feat: add freeform runnable, pre_run with umask 0002 default, add slice-positions param

Author: cmhulbert

runnables.yaml .fileglancer/runnables.yamlrunnables.yaml renamed to .fileglancer/runnables.yaml

@@ -2,20 +2,18 @@ name: Paintera Conversion Helper
 description: >-
   Convert N5/Zarr/HDF5 datasets to or from Paintera-style N5 datasets
   Submits a Spark job to the Janelia cluster via flintstone;
-repo_url: https://github.com/saalfeldlab/paintera-conversion-helper
 
 runnables:
   - id: to-paintera
     name: Convert Scalar Dataset To Paintera
     description: >-
-      Convert raw or label datasets into a Paintera-compatible N5 group with a multiscale
-      mipmap pyramid, running on N_NODES cluster worker nodes via flintstone.
+      Convert raw or label data into a Paintera-compatible N5 dataset with a multiscale pyramid.
     working_dir: repo
     resources:
       cpus: 1
       memory: "4 GB"
       walltime: "24:00"
-    pre_run: git submodule update --init --recursive
+    pre_run: umask 0002 && git submodule update --init --recursive
     command: >-
       ./startup-scripts/fileglancer-paintera-convert.sh to-paintera
     parameters:
@@ -35,6 +33,7 @@ runnables:
       - flag: --type
         name: Type
         type: enum
+        description: "The Paintera dataset type of the converted dataset"
         options:
           - raw
           - label
@@ -57,6 +56,13 @@ runnables:
         type: string
         required: false
         description: "Physical resolution x,y,z; overrides the input's resolution attribute. Example: 4,4,40"
+      - flag: --slice-positions
+        name: Slice positions
+        type: string
+        required: false
+        description: >-
+          Reduce an nD input to a 3D XYZ Paintera source. One entry per input axis in source dimension
+          order: x/y/z mark the spatial axes, an integer slices that axis at the given index. Example: z,y,x,0,10
       - flag: --scale
         name: Scale factors
         type: string
@@ -73,7 +79,7 @@ runnables:
         name: Reverse array attributes
         type: boolean
         default: false
-        description: "Reverse resolution/offset arrays, i.e. [x,y,z] -> [z,y,x]"
+        description: "Reverse resolution/offset arrays, i.e. [x,y,z] -> [z,y,x]. NOTE: N5-Zarr interop generally handles this automatically, especially for Zarr3. Only Reverse if you are sure it's necessary."
       - flag: --winner-takes-all-downsampling
         name: Winner-takes-all downsampling
         hidden: true
@@ -97,7 +103,7 @@ runnables:
       cpus: 1
       memory: "4 GB"
       walltime: "24:00"
-    pre_run: git submodule update --init --recursive
+    pre_run: umask 0002 && git submodule update --init --recursive
     command: >-
       ./startup-scripts/fileglancer-paintera-convert.sh to-scalar
     parameters:
@@ -175,3 +181,35 @@ runnables:
         type: boolean
         default: false
         description: "Apply the Paintera fragment-segment-assignment; ignored for non-Paintera inputs"
+
+  - id: freeform
+    name: Freeform Arguments
+    description: >-
+      Run to-paintera or to-scalar with hand-written arguments, for anything the guided forms
+      don't cover. Reports the Spark web UI URL and waits for the job to finish.
+    working_dir: repo
+    resources:
+      cpus: 1
+      memory: "4 GB"
+      walltime: "24:00"
+    pre_run: umask 0002 && git submodule update --init --recursive
+    command: >-
+      ./startup-scripts/fileglancer-paintera-convert.sh
+    parameters:
+      - flag: --n-nodes
+        name: Worker nodes
+        type: integer
+        required: true
+        min: 1
+        description: "Number of cluster worker nodes for the Spark job"
+      - name: Freeform (paste arguments)
+        type: string
+        raw: true
+        required: true
+        description: >-
+          Paste a paintera-convert invocation starting with the subcommand (to-paintera or to-scalar),
+          followed by its arguments.
+            Flags may use `--flag value` or `--flag=value`.
+            repeated values are whitespace-separated (e.g. --scale 2,2,2 2,2,2).
+            Shell operators (`;` `|` `&` `$` backticks) are not allowed.
+            Example: to-paintera --container=in.zarr -d labels/s0 --output-container=out.n5 --target-dataset=labels --type=label --scale 2,2,2 2,2,2 --block-size=32,32,32

startup-scripts/fileglancer-paintera-convert.sh

@@ -14,15 +14,15 @@
 # -> shutdown LSF chain and returns. We locate the run from flintstone's own output, then
 # poll the shared-filesystem logs and the driver job's LSF state.
 #
-# usage: fileglancer-paintera-convert.sh <subcommand> --n-nodes N [paintera-convert args...]
+# usage: fileglancer-paintera-convert.sh [--n-nodes N] <subcommand> [paintera-convert args...]
+#
+# `--n-nodes` may appear anywhere (Fileglancer emits flagged fields before positional ones); it is
+# pulled out and the first remaining token is taken as the subcommand.
 
 set -uo pipefail
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
-SUBCOMMAND="${1:?missing subcommand (to-paintera|to-scalar)}"
-shift
-
 # how often to poll, and how long to wait for the web UI URL before giving up on it (the
 # conversion keeps being waited on regardless)
 POLL_INTERVAL="${FG_POLL_INTERVAL:-30}"
@@ -31,19 +31,26 @@ URL_TIMEOUT="${FG_URL_TIMEOUT:-1800}"
 MAX_UNSEEN_POLLS="${FG_MAX_UNSEEN_POLLS:-20}"
 
 N_NODES=""
-PAINTERA_ARGS=()
+REST=()
 while [[ $# -gt 0 ]]; do
     case "$1" in
         --n-nodes) N_NODES="$2"; shift 2 ;;
         --n-nodes=*) N_NODES="${1#*=}"; shift ;;
-        *) PAINTERA_ARGS+=("$1"); shift ;;
+        *) REST+=("$1"); shift ;;
     esac
 done
 
 if [[ -z "$N_NODES" ]]; then
     echo "error: --n-nodes is required" 1>&2
     exit 1
 fi
+if [[ "${#REST[@]}" -eq 0 ]]; then
+    echo "error: missing subcommand (to-paintera|to-scalar)" 1>&2
+    exit 1
+fi
+
+SUBCOMMAND="${REST[0]}"
+PAINTERA_ARGS=("${REST[@]:1}")
 
 USER_NAME="${USER:-$(id -un)}"