstance(r, int):
             return r
@@ -736,8 +832,6 @@ class BaseJobs:
     @staticmethod
     def _stdout(results, output: str) -> int:
         # Standard Library
-        import csv
-        from io import StringIO
 
         from tabulate import tabulate
 
@@ -756,6 +850,30 @@ class BaseJobs:
             )
         return 0
 
+    @command
+    @argument(
+        "run_id",
+        type=str,
+        positional=False,
+        description="Specify the run_id that is going to be delete (required).",
+    )
+    @argument(
+        "workspace",
+        type=str,
+        description="Specify the workspace based on the signed in account (required).",
+    )
+    def delete(self, run_id: str, workspace: str) -> int:
+        """
+        Delete WES run as well as all the generated output files based on run ID.
+        """
+        try:
+            get_factory().load_resource(workspace).delete_run(run_id)
+        except requests.HTTPError as e:
+            cprint(f"Fail to delete Job {run_id} - '{str(e)}'.", "red")
+            return -1
+
+        return 0
+
 
 @command
 class Jobs(BaseJobs):

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/python/seqslab/wes/internal/parameters.py

@@ -6,7 +6,7 @@ import re
 import zipfile
 
 from seqslab.runsheet.runsheet import Run
-from seqslab.wes.internal.common import get_factory
+from seqslab.wes.resource.common import get_factory
 from seqslab.wes.template.base import (
     WorkflowBackendParamsClusterTemplate,
     WorkflowBackendParamsTemplate,
@@ -119,6 +119,7 @@ def workflow_params(
     is_runsheet_template: bool,
     is_single_end: bool,
     fq_sig: str,
+    opp_w_args: dict,
 ) -> dict:
     """
     Create workflow_params.json.
@@ -132,7 +133,9 @@ def workflow_params(
         with open(execs_json, "r") as f:
             t_content = json.loads(f.read())
 
-        params = WorkflowParamsTemplate().create(ex_template=t_content)
+        params = WorkflowParamsTemplate().create(
+            ex_template=t_content, opp_w_args=opp_w_args
+        )
 
         if is_runsheet_template:
             r1fqn, r2fqn = validate_label_column(run)
@@ -230,33 +233,13 @@ def workflow_backend_params(
             raise RuntimeError(
                 f"given call name {k} not in TRS registered call name list {calls}!"
             )
-
-        # general workflow>call handling
-        ids = k.split(">")
-        if len(ids) == 2:
-            clusters.append(
-                WorkflowBackendParamsClusterTemplate(
-                    run_time=resource.get_runtime_setting(v),
-                    call_name=ids[1],
-                    workflow_name=ids[0],
-                    kernel_version=kernel_version,
-                )
+        clusters.append(
+            WorkflowBackendParamsClusterTemplate(
+                run_time=resource.get_runtime_setting(v),
+                workflow_name=k,
+                kernel_version=kernel_version,
             )
-        else:
-            # main workflow name
-            if k == primary_workflow_name:
-                clusters.append(
-                    WorkflowBackendParamsClusterTemplate(
-                        run_time=resource.get_runtime_setting(v),
-                        call_name=k,
-                        kernel_version=kernel_version,
-                    )
-                )
-            else:
-                # raise exception for incorrect format of k
-                raise RuntimeError(
-                    f"given identifier {k} does not in format of in TRS registered call name list {calls}!"
-                )
+        )
 
     bk_template = WorkflowBackendParamsTemplate(
         graph=execs.get("graph"),

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/python/seqslab/wes/resource/base.py

@@ -55,6 +55,7 @@ class BaseResource(ABC):
     WES_RUNTIME_OPTIONS_URL = (
         f"{WES_BASE_URL}runtime-options/{{name}}?backend={{backend}}"
     )
+    WES_SCHEDULES_URL = f"{WES_BASE_URL}schedules/?backend={{backend}}"
 
     class Response(NamedTuple):
         status: int
@@ -313,6 +314,16 @@ class BaseResource(ABC):
                 raise requests.HTTPError(response.text)
             return json.loads(response.content)
 
+    def delete_run(self, run_id) -> int:
+        token = BaseAuth.get_token().get("tokens").get("access")
+        with requests.delete(
+            url=f"{self.WES_BASE_URL}runs/{run_id}",
+            headers={"Authorization": f"Bearer {token}"},
+        ) as response:
+            if response.status_code not in [204]:
+                raise requests.HTTPError(response.text)
+            return 0
+
     def list_runtime_options(self, page=1, page_size=10):
         try:
             token = BaseAuth.get_token().get("tokens").get("access")
@@ -344,3 +355,25 @@ class BaseResource(ABC):
             print(err)
             raise err
         return response.json()
+
+    def schedule_run(self, data) -> requests.Response:
+        try:
+            ctx = context.get_context()
+            backend = ctx.args.backend
+            token = BaseAuth.get_token().get("tokens").get("access")
+
+            response = requests.post(
+                url=self.WES_SCHEDULES_URL.format(backend=backend),
+                headers={"Authorization": f"Bearer {token}"},
+                json=data,
+            )
+
+            if response.status_code not in [requests.codes.created]:
+                raise requests.HTTPError(
+                    f"{response.status_code}: {repr(response.text)}"
+                )
+        except Exception as err:
+            print(err)
+            raise err
+
+        return response

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/python/seqslab/wes/template/base.py

@@ -1,6 +1,6 @@
 class WorkflowParamsTemplate:
-    def create(self, ex_template: dict) -> dict:
-        operator_pipelines = self.operator_pipelines(ex_template)
+    def create(self, ex_template: dict, opp_w_args: dict) -> dict:
+        operator_pipelines = self.operator_pipelines(ex_template, opp_w_args)
         return {
             "inputs": ex_template.get("inputs"),
             "datasets": ex_template.get("connections", None),
@@ -19,8 +19,7 @@ class WorkflowParamsTemplate:
             return self._flat_list(sub_v, r, layer)
         return {"list": r, "layer": layer}
 
-    @staticmethod
-    def operator_pipelines(ex_template: dict) -> dict:
+    def operator_pipelines(self, ex_template: dict, opp_w_args: dict) -> dict:
         """
         :param: parameter: parameter API response
         :return:
@@ -42,13 +41,20 @@ class WorkflowParamsTemplate:
             for pipeline in ex_template["operator_pipelines"]:
                 if pipeline["id"] == v:
                     tasks[k] = {
-                        "id": v,
+                        "id": self.norm_pl_key(v, opp_w_args),
                         "operators": pipeline["operators"],
                         "description": pipeline["description"],
                     }
                     continue
         return tasks
 
+    @staticmethod
+    def norm_pl_key(pl_key: str, opp_w_args: dict) -> str:
+        for opp in opp_w_args:
+            if pl_key.startswith(opp):
+                return opp
+        return pl_key
+
     @staticmethod
     def inputs_connections(inputs_connection: list = None) -> dict:
         """
@@ -115,14 +121,11 @@ def WorkflowBackendParamsTemplate(
 
 
 def WorkflowBackendParamsClusterTemplate(
-    run_time: dict, call_name: str, kernel_version: str, workflow_name: str = ""
+    run_time: dict, kernel_version: str, workflow_name: str = ""
 ) -> dict:
     if kernel_version:
         opts = run_time["options"]
         opts.append(f"seqslab.kernel.version {kernel_version}")
         run_time.update({"options": opts})
-    if workflow_name:
-        run_time.update({"call": call_name, "workflow": workflow_name})
-    else:
-        run_time.update({"call": call_name})
+    run_time.update({"call": workflow_name})
     return run_time

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4/python/seqslab_cli.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seqslab-cli
-Version: 3.3.3
+Version: 3.3.4
 Summary: Atgenomix SeqsLab Command Line Tool
 Home-page: https://github.com/AnomeGAP/seqslab-cli
 Author: Allen Chang

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/python/seqslab_cli.egg-info/SOURCES.txt

@@ -83,11 +83,11 @@ python/seqslab/user/resource/base.py
 python/seqslab/wes/__init__.py
 python/seqslab/wes/commands.py
 python/seqslab/wes/internal/__init__.py
-python/seqslab/wes/internal/common.py
 python/seqslab/wes/internal/parameters.py
 python/seqslab/wes/resource/__init__.py
 python/seqslab/wes/resource/azure.py
 python/seqslab/wes/resource/base.py
+python/seqslab/wes/resource/common.py
 python/seqslab/wes/template/__init__.py
 python/seqslab/wes/template/base.py
 python/seqslab/wes/template/template.py

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/python/seqslab_cli.egg-info/requires.txt

@@ -28,3 +28,5 @@ aiohttp_retry==2.8.3
 requests~=2.31.0
 setuptools~=69.5.1
 jsonpath-ng==1.6.0
+tzlocal==5.2
+pytz==2021.3

{seqslab-cli-3.3.3 → seqslab-cli-3.3.4}/requirements.txt

@@ -24,3 +24,5 @@ aiohttp_retry==2.8.3
 requests~=2.31.0
 setuptools~=69.5.1
 jsonpath-ng==1.6.0
+tzlocal==5.2
+pytz==2021.3