Use Jinja2 template in interactive app command

config-example.yaml

@@ -2,7 +2,7 @@ job_root_dir: /tmp/jobs
 destination_picker: bartender.picker:pick_first
 applications:
   wc:
-    command: wc $config
+    command: wc config
     config: README.md
 destinations:
   local:

config-haddock3.yaml

@@ -30,8 +30,8 @@ interactive_applications:
   rescore:
     command: >
       haddock3-re score \
-        --w_elec $w_elec --w_vdw $w_vdw --w_desolv $w_desolv --w_bsa $w_bsa --w_air $w_air \
-        $capri_dir
+        --w_elec {{w_elec|q}} --w_vdw {{w_vdw|q}} --w_desolv {{w_desolv|q}} --w_bsa {{w_bsa|q}} --w_air {{w_air|q}} \
+        {{ capri_dir }}
     description: Rescore a HADDOCK run with different weights.
     input:
       $schema: https://json-schema.org/draft/2020-12/schema
@@ -60,9 +60,15 @@ interactive_applications:
   reclustrmsd:
     command: >
       haddock3-re clustrmsd
-      --criterion $criterion
-      --n_clusters $n_clusters --clust_cutoff $clust_cutoff --min_population $min_population
-      $clustrmsd_dir
+      {% if criterion == 'maxclust' -%}
+      --n_clusters {{n_clusters|q}}
+      {% else -%}
+      --clust_cutoff {{clust_cutoff|q}}
+      {% endif -%}
+      {% if min_population -%}
+      --min_population {{min_population|q}}
+      {% endif -%}
+      {{clustrmsd_dir|q}}
     description: Recluster a HADDOCK run with RSMD and different parameters.
     input:
       $schema: https://json-schema.org/draft/2020-12/schema
@@ -72,24 +78,22 @@ interactive_applications:
           type: string
         criterion:
           type: string
+          enum: [maxclust, distance]
         clust_cutoff:
           type: number
         n_clusters:
           type: number
         min_population:
           type: number
       required:
-      - clustrmsd_dir
       - criterion
-      - clust_cutoff
-      - n_clusters
-      - min_population
+      - clustrmsd_dir
       type: object
   reclustfcc:
     command: >
       haddock3-re clustfcc
-      --clust_cutoff $clust_cutoff --strictness $strictness --min_population $min_population
-      $clustfcc_dir
+      --clust_cutoff {{clust_cutoff|q}} --strictness {{strictness|q}} --min_population {{min_population|q}}
+      {{clustfcc_dir|q}}
     description: Recluster a HADDOCK run with FCC and different parameters.
     input:
       $schema: https://json-schema.org/draft/2020-12/schema

pyproject.toml

@@ -32,6 +32,7 @@ python-jose = {extras = ["cryptography"], version = "^3.3.0"}
 # poetry has upper limit for jsonschema, so lowering ourselves to it
 # unreleased poetry > 1.6.1 will use latest fastjsonschema
 jsonschema = "<4.18.0"
+jinja2 = "^3.1.2"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.0"

src/bartender/web/api/job/interactive_apps.py

@@ -2,9 +2,9 @@
 from asyncio.subprocess import PIPE
 from pathlib import Path
 from shlex import quote
-from string import Template
 from typing import Any
 
+from jinja2 import Environment
 from jsonschema import Draft202012Validator
 from pydantic import BaseModel
 
@@ -50,6 +50,12 @@ async def _shell(job_dir: Path, command: str, timeout: float) -> InteractiveAppR
     )
 
 
+template_environment = (
+    Environment()  # noqa: S701 -- used to generate shell commands not HTML
+)
+template_environment.filters["q"] = lambda variable: quote(str(variable))
+
+
 def build_command(
     payload: dict[Any, Any],
     app: InteractiveApplicationConfiguration,
@@ -68,11 +74,8 @@ def build_command(
     validator = Draft202012Validator(app.input)
     validator.validate(payload)
 
-    # TODO to allow nested payload we could use a Jinja2 template
-    # but need to be careful with newlines
-    return Template(app.command).substitute(
-        {key: quote(str(value)) for key, value in payload.items()},
-    )
+    template = template_environment.from_string(app.command)
+    return template.render(**payload)
 
 
 async def run(

tests/web/test_interactive_apps.py

@@ -14,7 +14,7 @@
 @pytest.fixture
 def app_config() -> InteractiveApplicationConfiguration:
     return InteractiveApplicationConfiguration(
-        command="cat ${input_file} | wc -m  > ${output_file}",
+        command="cat {{ input_file|q }} | wc -m  > {{ output_file|q }}",
         input={
             "$schema": "https://json-schema.org/draft/2020-12/schema",
             "type": "object",
@@ -77,3 +77,35 @@ def test_build_command(
 ) -> None:
     command = build_command(payload, app_config)
     assert command == expected
+
+
+@pytest.mark.parametrize(
+    "payload, expected",
+    [
+        (
+            {},
+            "ls",
+        ),
+        (
+            {"recursive": True},
+            "ls --recursive",
+        ),
+        (
+            {"recursive": False},
+            "ls",
+        ),
+    ],
+)
+def test_build_command_optional_field(payload: dict[Any, Any], expected: str) -> None:
+    config = InteractiveApplicationConfiguration(
+        command="ls{% if recursive %} --recursive{% endif %}",
+        input={
+            "$schema": "https://json-schema.org/draft/2020-12/schema",
+            "type": "object",
+            "properties": {
+                "recursive": {"type": "boolean"},
+            },
+        },
+    )
+    command = build_command(payload, config)
+    assert command == expected