First work in creating a first dataset loader

Co-authored-by: LouisK92 <[email protected]>
openproblems-bio · Aug 26, 2024 · 72fd831 · 72fd831
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diff --git a/.gitignore b/.gitignore
@@ -13,4 +13,5 @@ singularity_container/
 
 target
 .nextflow
-.resources_test
+resources_test
+resources
diff --git a/README.md b/README.md
diff --git a/src/api/comp_control_method.yaml b/src/api/comp_control_method.yaml
diff --git a/src/api/comp_data_loader.yaml b/src/api/comp_data_loader.yaml
@@ -0,0 +1,23 @@
+
+info:
+  type: data_processor
+  type_info:
+    label: Data loader
+    summary: A data loader component which downloads data from a resource and stores it as a zarr file.
+    description: |
+      TODO: fill in
+arguments:
+  - name: "--dataset_organism"
+    type: string
+    direction: input
+    required: true
+  - name: "--output"
+    __merge__: file_raw_data.yaml
+    direction: output
+    required: true
+# test_resources:
+#   - path: /resources_test/common/pancreas
+#     dest: resources_test/common/pancreas
+#   - type: python_script
+#     path: /common/component_tests/run_and_check_output.py
+
diff --git a/src/api/comp_data_processor.yaml b/src/api/comp_data_processor.yaml
diff --git a/src/api/comp_method.yaml b/src/api/comp_method.yaml
diff --git a/src/api/comp_metric.yaml b/src/api/comp_metric.yaml
diff --git a/src/api/file_common_dataset.yaml b/src/api/file_common_dataset.yaml
diff --git a/src/api/file_prediction.yaml b/src/api/file_prediction.yaml