Replace "inputs" with "algorithm_inputs" where appropriate, also appl…

…ies for "outputs"
DIAGNijmegen · Jan 8, 2024 · f62fcb7 · f62fcb7
1 parent 04b3199
commit f62fcb7
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Showing 10 changed files with 49 additions and 40 deletions.
diff --git a/README.md b/README.md
@@ -48,7 +48,7 @@ a directory `dist/` (default).
                 "archive": {
                     "url": "https://grand-challenge.org/archives/archive-slug/"
                 },
-                "inputs": [
+                "algorithm_inputs": [
                     {
                         "slug": "input-ci-slug",
                         "kind": "Segmentation",
@@ -62,7 +62,7 @@ a directory `dist/` (default).
                         "relative_path": "another-input-value.json"
                     }
                 ],
-                "outputs": [
+                "algorithm_outputs": [
                     {
                         "slug": "output-ci-slug",
                         "kind": "Image",
@@ -82,15 +82,15 @@ a directory `dist/` (default).
                 "archive": {
                     "url": "https://grand-challenge.org/archives/another-archive-slug/"
                 },
-                "inputs": [
+                "algorithm_inputs": [
                     {
                         "slug": "input-ci-slug",
                         "kind": "Image",
                         "super_kind": "Image",
                         "relative_path": "images/input-value"
                     }
                 ],
-                "outputs": [
+                "algorithm_outputs": [
                     {
                         "slug": "another-output-ci-slug",
                         "kind": "Anything",

diff --git a/grand_challenge_forge/forge.py b/grand_challenge_forge/forge.py
@@ -111,7 +111,7 @@ def generate_upload_to_archive_script(
 
     # Map the expected case, but only create after the script
     expected_cases, create_files_func = _gen_expected_archive_cases(
-        inputs=context["phase"]["inputs"],
+        inputs=context["phase"]["algorithm_inputs"],
         output_directory=script_dir,
     )
     context["phase"]["expected_cases"] = expected_cases
@@ -174,7 +174,7 @@ def generate_example_algorithm(
 
     # Create input files
     input_dir = algorithm_dir / "test" / "input"
-    for input_ci in context["phase"]["inputs"]:
+    for input_ci in context["phase"]["algorithm_inputs"]:
         create_civ_stub_file(
             target_dir=input_dir / input_ci["relative_path"],
             component_interface=input_ci,
@@ -226,9 +226,13 @@ def generate_predictions(context, evaluation_dir, n=3):
         predictions.append(
             {
                 "pk": str(uuid.uuid4()),
-                "inputs": [ci_to_civ(ci) for ci in context["phase"]["inputs"]],
+                "inputs": [
+                    ci_to_civ(ci)
+                    for ci in context["phase"]["algorithm_inputs"]
+                ],
                 "outputs": [
-                    ci_to_civ(ci) for ci in context["phase"]["outputs"]
+                    ci_to_civ(ci)
+                    for ci in context["phase"]["algorithm_outputs"]
                 ],
                 "status": "Succeeded",
                 "started_at": "2023-11-29T10:31:25.691799Z",

diff --git a/...enge_forge/partials/example-algorithm/example-algorithm{{cookiecutter._}}/inference.py.j2 b/...enge_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.inputs | has_json or cookiecutter.phase.outputs | has_json -%}
+{% if cookiecutter.phase.algorithm_inputs | has_json or cookiecutter.phase.algorithm_outputs | has_json -%}
 import json
 {%- endif %}
-{% if cookiecutter.phase.inputs | has_image or cookiecutter.phase.outputs | has_image -%}
+{% if cookiecutter.phase.algorithm_inputs | has_image or cookiecutter.phase.algorithm_outputs | has_image -%}
 from glob import glob
 import SimpleITK
 import numpy
@@ -35,7 +35,7 @@ RESOURCE_PATH = Path("resources")
 
 def run():
     # Read the input
-    {% for ci in cookiecutter.phase.inputs -%}
+    {% for ci in cookiecutter.phase.algorithm_inputs -%}
     {% set py_slug = ci.slug | replace("-", "_") -%}
     {% if ci | is_image -%}
     {{ py_slug }} = load_image_file_as_array(
@@ -55,7 +55,7 @@ def run():
         print(f.read())
 
     # For now, let us set make bogus predictions
-    {%- for ci in cookiecutter.phase.outputs %}
+    {%- for ci in cookiecutter.phase.algorithm_outputs %}
     {{ ci.slug | replace("-", "_")}} =
         {%- if ci | is_image %} numpy.eye(4, 2)
         {%- elif ci | is_json %} {"content": "should match the required format"}
@@ -64,7 +64,7 @@ def run():
     {%- endfor %}
 
     # Save your output
-    {% for ci in cookiecutter.phase.outputs -%}
+    {% for ci in cookiecutter.phase.algorithm_outputs -%}
     {% set py_slug = ci.slug | replace("-", "_") -%}
     {% if ci | is_image -%}
     write_array_as_image_file(
@@ -86,23 +86,23 @@ def run():
     {% endif -%}
     {% endfor %}
     return 0
-{%- if cookiecutter.phase.inputs | has_json %}
+{%- if cookiecutter.phase.algorithm_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.outputs | has_json %}
+{%- if cookiecutter.phase.algorithm_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.inputs | has_image %}
+{%- if cookiecutter.phase.algorithm_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.outputs | has_image %}
+{%- if cookiecutter.phase.algorithm_outputs | has_image %}
 
 
 def write_array_as_image_file(*, location, array):
@@ -129,7 +129,7 @@ def write_array_as_image_file(*, location, array):
         useCompression=True,
     )
 {%- endif %}
-{%- if cookiecutter.phase.inputs | has_file %}
+{%- if cookiecutter.phase.algorithm_inputs | has_file %}
 
 
 # Note to the challenge hosts:
@@ -140,7 +140,7 @@ def load_file(*, location):
     with open(location) as f:
         return f.read()
 {%- endif %}
-{%- if cookiecutter.phase.outputs | has_file %}
+{%- if cookiecutter.phase.algorithm_outputs | has_file %}
 
 
 # Note to the challenge hosts:

diff --git a/..._forge/partials/example-algorithm/example-algorithm{{cookiecutter._}}/requirements.txt.j2 b/..._forge/partials/example-algorithm/example-algorithm{{cookiecutter._}}/requirements.txt.j2
@@ -1,4 +1,4 @@
-{% if cookiecutter.phase.inputs | has_image or cookiecutter.phase.outputs | has_image -%}
+{% if cookiecutter.phase.algorithm_inputs | has_image or cookiecutter.phase.algorithm_outputs | has_image -%}
 SimpleITK
 numpy
 {%- endif %}
diff --git a/...ials/example-evaluation-method/example-evaluation-method{{cookiecutter._}}/evaluate.py.j2 b/...ials/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.inputs | has_image -%}
+{% if cookiecutter.phase.algorithm_inputs | has_image -%}
 from glob import glob
 import SimpleITK
 {%- endif %}
@@ -69,7 +69,7 @@ def process(job):
 
 
     # Firstly, find the location of the results
-    {% for ci in cookiecutter.phase.outputs %}
+    {% for ci in cookiecutter.phase.algorithm_outputs %}
     {%- set py_slug = ci.slug | replace("-", "_") -%}
     {{ py_slug }}_location = get_file_location(
             job_pk=job["pk"],
@@ -79,7 +79,7 @@ def process(job):
     {% endfor %}
 
     # Secondly, read the results
-    {% for ci in cookiecutter.phase.outputs -%}
+    {% for ci in cookiecutter.phase.algorithm_outputs -%}
     {% set py_slug = ci.slug | replace("-", "_") -%}
     {% if ci | is_image -%}
     {{ py_slug }} = load_image_file(
@@ -100,7 +100,7 @@ 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 -%}
+    {% for ci in cookiecutter.phase.algorithm_inputs -%}
     {% set py_slug = ci.slug | replace("-", "_") -%}
     {% if ci | is_image -%}
     {{ py_slug }}_image_name = get_image_name(
@@ -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.inputs | has_image or cookiecutter.phase.outputs | has_image %}
+{%- if cookiecutter.phase.algorithm_inputs | has_image or cookiecutter.phase.algorithm_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.outputs | has_json %}
+{%- if cookiecutter.phase.algorithm_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.outputs | has_image %}
+{%- if cookiecutter.phase.algorithm_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.outputs | has_file %}
+{%- if cookiecutter.phase.algorithm_outputs | has_file %}
 
 
 def load_file(*, location):

diff --git a/...example-evaluation-method/example-evaluation-method{{cookiecutter._}}/requirements.txt.j2 b/...example-evaluation-method/example-evaluation-method{{cookiecutter._}}/requirements.txt.j2
@@ -1,4 +1,4 @@
-{% if cookiecutter.phase.inputs | has_image or cookiecutter.phase.outputs | has_image -%}
+{% if cookiecutter.phase.algorithm_inputs | has_image or cookiecutter.phase.algorithm_outputs | has_image -%}
 SimpleITK
 numpy
 {%- endif %}
diff --git a/...o-archive-script/upload-to-archive-{{cookiecutter.phase.archive.slug}}/upload_files.py.j2 b/...o-archive-script/upload-to-archive-{{cookiecutter.phase.archive.slug}}/upload_files.py.j2
@@ -33,7 +33,7 @@ Happy uploading!
 from pathlib import Path
 
 import gcapi
-{% if cookiecutter.phase.inputs | has_json -%}
+{% if cookiecutter.phase.algorithm_inputs | has_json -%}
 import json
 {%- endif %}
 
@@ -42,7 +42,7 @@ API_TOKEN = "REPLACE-ME-WITH-YOUR-TOKEN"
 ARCHIVE_SLUG = "{{ cookiecutter.phase.archive.slug }}"
 
 EXPECTED_CASES = [
-    # for: {% for ci in cookiecutter.phase.inputs -%}{{ ci.slug }}{%- if not loop.last -%}, {% endif -%}{% endfor %}
+    # for: {% for ci in cookiecutter.phase.algorithm_inputs -%}{{ ci.slug }}{%- if not loop.last -%}, {% endif -%}{% endfor %}
 {%- for expected_cases in cookiecutter.phase.expected_cases %}
     {{ expected_cases }},
 {%- endfor %}
@@ -86,7 +86,7 @@ def upload_files():
 
 def map_case_content_to_interfaces(case):
     return {
-        {%- for ci in cookiecutter.phase.inputs %}
+        {%- for ci in cookiecutter.phase.algorithm_inputs %}
         {%- if ci | is_json %}
         "{{ ci.slug }}": json.loads(Path(case[{{ loop.index - 1}}]).read_text()),
         {%- else %}

diff --git a/grand_challenge_forge/quality_control.py b/grand_challenge_forge/quality_control.py
@@ -75,7 +75,7 @@ def _test_example_algorithm(phase_context, algorithm_dir, number_run):
     _test_subprocess(script_dir=algorithm_dir, number_run=number_run)
 
     # Check if output is generated (ignore content)
-    for output in phase_context["phase"]["outputs"]:
+    for output in phase_context["phase"]["algorithm_outputs"]:
         expected_file = output_dir / output["relative_path"]
         if not expected_file.exists():
             raise QualityFailureError(

diff --git a/grand_challenge_forge/schemas.py b/grand_challenge_forge/schemas.py
@@ -48,16 +48,21 @@
                         "properties": {
                             "slug": {"type": "string"},
                             "archive": ARCHIVE_SCHEMA,
-                            "inputs": {
+                            "algorithm_inputs": {
                                 "type": "array",
                                 "items": COMPONENT_INTERFACE_SCHEMA,
                             },
-                            "outputs": {
+                            "algorithm_outputs": {
                                 "type": "array",
                                 "items": COMPONENT_INTERFACE_SCHEMA,
                             },
                         },
-                        "required": ["slug", "archive", "inputs", "outputs"],
+                        "required": [
+                            "slug",
+                            "archive",
+                            "algorithm_inputs",
+                            "algorithm_outputs",
+                        ],
                         "additionalProperties": True,  # Allow additional properties
                     },
                 },

diff --git a/tests/utils.py b/tests/utils.py
@@ -27,7 +27,7 @@
                     "slug": "archive-slug",
                     "url": "https://grand-challenge.org/archives/archive-slug/"
                 },
-                "inputs": [
+                "algorithm_inputs": [
                     {
                         "slug": "input-ci-slug",
                         "kind": "Segmentation",
@@ -53,7 +53,7 @@
                         "relative_path": "yet-another-non-json-input-value"
                     }
                 ],
-                "outputs": [
+                "algorithm_outputs": [
                     {
                         "slug": "output-ci-slug",
                         "kind": "Image",
@@ -86,15 +86,15 @@
                     "slug": "another-archive-slug",
                     "url": "https://grand-challenge.org/archives/another-archive-slug/"
                 },
-                "inputs": [
+                "algorithm_inputs": [
                     {
                         "slug": "input-ci-slug",
                         "kind": "Image",
                         "super_kind": "Image",
                         "relative_path": "images/input-value"
                     }
                 ],
-                "outputs": [
+                "algorithm_outputs": [
                     {
                         "slug": "another-output-ci-slug",
                         "kind": "Anything",