bug: Fixes deserialization issues with attachments and outputs

kreshuklab · Sep 25, 2024 · 0c58bba · 0c58bba
1 parent ad2e830
commit 0c58bba
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Showing 4 changed files with 10 additions and 3 deletions.
diff --git a/bioimg_runtime/src/zoo_model.rs b/bioimg_runtime/src/zoo_model.rs
@@ -115,7 +115,7 @@ impl ZooModel{
             .collect::<Result<_, _>>()?;
 
         let attachments: Vec<FileSource> = model_rdf.attachments.into_iter()
-            .map(|att| match att{
+            .map(|att| match att.source{
                 rdf::FileReference::Url(_) => return Err(ModelLoadingError::UrlFileReferenceNotSupportedYet),
                 rdf::FileReference::Path(fs_path) => {
                     Ok(FileSource::FileInZipArchive { outer_path: Arc::from(path), inner_path: Arc::from(String::from(fs_path).as_str()) })
@@ -173,7 +173,7 @@ impl ZooModel {
             cov.dump(&mut writer)
         }).collect::<Result<Vec<_>, _>>()?;
         let attachments = self.attachments.iter().map(|file|{
-            file.rdf_dump_as_file_reference(&mut writer)
+            file.dump_as_file_description(&mut writer)
         }).collect::<Result<Vec<_>, _>>()?;
         let icon: Option<rdf::Icon> = match &self.icon{
             Some(icon) => Some(icon.dump(&mut writer)?),

diff --git a/bioimg_spec/src/rdf/model/model_rdf_0_5.rs b/bioimg_spec/src/rdf/model/model_rdf_0_5.rs
@@ -1,3 +1,4 @@
+use crate::rdf::FileDescription;
 use crate::rdf::{
     self,
     version::Version_0_5_x, Author2, CiteEntry2, CoverImageSource, FileReference, HttpUrl, Icon, LicenseId,
@@ -31,7 +32,7 @@ pub struct ModelRdfV0_5 {
 
     /// file attachments
     #[serde(default)]
-    pub attachments: Vec<FileReference>,
+    pub attachments: Vec<FileDescription>,
 
     /// citations
     pub cite: NonEmptyList<CiteEntry2>,

diff --git a/bioimg_spec/src/rdf/model/output_tensor.rs b/bioimg_spec/src/rdf/model/output_tensor.rs
@@ -24,6 +24,10 @@ pub struct OutputTensorDescr {
 }
 
 
+fn _default_to_output() -> TensorId{
+    TensorId::try_from("output").unwrap()
+}
+
 #[derive(Serialize, Deserialize, Debug, Clone)]
 #[serde(try_from = "OutputTensorMetadataMsg")]
 #[serde(into = "OutputTensorMetadataMsg")]
@@ -41,6 +45,7 @@ impl OutputTensorMetadata{
 
 #[derive(Serialize, Deserialize, Debug, Clone)]
 pub struct OutputTensorMetadataMsg{
+    #[serde(default="_default_to_output")]
     pub id: TensorId,
     #[serde(default)]
     pub postprocessing: Vec<PostprocessingDescr>,

diff --git a/bioimg_spec/src/rdf/model/preprocessing/scale_range.rs b/bioimg_spec/src/rdf/model/preprocessing/scale_range.rs
@@ -104,6 +104,7 @@ pub struct ScaleRangeDescr{
     /// Epsilon for numeric stability.
     /// `out = (tensor - v_lower) / (v_upper - v_lower + eps)`;
     /// with `v_lower,v_upper` values at the respective percentiles.
+    #[serde(default)]
     pub eps: PreprocessingEpsilon,
 
     // Tensor name to compute the percentiles from. Default: The tensor itself.