document biosim_pipeline commands.

python-utils/README.md

@@ -1,130 +1 @@
-create a .env file with the following:
-
-```properties
-CLIENT_ID=<<auth-provider-client-id>>
-CLIENT_SECRET=<<auth-provider-client-secret>>
-AUTH_HOST=auth.biosimulations.org
-AUTH_AUDIENCE=api.biosimulations.org
-API_BASE_URL=https://api.biosimulations.org
-RUN_APP_BASE_URL=https://run.biosimulations.org
-
-OMEX_SOURCE_DIR=<<path-to-source-omex-files>>
-OMEX_OUTPUT_DIR=<<path-to-output-artifacts>>
-```
-
-```bash
-poetry run python vcutils/biosimulations_pipeline/cli.py --help
-```
-
-```
-    Usage: cli.py [OPTIONS] COMMAND [ARGS]...
-    
-    Options:
-      --install-completion [bash|zsh|fish|powershell|pwsh]
-                                      Install completion for the specified shell.
-      --show-completion [bash|zsh|fish|powershell|pwsh]
-                                      Show completion for the specified shell, to
-                                      copy it or customize the installation.
-      --help                          Show this message and exit.
-    
-    Commands:
-      compare_runs    compare downloaded runs
-      download_runs   download runs (results.zip) from BioSimulations
-      publish         publish validated projects to BioSimulations
-      refresh_status  fetch status of runs and update biosimulations_runs.ndjson
-      upload_omex     upload and run OMEX files at BioSimulations
-    
-```
-
-## upload OMEX files
-
-```bash
-poetry run python vcutils/biosimulations_pipeline/cli.py upload_omex --help
-```
-
-```
-Usage: cli.py upload_omex [OPTIONS]
-
-  upload and run OMEX files at BioSimulations
-
-Options:
-  --simulator [tellurium|copasi|amici|vcell|pysces|libsbmlsim]
-                                  simulator to run  [default: Simulator.vcell]
-  --project-id TEXT               filter by project_id
-  --omex-src-dir PATH             defaults env.OMEX_SOURCE_DIR
-  --out-dir PATH                  defaults to env.OMEX_OUTPUT_DIR
-  --help                          Show this message and exit.
-
-```
-
-## download runs
-
-```bash
-poetry run python vcutils/biosimulations_pipeline/cli.py download_runs --help
-```
-
-```
-Usage: cli.py download_runs [OPTIONS]
-
-  download runs (results.zip) from BioSimulations
-
-Options:
-  --omex-src-dir PATH             defaults env.OMEX_SOURCE_DIR
-  --out-dir PATH                  defaults to env.OMEX_OUTPUT_DIR
-  --project-id TEXT               filter by project_id
-  --simulator [tellurium|copasi|amici|vcell|pysces|libsbmlsim]
-                                  filter by simulator
-  --help                          Show this message and exit.
-```
-
-## refresh status
-
-```bash
-poetry run python vcutils/biosimulations_pipeline/cli.py refresh_status --help
-```
-
-```
-Usage: cli.py refresh_status [OPTIONS]
-
-  fetch status of runs and update biosimulations_runs.ndjson
-
-Options:
-  --out-dir PATH  defaults to env.OMEX_OUTPUT_DIR
-  --help          Show this message and exit.
-```
-
-## compare runs
-
-```bash
-poetry run python vcutils/biosimulations_pipeline/cli.py compare_runs --help
-```
-
-```
-Usage: cli.py compare_runs [OPTIONS]
-
-  compare downloaded runs
-
-Options:
-  --omex-src-dir PATH  defaults env.OMEX_SOURCE_DIR
-  --out-dir PATH       defaults to env.OMEX_OUTPUT_DIR
-  --project-id TEXT    filter by project_id
-  --help               Show this message and exit.
-```
-
-## publish
-
-```bash
-poetry run python vcutils/biosimulations_pipeline/cli.py publish --help
-```
-
-```
-Usage: cli.py publish [OPTIONS]
-
-  publish validated projects to BioSimulations
-
-Options:
-  --omex-src-dir PATH  defaults env.OMEX_SOURCE_DIR
-  --out-dir PATH       defaults to env.OMEX_OUTPUT_DIR
-  --project-id TEXT    filter by project_id
-  --help               Show this message and exit.
-```
+See [Managed Biosim pipeline](vcutils/biosim_pipeline/README.md) for details about series of commands to upload/run, check status, download, compare results, and publish models to BioSimulations.

python-utils/vcutils/biosim_pipeline/README.md

@@ -0,0 +1,120 @@
+
+# Managed Biosim pipeline
+
+## Command Overview
+
+1. [upload OMEX files](#upload-omex-files)
+2. [refresh status](#refresh-status)
+3. [download runs](#download-runs)
+4. [compare runs](#compare-runs)
+5. [publish](#publish)
+
+## Setup
+
+create a .env file with the following:
+
+```properties
+CLIENT_ID=<<auth-provider-client-id>>
+CLIENT_SECRET=<<auth-provider-client-secret>>
+AUTH_HOST=auth.biosimulations.org
+AUTH_AUDIENCE=api.biosimulations.org
+API_BASE_URL=https://api.biosimulations.org
+RUN_APP_BASE_URL=https://run.biosimulations.org
+
+OMEX_SOURCE_DIR=<<path-to-source-omex-files>>
+OMEX_OUTPUT_DIR=<<path-to-output-artifacts>>
+```
+
+## upload OMEX files
+
+```bash
+poetry run python main.py upload_omex --help
+```
+
+```
+Usage: main.py upload_omex [OPTIONS]
+
+  upload and run OMEX files at BioSimulations
+
+Options:
+  --simulator [tellurium|copasi|amici|vcell|pysces|libsbmlsim]
+                                  simulator to run  [default: Simulator.vcell]
+  --project-id TEXT               filter by project_id
+  --omex-src-dir PATH             defaults env.OMEX_SOURCE_DIR
+  --out-dir PATH                  defaults to env.OMEX_OUTPUT_DIR
+  --help                          Show this message and exit.
+
+```
+
+## refresh status
+
+```bash
+poetry run python main.py refresh_status --help
+```
+
+```
+Usage: main.py refresh_status [OPTIONS]
+
+  fetch status of runs and update biosimulations_runs.ndjson
+
+Options:
+  --out-dir PATH  defaults to env.OMEX_OUTPUT_DIR
+  --help          Show this message and exit.
+```
+
+## download runs
+
+```bash
+poetry run python main.py download_runs --help
+```
+
+```
+Usage: main.py download_runs [OPTIONS]
+
+  download runs (results.zip) from BioSimulations
+
+Options:
+  --omex-src-dir PATH             defaults env.OMEX_SOURCE_DIR
+  --out-dir PATH                  defaults to env.OMEX_OUTPUT_DIR
+  --project-id TEXT               filter by project_id
+  --simulator [tellurium|copasi|amici|vcell|pysces|libsbmlsim]
+                                  filter by simulator
+  --help                          Show this message and exit.
+```
+
+
+## compare runs
+
+```bash
+poetry run python main.py compare_runs --help
+```
+
+```
+Usage: main.py compare_runs [OPTIONS]
+
+  compare downloaded runs
+
+Options:
+  --omex-src-dir PATH  defaults env.OMEX_SOURCE_DIR
+  --out-dir PATH       defaults to env.OMEX_OUTPUT_DIR
+  --project-id TEXT    filter by project_id
+  --help               Show this message and exit.
+```
+
+## publish
+
+```bash
+poetry run python main.py publish --help
+```
+
+```
+Usage: main.py publish [OPTIONS]
+
+  publish validated projects to BioSimulations
+
+Options:
+  --omex-src-dir PATH  defaults env.OMEX_SOURCE_DIR
+  --out-dir PATH       defaults to env.OMEX_OUTPUT_DIR
+  --project-id TEXT    filter by project_id
+  --help               Show this message and exit.
+```

python-utils/vcutils/biosimulations_pipeline/biosim_api.py → python-utils/vcutils/biosim_pipeline/biosim_api.py

@@ -6,8 +6,8 @@
 import requests
 from pydantic import BaseModel
 
-from data_manager import DataManager
-from datamodels import SourceOmex, Simulator, SimulationRun, BiosimulationsProject
+from vcutils.biosim_pipeline.data_manager import DataManager
+from vcutils.biosim_pipeline.datamodels import SourceOmex, Simulator, SimulationRun, BiosimulationsProject
 
 
 class _SimulationRunApiRequest(BaseModel):

python-utils/vcutils/biosimulations_pipeline/data_manager.py → python-utils/vcutils/biosim_pipeline/data_manager.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Optional
 
-from vcutils.biosimulations_pipeline.datamodels import (
+from vcutils.biosim_pipeline.datamodels import (
     BiosimulationsProject,
     SourceOmex,
     SimulationRun,