Reconstruct ecpac call for re-running; Refactoring

src/ecpac/cli.py

@@ -0,0 +1,34 @@
+import pathlib as pl
+from typing import Optional
+
+import click
+
+
+def check_exist_file(path: pl.Path, label: str = "") -> bool:
+    """Check if a file exists. Or print a message if it doesn't."""
+    if path.exists() and path.is_file():
+        return True
+    click.secho(f'Error: {label} file does not exist! "{path}"', fg="red")
+    return False
+
+
+def check_exist_dir(path: pl.Path, label: str = "") -> bool:
+    """Check if a directory exists. Or print a message if it doesn't."""
+    if path.exists() and path.is_dir():
+        return True
+    click.secho(f'Error: {label} directory does not exist! "{path}"', fg="red")
+    return False
+
+
+def option_or_prompt(opt: Optional[str], prompt: str, default: Optional[str] = None) -> str:
+    """Prompt the user for input if the option is not provided."""
+    if opt is not None:
+        return opt
+    return click.prompt(prompt, default=default, type=str)
+
+
+def option_or_confirm(opt: Optional[bool], prompt: str, default: Optional[bool] = False) -> bool:
+    """Prompt the user for input (confirmation boolean) if the option is not provided."""
+    if opt is not None:
+        return opt
+    return click.confirm(prompt, default=default)

src/ecpac/consts.py

@@ -0,0 +1,72 @@
+import os
+import pathlib as pl
+
+ID_PIPELINE_DEFAULT = "default"
+FILENAME_JOB = "job.sh"
+FOLDERNAME_OUTPUT = "output"
+
+# Grab from $PROJECT, which is "/ocean/projects/{med000000p}/{username}"
+ENV_PROJECT = os.environ.get("PROJECT", "")
+PSC_PROJECT_USER = pl.Path(ENV_PROJECT)
+PSC_OUTPUT_DEFAULT = PSC_PROJECT_USER / "ecpac_runs"
+PSC_IMAGE_DEFAULT = PSC_PROJECT_USER / "images/cpac.sif"
+
+CPAC_ANALYSIS_LEVELS = ("participant", "group", "test_config")
+ANALYSIS_LEVEL_DEFAULT = "participant"
+CPAC_PRECONFIGS = [
+    "abcd-options",
+    "abcd-prep",
+    "anat-only",
+    "benchmark-FNIRT",
+    "blank",
+    "ccs-options",
+    "default",
+    "default-deprecated",
+    "fmriprep-options",
+    "fx-options",
+    "monkey",
+    "ndmg",
+    "nhp-macaque",
+    "preproc",
+    "rbc-options",
+    "rodent",
+]
+
+
+BASH_TEMPLATE_JOB = """\
+#!/usr/bin/bash
+#SBATCH --job-name {job_name}
+#SBATCH --output {stdout_file}
+#SBATCH --nodes 1
+#SBATCH --partition RM-shared
+#SBATCH --time {duration_str}
+#SBATCH --ntasks-per-node {threads}
+#SBATCH --mem {memory_mb}
+
+set -x
+
+cd {wd}
+
+singularity run \
+--cleanenv \
+{cpac_bin_opt} \
+-B {path_input}:{path_input}:ro \
+-B {path_output}:{path_output} \
+{image} {path_input} {path_output} {analysis_level} \
+--skip_bids_validator \
+--n_cpus {cpac_threads} \
+--mem_gb {cpac_memory_gb} \
+--participant_label {subject} \
+{pipeline} \
+{extra_cpac_args}
+"""
+
+BASH_TEMPLATE_PIPELINE_PRECONFIG = "--preconfig {pipeline}"
+BASH_TEMPLATE_PIPELINE_CONFIG_FILE = "--pipeline-file {pipeline}"
+
+
+BASH_TEMPLATE_JOB_CPAC_BIN = """\
+-B {cpac_bin}/CPAC:/code/CPAC \
+-B {cpac_bin}/dev/docker_data/run.py:/code/run.py \
+-B {cpac_bin}/dev/docker_data:/cpac_resources \
+"""