Merge pull request #54 from sdsc-ordes/fix/ontology-sync

fix: ontology sync

Author: vancauwe

src/catplus-common/src/graph/namespaces/cat.rs

@@ -57,7 +57,7 @@ namespace! {
     Observation,
     optimizationType,
     order,
-    Peak,
+    peak,
     PeakList,
     Plate,
     ProcessedDataDocument,

src/catplus-common/src/graph/utils.rs

@@ -1,3 +1,4 @@
+use crate::graph::namespaces::cat_resource;
 use base64::{engine::general_purpose, Engine as _};
 use sha2::{Digest, Sha256};
 use sophia_api::{
@@ -20,3 +21,9 @@ pub(crate) fn hash_identifier(identifier: &str) -> String {
     let result = hasher.finalize();
     general_purpose::URL_SAFE_NO_PAD.encode(result)
 }
+
+pub fn generate_resource_identifier_uri(resource_id: String) -> SimpleTerm<'static> {
+    let mut uri = cat_resource::ns.clone().as_str().to_owned();
+    uri.push_str(&hash_identifier(&resource_id));
+    IriRef::new_unchecked(uri).try_into_term().expect("Failed to convert to SimpleTerm")
+}

src/catplus-common/src/models/agilent.rs

@@ -1,8 +1,8 @@
 use crate::{
     graph::{
         insert_into::{InsertIntoGraph, Link},
-        namespaces::{allodc, allores, allorole, cat, cat_resource, obo, purl, qb, qudt},
-        utils::hash_identifier,
+        namespaces::{allodc, allores, allorole, cat, obo, purl, qb, qudt},
+        utils::generate_resource_identifier_uri,
     },
     models::{core::PeakList, enums::Unit},
 };
@@ -100,9 +100,6 @@ impl InsertIntoGraph for MeasurementAggregateDocument {
 pub struct MeasurementDocument {
     #[serde(rename = "measurement identifier")]
     pub measurement_identifier: String,
-    // TO-DO: needs further definition to be integrated
-    // #[serde(rename = "chromatography column document")]
-    // pub chromatography_column_document: ChromatographyColumnDocument,
     #[serde(rename = "device control aggregate document")]
     pub device_control_aggregate_document: DeviceSystemDocument,
     #[serde(rename = "sample document")]
@@ -148,23 +145,6 @@ impl InsertIntoGraph for MeasurementDocument {
     }
 }
 
-#[derive(Clone, Debug, Serialize, Deserialize)]
-pub struct ChromatographyColumnDocument {}
-
-impl InsertIntoGraph for ChromatographyColumnDocument {
-    fn insert_into(&self, graph: &mut LightGraph, iri: SimpleTerm) -> anyhow::Result<()> {
-        for (pred, value) in
-            [(rdf::type_, &cat::ChromatographyColumnDocument.as_simple() as &dyn InsertIntoGraph)]
-        {
-            value.attach_into(
-                graph,
-                Link { source_iri: iri.clone(), pred: pred.as_simple(), target_iri: None },
-            )?;
-        }
-        Ok(())
-    }
-}
-
 #[derive(Clone, Debug, Serialize, Deserialize)]
 pub struct DeviceSystemDocument {
     #[serde(alias = "device document", alias = "device control document")]
@@ -215,9 +195,7 @@ pub struct DeviceDocument {
 impl InsertIntoGraph for DeviceDocument {
     fn get_uri(&self) -> SimpleTerm<'static> {
         // build URI based on self.device_identifier
-        let mut uri = cat_resource::ns.clone().as_str().to_owned();
-        uri.push_str(&hash_identifier(&self.device_identifier));
-        IriRef::new_unchecked(uri).try_into_term().unwrap()
+        generate_resource_identifier_uri(self.device_identifier.clone())
     }
 
     fn insert_into(&self, graph: &mut LightGraph, iri: SimpleTerm) -> anyhow::Result<()> {
@@ -296,6 +274,11 @@ pub struct AgilentProduct {
 }
 
 impl InsertIntoGraph for AgilentProduct {
+    fn get_uri(&self) -> SimpleTerm<'static> {
+        //same as in synth.rs set_product_uri function
+        //same as in bravo.rs get_uri function for BravoProduct
+        generate_resource_identifier_uri(self.product_identifier.clone())
+    }
     fn insert_into(&self, graph: &mut LightGraph, iri: SimpleTerm) -> anyhow::Result<()> {
         for (pred, value) in [
             (rdf::type_, &cat::Product.as_simple() as &dyn InsertIntoGraph),

src/catplus-common/src/models/bravo.rs

@@ -2,6 +2,7 @@ use crate::{
     graph::{
         insert_into::{InsertIntoGraph, Link},
         namespaces::{alloprop, alloqual, allores, cat, purl},
+        utils::generate_resource_identifier_uri,
     },
     models::{
         core::{Chemical, Observation, Plate, Well},
@@ -13,6 +14,7 @@ use serde::{Deserialize, Serialize};
 use sophia::{
     api::ns::{rdf, xsd},
     inmem::graph::LightGraph,
+    iri::IriRef,
 };
 use sophia_api::term::{SimpleTerm, Term};
 
@@ -60,7 +62,7 @@ pub struct BravoAction {
     pub start_duration: Option<Observation>,
     pub ending_duration: Option<Observation>,
     pub order: Option<String>,
-    pub product_identification: ProductIdentification,
+    pub product_identification: BravoProduct,
 }
 
 impl InsertIntoGraph for BravoAction {
@@ -191,14 +193,19 @@ impl InsertIntoGraph for BravoWell {
 
 #[derive(Clone, Debug, Serialize, Deserialize)]
 #[serde(rename_all = "camelCase")]
-pub struct ProductIdentification {
+pub struct BravoProduct {
     #[serde(rename = "sampleID")]
     pub sample_id: String,
     // Peak identifier is added on the action, not on the product
     pub peak_identifier: String,
 }
 
-impl InsertIntoGraph for ProductIdentification {
+impl InsertIntoGraph for BravoProduct {
+    fn get_uri(&self) -> SimpleTerm<'static> {
+        //same as in synth.rs set_product_uri function
+        //same as in agilent.rs get_uri function for AgilentProduct
+        generate_resource_identifier_uri(self.sample_id.clone())
+    }
     fn insert_into(&self, graph: &mut LightGraph, iri: SimpleTerm) -> anyhow::Result<()> {
         for (pred, value) in [
             (rdf::type_, &cat::Product.as_simple() as &dyn InsertIntoGraph),

src/catplus-common/src/models/core.rs

@@ -154,13 +154,27 @@ impl InsertIntoGraph for PeakList {
     fn insert_into(&self, graph: &mut LightGraph, iri: SimpleTerm) -> anyhow::Result<()> {
         for (pred, value) in [
             (rdf::type_, &cat::PeakList.as_simple() as &dyn InsertIntoGraph),
-            (cat::Peak, &self.peak),
+            (cat::peak, &self.peak),
         ] {
             value.attach_into(
                 graph,
                 Link { source_iri: iri.clone(), pred: pred.as_simple(), target_iri: None },
             )?;
         }
+        let product = cat::Product.as_simple();
+        let rdf_type = rdf::type_.as_simple();
+
+        let product_object = graph.triples().filter_map(Result::ok).find_map(|[s, p, o]| {
+            if *p == rdf_type && *o == product {
+                Some(s.clone())
+            } else {
+                None
+            }
+        });
+
+        if let Some(subject) = product_object {
+            graph.insert(iri.clone(), cat::hasProduct.as_simple(), subject)?;
+        }
         Ok(())
     }
 }

src/catplus-common/src/models/synth.rs

@@ -1,8 +1,8 @@
 use crate::{
     graph::{
         insert_into::{InsertIntoGraph, Link},
-        namespaces::{alloproc, alloprop, alloqual, allores, cat, cat_resource, purl, qudt},
-        utils::hash_identifier,
+        namespaces::{alloproc, alloprop, alloqual, allores, cat, purl, qudt},
+        utils::generate_resource_identifier_uri,
     },
     models::{
         core::{Chemical, Observation, Plate},
@@ -31,12 +31,16 @@ pub struct SynthBatch {
     pub actions: Vec<SynthAction>,
 }
 
+fn set_product_uri(product_id: String) -> SimpleTerm<'static> {
+    //same as in agilent.rs get_uri function for AgilentProduct
+    //same as in bravo.rs get_uri function for BravoProduct
+    generate_resource_identifier_uri(product_id.clone())
+}
+
 impl InsertIntoGraph for SynthBatch {
     fn get_uri(&self) -> SimpleTerm<'static> {
         // build URI based on self.batch_id
-        let mut uri = cat_resource::ns.clone().as_str().to_owned();
-        uri.push_str(&hash_identifier(&self.batch_id));
-        IriRef::new_unchecked(uri).try_into_term().unwrap()
+        generate_resource_identifier_uri(self.batch_id.clone())
     }
 
     fn insert_into(&self, graph: &mut LightGraph, iri: SimpleTerm) -> anyhow::Result<()> {
@@ -64,7 +68,8 @@ impl InsertIntoGraph for SynthBatch {
                             // Create the product_id from container_id and position
                             let product_id =
                                 format!("{}-{}", &well.has_plate.container_id, well.position);
-                            let new_product_uri = well.get_uri();
+                            //let new_product_uri = well.get_uri();
+                            let new_product_uri = set_product_uri(product_id.clone());
                             for (pred, value) in [
                                 (
                                     rdf::type_,
@@ -169,7 +174,7 @@ impl InsertIntoGraph for SynthAction {
             (allores::AFR_0001606, &self.method_name.as_simple()),
             (allores::AFR_0001723, &self.equipment_name.as_simple()),
             (cat::subEquipmentName, &self.sub_equipment_name.as_simple()),
-            (cat::speedInRPM, &self.speed_shaker),
+            (alloprop::AFX_0000211, &self.speed_shaker),
             (cat::temperatureTumbleStirrer, &self.temperature_tumble_stirrer),
             (alloprop::AFX_0000211, &self.speed_tumble_stirrer),
             (cat::vacuum, &self.vacuum),