commit

README.md

@@ -4,6 +4,28 @@ Helper utils for omics
 
 * Free software: MIT license
 
+## Usage
+
+### Prepare the workflow
+
+In order to use a nextflow workflow with AWS Omics, you need to prepare it first.
+
+* All images must be stored in *your* ecr repository. You can use the `create-ecr-repos` command to create the repos and
+  push the images.
+* All parameters must be defined in the `nextflow_schema.json` file. You can use the `create-workflow` command to create
+  the workflow.
+* The workflow must be zipped and uploaded to AWS Omics. You can use the `create-workflow` command to create the
+  workflow.
+
+```bash
+omicsx create-ecr-repos --nf-workflow <your-nextflow-workflow-directory> \
+  --aws-region <your-aws-region>
+
+omicsx create-workflow --nf-workflow <your-nextflow-workflow-directory> \
+  --name <your-workflow-name> \
+  --aws-region <your-aws-region>
+```
+
 # CLI
 
 **Usage**:
@@ -101,6 +123,32 @@ $ omicsx create-workflow [OPTIONS] NF_WORKFLOW NAME
 * `--aws-profile TEXT`: [default: default]
 * `--help`: Show this message and exit.
 
+## `list-workflows`
+
+List existing omics workflows
+
+**Options**:
+
+* `--aws-region TEXT`: [default: us-east-1]
+* `--aws-profile TEXT`: [default: default]
+* `--help`: Show this message and exit.
+
+## `list-runs`
+
+List existing omics runs
+
+**Usage**:
+
+```console
+$ list-runs [OPTIONS]
+```
+
+**Options**:
+
+* `--aws-region TEXT`: [default: us-east-1]
+* `--aws-profile TEXT`: [default: default]
+* `--help`: Show this message and exit.
+
 ## `run-cost`
 
 Calculate the cost of a run. If the run is still running, it will calculate the current cost. If the run is complete, it

bioanalyze_omics/cli.py

@@ -113,6 +113,38 @@ def create_ecr_repos(
     return
 
 
+@app.command()
+def list_workflows(
+    aws_region: Annotated[
+        Optional[str],
+        typer.Option(help="AWS Region", default=AWS_REGION),
+    ] = AWS_REGION,
+    aws_profile: Annotated[
+        Optional[str], typer.Option(help="AWS Profile", default="default")
+    ] = "default",
+):
+    """List existing omics workflows"""
+    omics_workflow = workflows.OmicsWorkflow(aws_region=aws_region)
+    omics_workflow.list_workflows()
+    return
+
+
+@app.command()
+def list_runs(
+    aws_region: Annotated[
+        Optional[str],
+        typer.Option(help="AWS Region", default=AWS_REGION),
+    ] = AWS_REGION,
+    aws_profile: Annotated[
+        Optional[str], typer.Option(help="AWS Profile", default="default")
+    ] = "default",
+):
+    """List existing omics runs"""
+    omics_run = runs.OmicsRun(aws_region=aws_region)
+    omics_run.list_runs()
+    return
+
+
 @app.command()
 def create_workflow(
     nf_workflow: Annotated[

bioanalyze_omics/resources/ecr.py

@@ -12,6 +12,8 @@
 
 from bioanalyze_omics.nf import NextflowWorkflow
 from bioanalyze_omics.resources.account import get_aws_account_id
+from rich.console import Console
+from rich.table import Table
 
 import logging
 from rich.logging import RichHandler

bioanalyze_omics/resources/runs.py

@@ -16,6 +16,8 @@
 import requests
 from copy import deepcopy
 import pandas as pd
+from rich.console import Console
+from rich.table import Table
 
 MINIMUM_STORAGE_CAPACITY_GIB = 1200
 
@@ -218,6 +220,33 @@ def gen_run_df(self, run: Any) -> pd.DataFrame:
         run_df = pd.DataFrame.from_records([run])
         return run_df
 
+    def list_runs(self):
+        response = self.omics_client.list_runs()
+        if 'items' not in response:
+            return []
+        table = Table(title="Runs")
+        table.add_column("RunId")
+        table.add_column("WorkflowId")
+        table.add_column("Name")
+        table.add_column("Status")
+        table.add_column("CreationTime")
+        table.add_column("StartTime")
+        table.add_column("StopTime")
+        for run in response['items']:
+            table.add_row(
+                run['id'],
+                run['workflowId'],
+                run['name'],
+                run['status'],
+                run['creationTime'].strftime("%Y/%m/%d, %H:%M:%S"),
+                run['startTime'].strftime("%Y/%m/%d, %H:%M:%S"),
+                run['stopTime'].strftime("%Y/%m/%d, %H:%M:%S"),
+
+            )
+        console = Console()
+        console.print(table)
+        return response['items']
+
 
 def calculate_cost(
     run_id: str,

bioanalyze_omics/resources/workflows.py

@@ -13,6 +13,8 @@
 from urllib.parse import urlparse
 from zipfile import ZipFile, ZIP_DEFLATED
 from typing import Dict, List, Any
+from rich.console import Console
+from rich.table import Table
 
 import boto3
 import botocore.exceptions
@@ -144,3 +146,24 @@ def create_workflow(
             name=name,
         )
         return workflow
+
+    def list_workflows(self):
+        response = self.omics_client.list_workflows()
+        if 'items' not in response:
+            return []
+        table = Table(title="Workflows")
+        table.add_column("ID")
+        table.add_column("Name")
+        table.add_column("CreationTime")
+        for workflow in response['items']:
+            table.add_row(workflow['id'], workflow['name'], workflow['creationTime'].strftime("%Y/%m/%d, %H:%M:%S"))
+        console = Console()
+        console.print(table)
+        return response['items']
+
+    def submit_workflow(self, workflow_id: str, parameters: Dict[str, Any]):
+        response = self.omics_client.submit_workflow(
+            id=workflow_id,
+            parameterOverrides=parameters,
+        )
+        return response