Replace enrichment of context with template filters

grand_challenge_forge/forge.py

@@ -13,11 +13,11 @@
 from grand_challenge_forge.generation_utils import (
     ci_to_civ,
     create_civ_stub_file,
-    enrich_phase_context,
+    extract_slug,
 )
 from grand_challenge_forge.schemas import validate_pack_context
 from grand_challenge_forge.utils import cookiecutter_context as cc
-from grand_challenge_forge.utils import extract_slug, remove_j2_suffix
+from grand_challenge_forge.utils import remove_j2_suffix
 
 logger = logging.getLogger(__name__)
 
@@ -100,13 +100,15 @@ def generate_upload_to_archive_script(
 ):
     context = deepcopy(context)
 
-    enrich_phase_context(context)
-
-    # Cannot use filters in directory names so generate it here
-    archive_slug = extract_slug(context["phase"]["archive"]["url"])
-    context["phase"]["archive"]["slug"] = archive_slug
+    # Cannot always use filters in directory names so generate it here
+    context["phase"]["archive"]["slug"] = extract_slug(
+        context["phase"]["archive"]["url"]
+    )
 
-    script_dir = output_directory / f"upload-to-archive-{archive_slug}"
+    script_dir = (
+        output_directory
+        / f"upload-to-archive-{context['phase']['archive']['slug']}"
+    )
 
     # Map the expected case, but only create after the script
     expected_cases, create_files_func = _gen_expected_archive_cases(
@@ -161,14 +163,6 @@ def create_files():
 def generate_example_algorithm(
     context, output_directory, quality_control_registry=None
 ):
-    context = deepcopy(context)
-
-    enrich_phase_context(context)
-
-    # Cannot use filters in directory names so generate it here
-    archive_slug = extract_slug(context["phase"]["archive"]["url"])
-    context["phase"]["archive"]["slug"] = archive_slug
-
     algorithm_dir = generate_files(
         repo_dir=PARTIALS_PATH / "example-algorithm",
         context=cc(context),
@@ -201,9 +195,6 @@ def quality_check():
 def generate_example_evaluation(
     context, output_directory, quality_control_registry=None
 ):
-    context = deepcopy(context)
-    enrich_phase_context(context)
-
     evaluation_dir = generate_files(
         repo_dir=PARTIALS_PATH / "example-evaluation-method",
         context=cc(context),

grand_challenge_forge/generation_utils.py

@@ -1,4 +1,5 @@
 import os
+import re
 import shutil
 import uuid
 from pathlib import Path
@@ -7,33 +8,42 @@
 RESOURCES_PATH = SCRIPT_PATH / "resources"
 
 
-def enrich_phase_context(context):
-    """Enriches the "phase" value of the context to simplify templating"""
-    phase_context = context["phase"]
+def is_json(component_interface):
+    return component_interface["relative_path"].endswith(".json")
 
-    for ci in [
-        *phase_context["inputs"],
-        *phase_context["outputs"],
-    ]:
-        ci["is_json"] = ci["relative_path"].endswith(".json")
-        ci["is_image"] = ci["super_kind"] == "Image"
-        ci["is_file"] = ci["super_kind"] == "File" and not ci[
-            "relative_path"
-        ].endswith(".json")
 
-    for _type in ["json", "image", "file"]:
-        for in_out in ["input", "output"]:
-            phase_context[f"has_{in_out}_{_type}"] = any(
-                ci[f"is_{_type}"] for ci in phase_context[f"{in_out}s"]
-            )
+def is_image(component_interface):
+    return component_interface["super_kind"] == "Image"
+
+
+def is_file(component_interface):
+    return component_interface[
+        "super_kind"
+    ] == "File" and not component_interface["relative_path"].endswith(".json")
+
+
+def extract_slug(url):
+    # Define a regex pattern to match the slug in the URL
+    pattern = r"/([^/]+)/*$"
+
+    # Use re.search to find the match
+    match = re.search(pattern, url)
+
+    # If a match is found, extract and return the slug
+    if match:
+        slug = match.group(1)
+        return slug
+    else:
+        # Return None or handle the case where no match is found
+        return None
 
 
 def create_civ_stub_file(*, target_dir, component_interface):
     """Creates a stub based on a component interface"""
     target_dir.parent.mkdir(parents=True, exist_ok=True)
-    if component_interface["is_json"]:
+    if is_json(component_interface):
         src = RESOURCES_PATH / "example.json"
-    elif component_interface["is_image"]:
+    elif is_image(component_interface):
         target_dir = target_dir / f"{str(uuid.uuid4())}.mha"
         target_dir.parent.mkdir(parents=True, exist_ok=True)
         src = RESOURCES_PATH / "example.mha"

grand_challenge_forge/partials/example-algorithm/example-algorithm{{cookiecutter._}}/inference.py.j2

@@ -18,10 +18,10 @@ Any container that shows the same behavior will do, this is purely an example of
 Happy programming!
 """
 from pathlib import Path
-{% if cookiecutter.phase.has_input_json or cookiecutter.phase.has_output_json -%}
+{% if cookiecutter.phase.inputs | has_json or cookiecutter.phase.outputs | has_json -%}
 import json
 {%- endif %}
-{% if cookiecutter.phase.has_input_image or cookiecutter.phase.has_output_image -%}
+{% if cookiecutter.phase.inputs | has_image or cookiecutter.phase.outputs | has_image -%}
 from glob import glob
 import SimpleITK
 import numpy
@@ -37,12 +37,12 @@ def run():
     # Read the input
     {% for ci in cookiecutter.phase.inputs -%}
     {% set py_slug = ci.slug | replace("-", "_") -%}
-    {% if ci.is_image -%}
+    {% if ci | is_image -%}
     {{ py_slug }} = load_image_file_as_array(
         location=INPUT_PATH / "{{ ci.relative_path }}",
     )
     {% endif -%}
-    {% if ci.is_json -%}
+    {% if ci | is_json -%}
     {{ py_slug }} = load_json_file(
          location=INPUT_PATH / "{{ ci.relative_path }}",
     )
@@ -57,52 +57,52 @@ def run():
     # For now, let us set make bogus predictions
     {%- for ci in cookiecutter.phase.outputs %}
     {{ ci.slug | replace("-", "_")}} =
-        {%- if ci.is_image %} numpy.eye(4, 2)
-        {%- elif ci.is_json %} {"content": "should match the required format"}
-        {%- elif ci.is_file %} "content: should match the required format"
+        {%- if ci | is_image %} numpy.eye(4, 2)
+        {%- elif ci | is_json %} {"content": "should match the required format"}
+        {%- elif ci | is_file %} "content: should match the required format"
         {% endif %}
     {%- endfor %}
 
     # Save your output
     {% for ci in cookiecutter.phase.outputs -%}
     {% set py_slug = ci.slug | replace("-", "_") -%}
-    {% if ci.is_image -%}
+    {% if ci | is_image -%}
     write_array_as_image_file(
         location=OUTPUT_PATH / "{{ ci.relative_path }}",
         array={{ py_slug }},
     )
     {% endif -%}
-    {% if ci.is_json -%}
+    {% if ci | is_json -%}
     write_json_file(
         location=OUTPUT_PATH / "{{ ci.relative_path }}",
         content={{ py_slug }}
     )
     {% endif -%}
-    {% if ci.is_file -%}
+    {% if ci | is_file -%}
     write_file(
         location=OUTPUT_PATH / "{{ ci.relative_path }}",
         content={{ py_slug }}
     )
     {% endif -%}
     {% endfor %}
     return 0
-{%- if cookiecutter.phase.has_input_json %}
+{%- if cookiecutter.phase.inputs | has_json %}
 
 
 def load_json_file(*, location):
     # Reads a json file
     with open(location, 'r') as f:
         return json.loads(f.read())
 {%- endif %}
-{%- if cookiecutter.phase.has_output_json %}
+{%- if cookiecutter.phase.outputs | has_json %}
 
 
 def write_json_file(*, location, content):
     # Writes a json file
     with open(location, 'w') as f:
         f.write(json.dumps(content, indent=4))
 {%- endif %}
-{%- if cookiecutter.phase.has_input_image %}
+{%- if cookiecutter.phase.inputs | has_image %}
 
 
 def load_image_file_as_array(*, location):
@@ -113,7 +113,7 @@ def load_image_file_as_array(*, location):
     # Convert it to a Numpy array
     return SimpleITK.GetArrayFromImage(result)
 {%- endif %}
-{%- if cookiecutter.phase.has_output_image %}
+{%- if cookiecutter.phase.outputs | has_image %}
 
 
 def write_array_as_image_file(*, location, array):
@@ -126,7 +126,7 @@ def write_array_as_image_file(*, location, array):
         useCompression=True,
     )
 {%- endif %}
-{%- if cookiecutter.phase.has_input_file %}
+{%- if cookiecutter.phase.inputs | has_file %}
 
 
 # Note to the challenge hosts:
@@ -137,7 +137,7 @@ def load_file(*, location):
     with open(location) as f:
         return f.read()
 {%- endif %}
-{%- if cookiecutter.phase.has_output_file %}
+{%- if cookiecutter.phase.outputs | has_file %}
 
 
 # Note to the challenge hosts:

grand_challenge_forge/partials/example-algorithm/example-algorithm{{cookiecutter._}}/requirements.txt.j2

@@ -1,4 +1,4 @@
-{% if cookiecutter.phase.has_input_image or cookiecutter.phase.has_output_image -%}
+{% if cookiecutter.phase.inputs | has_image or cookiecutter.phase.outputs | has_image -%}
 SimpleITK
 numpy
 {%- endif %}

grand_challenge_forge/partials/example-evaluation-method/example-evaluation-method{{cookiecutter._}}/evaluate.py.j2

@@ -18,7 +18,7 @@ Any container that shows the same behavior will do, this is purely an example of
 Happy programming!
 """
 import json
-{% if cookiecutter.phase.has_input_image -%}
+{% if cookiecutter.phase.inputs | has_image -%}
 from glob import glob
 import SimpleITK
 {%- endif %}
@@ -81,17 +81,17 @@ def process(job):
     # Secondly, read the results
     {% for ci in cookiecutter.phase.outputs -%}
     {% set py_slug = ci.slug | replace("-", "_") -%}
-    {% if ci.is_image -%}
+    {% if ci | is_image -%}
     {{ py_slug }} = load_image_file(
         location={{ py_slug }}_location,
     )
     {% endif -%}
-    {% if ci.is_json -%}
+    {% if ci | is_json -%}
     {{ py_slug }} = load_json_file(
         location={{ py_slug }}_location,
     )
     {% endif -%}
-    {% if ci.is_file -%}
+    {% if ci | is_file -%}
     {{ py_slug }} = load_file(
         location={{ py_slug }}_location,
     )
@@ -102,7 +102,7 @@ def process(job):
     # Thirdly, retrieve the input image name to match it with an image in your ground truth
     {% for ci in cookiecutter.phase.inputs -%}
     {% set py_slug = ci.slug | replace("-", "_") -%}
-    {% if ci.is_image -%}
+    {% if ci | is_image -%}
     {{ py_slug }}_image_name = get_image_name(
             values=job["inputs"],
             slug="{{ ci.slug }}",
@@ -138,7 +138,7 @@ def read_predictions():
     # The prediction file tells us the location of the users' predictions
     with open(INPUT_DIRECTORY / "predictions.json") as f:
         return json.loads(f.read())
-{%- if cookiecutter.phase.has_input_image or cookiecutter.phase.has_output_image %}
+{%- if cookiecutter.phase.inputs | has_image or cookiecutter.phase.outputs | has_image %}
 
 
 def get_image_name(*, values, slug):
@@ -164,15 +164,15 @@ def get_file_location(*, job_pk, values, slug):
     # Where a job's output file will be located in the evaluation container
     relative_path = get_interface_relative_path(values=values, slug=slug)
     return INPUT_DIRECTORY / job_pk / "output" / relative_path
-{%- if cookiecutter.phase.has_output_json %}
+{%- if cookiecutter.phase.outputs | has_json %}
 
 
 def load_json_file(*, location):
     # Reads a json file
     with open(location) as f:
         return json.loads(f.read())
 {%- endif %}
-{%- if cookiecutter.phase.has_output_image %}
+{%- if cookiecutter.phase.outputs | has_image %}
 
 
 def load_image_file(*, location):
@@ -183,7 +183,7 @@ def load_image_file(*, location):
     # Convert it to a Numpy array
     return SimpleITK.GetArrayFromImage(result)
 {%- endif %}
-{%- if cookiecutter.phase.has_output_file %}
+{%- if cookiecutter.phase.outputs | has_file %}
 
 
 def load_file(*, location):

grand_challenge_forge/partials/example-evaluation-method/example-evaluation-method{{cookiecutter._}}/requirements.txt.j2

@@ -1,4 +1,4 @@
-{% if cookiecutter.phase.has_input_image or cookiecutter.phase.has_output_image -%}
+{% if cookiecutter.phase.inputs | has_image or cookiecutter.phase.outputs | has_image -%}
 SimpleITK
 numpy
 {%- endif %}

grand_challenge_forge/partials/filters.py

@@ -1,8 +1,48 @@
 from cookiecutter.utils import simple_filter
 
-from grand_challenge_forge.utils import extract_slug as util_extract_slug
+from grand_challenge_forge import generation_utils
 
+custom_filters = []
 
-@simple_filter
+
+def register_simple_filter(func):
+    func = simple_filter(func)
+    custom_filters.append(
+        f"grand_challenge_forge.partials.filters.{func.__name__}"
+    )
+    return func
+
+
+@register_simple_filter
 def extract_slug(url):
-    return util_extract_slug(url)
+    return generation_utils.extract_slug(url)
+
+
+@register_simple_filter
+def is_json(arg):
+    return generation_utils.is_json(arg)
+
+
+@register_simple_filter
+def has_json(arg):
+    return any(generation_utils.is_json(item) for item in arg)
+
+
+@register_simple_filter
+def is_image(arg):
+    return generation_utils.is_image(arg)
+
+
+@register_simple_filter
+def has_image(arg):
+    return any(generation_utils.is_image(item) for item in arg)
+
+
+@register_simple_filter
+def is_file(arg):
+    return generation_utils.is_file(arg)
+
+
+@register_simple_filter
+def has_file(arg):
+    return any(generation_utils.is_file(item) for item in arg)