improve demo page

cleanup code, remove comments

js/index.html

@@ -57,8 +57,7 @@ <h1 class="text-xl font-semibold">Nanopublication dev</h1>
     </div>
 
     <script type="module">
-      // import init, { get_np_server, Nanopub, NpProfile } from "https://unpkg.com/@nanopub/sign";
-      import init, { Nanopub, NpProfile, get_np_server, KeyPair } from "./pkg/web.js";
+      import init, { Nanopub, NpProfile, getNpServer, KeyPair } from "./pkg/web.js";
 
       const privKey=`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`;
 

lib/docs/introduction.md

@@ -22,10 +22,15 @@ On all platforms:
 - 🪟 Windows
 - 🦊 Web browsers
 
-The library automatically handles most RDF serializations supporting graphs for the nanopub:
+The library automatically handles most RDF serializations supporting quads for the nanopub:
 
 - TriG
 - Nquads
 - JSON-LD
 
+When signing a nanopub, some metadata in the pubinfo graph are created automatically if they are not already set in the RDF provided:
+
+- Date and time of the Nanopublication creation using `dct:created`.
+- ORCID of the creator using `dct:creator`, if an ORCID was provided in the profile used to sign the Nanopublication (we also check if the ORCID has been set with `prov:wasAttributedTo`, or `pav:createdBy`)
+
 > 💡 If you are facing any problem, or have ideas to help improve this project, please [create an issue](https://github.com/vemonet/nanopub-rs/issues) on GitHub.

lib/src/extract.rs

@@ -46,11 +46,6 @@ impl fmt::Display for NpInfo {
     }
 }
 
-// TODO: separate funtion just to extract uri and ns (to pass to serialize_rdf())
-// pub fn extract_np_uri(dataset: &LightDataset) -> Result<(String, String), NpError> {
-//     let mut np_url: String = "".to_string();
-// }
-
 /// Extract graphs URLs from a nanopub: nanopub URL, head, assertion, prov, pubinfo
 pub fn extract_np_info(dataset: &LightDataset, check_pubinfo: bool) -> Result<NpInfo, NpError> {
     let mut np_url: String = "".to_string();
@@ -129,6 +124,7 @@ pub fn extract_np_info(dataset: &LightDataset, check_pubinfo: bool) -> Result<Np
 
     // Getting potential ns from head graph (removing the last frag from head)
     let original_ns = &head_iri[..np_iri.len()];
+    let np_ns = Namespace::new_unchecked(original_ns.to_string());
 
     // Remove last char if it is # or / to get the URI
     let np_iri: Iri<String> =
@@ -157,7 +153,6 @@ pub fn extract_np_info(dataset: &LightDataset, check_pubinfo: bool) -> Result<Np
 
     // Get the base URI and separators from the namespace
     let re_trusty_ns = Regex::new(r"^(.*?)(/|#|\.)?(RA[a-zA-Z0-9-_]*)?([#/\.])?$")?;
-    // let re = Regex::new(r"^(.*?)(RA.*)?$")?;
     if let Some(caps) = re_trusty_ns.captures(original_ns) {
         // The first group captures everything up to a '/' or '#', non-greedy.
         base_uri = caps.get(1).map_or("", |m| m.as_str()).to_string();
@@ -167,7 +162,6 @@ pub fn extract_np_info(dataset: &LightDataset, check_pubinfo: bool) -> Result<Np
             .map_or(separator_before_trusty, |m| m.as_str().to_string())
             .to_string();
         // The last group captures everything after 'RA', if present.
-        // trusty_hash = caps.get(3).map_or("", |m| m.as_str()).to_string();
         separator_after_trusty = caps
             .get(4)
             .map_or(separator_after_trusty, |m| m.as_str().to_string())
@@ -176,14 +170,7 @@ pub fn extract_np_info(dataset: &LightDataset, check_pubinfo: bool) -> Result<Np
     if trusty_hash.is_empty() && separator_after_trusty.is_empty() {
         separator_after_trusty = "#".to_string()
     };
-
-    let np_ns = Namespace::new_unchecked(original_ns.to_string());
-    // println!(
-    //     "DEBUG: Extracted URI and namespace: {} {} {}",
-    //     np_iri,
-    //     np_ns.get("")?,
-    //     trusty_hash
-    // );
+    // println!("DEBUG: Extracted URIs: {} {} {}", np_iri, np_ns.get("")?, trusty_hash);
 
     // Generate normalized namespace without trusty
     let norm_ns = if !trusty_hash.is_empty() {
@@ -319,7 +306,7 @@ pub fn extract_np_info(dataset: &LightDataset, check_pubinfo: bool) -> Result<Np
         ));
     }
 
-    let np_info = NpInfo {
+    Ok(NpInfo {
         uri: np_iri,
         ns: np_ns,
         normalized_ns: norm_ns,
@@ -336,86 +323,5 @@ pub fn extract_np_info(dataset: &LightDataset, check_pubinfo: bool) -> Result<Np
         public_key: pubkey.unwrap_or("".to_string()),
         algo: algo.unwrap_or("".to_string()),
         orcid: orcid.unwrap_or("".to_string()),
-    };
-    // let _ = check_np_info(dataset, &np_info, check_pubinfo);
-    Ok(np_info)
-}
-
-pub fn check_np_info(
-    dataset: &LightDataset,
-    np_info: &NpInfo,
-    check_pubinfo: bool,
-) -> Result<(), NpError> {
-    // Check minimal required triples in assertion, prov, pubinfo graphs
-    if dataset
-        .quads_matching(Any, Any, Any, [Some(np_info.assertion.clone())])
-        .next()
-        .is_none()
-    {
-        return Err(NpError(
-            "Invalid Nanopub: no triples in the assertion graph.".to_string(),
-        ));
-    }
-    if dataset
-        .quads_matching(Any, Any, Any, [Some(np_info.prov.clone())])
-        .next()
-        .is_none()
-    {
-        return Err(NpError(
-            "Invalid Nanopub: no triples in the provenance graph.".to_string(),
-        ));
-    }
-    if dataset
-        .quads_matching(
-            [np_info.assertion.clone()],
-            Any,
-            Any,
-            [Some(np_info.prov.clone())],
-        )
-        .next()
-        .is_none()
-    {
-        return Err(NpError("Invalid Nanopub: no triples with the assertion graph as subject in the provenance graph.".to_string()));
-    }
-    if check_pubinfo {
-        if dataset
-            .quads_matching(Any, Any, Any, [Some(np_info.pubinfo.clone())])
-            .next()
-            .is_none()
-        {
-            return Err(NpError(
-                "Invalid Nanopub: no triples in the pubinfo graph.".to_string(),
-            ));
-        }
-        if dataset
-            .quads_matching(
-                [
-                    np_info.uri.clone(),
-                    Iri::new_unchecked(np_info.ns.get("")?.to_string()),
-                ],
-                Any,
-                Any,
-                [Some(np_info.pubinfo.clone())],
-            )
-            .next()
-            .is_none()
-        {
-            return Err(NpError(
-                "Invalid Nanopub: no triples with the nanopub URI as subject in the pubinfo graph."
-                    .to_string(),
-            ));
-        };
-    }
-    let mut graph_names = HashSet::new();
-    for g in dataset.graph_names() {
-        if let Some(graph_name) = g?.iri() {
-            graph_names.insert(graph_name.to_string());
-        }
-    }
-    if graph_names.len() != 4 {
-        return Err(NpError(
-            format!("Invalid Nanopub: it should have 4 graphs (head, assertion, provenance, pubinfo), but the given nanopub has {} graphs.", graph_names.len())
-        ));
-    }
-    Ok(())
+    })
 }

lib/src/nanopub.rs

@@ -1,7 +1,7 @@
-use crate::constants::{BOLD, END, NP_PREF_NS, NP_TEMP_URI, TEST_SERVER};
+use crate::constants::{BOLD, END, NP_TEMP_URI, TEST_SERVER};
 use crate::error::NpError;
 use crate::extract::extract_np_info;
-use crate::profile::{get_keys, get_pubkey_str, NpProfile};
+use crate::profile::NpProfile;
 use crate::publish::{fetch_np, publish_np};
 use crate::sign::{make_trusty, normalize_dataset, replace_bnodes, replace_ns_in_quads};
 use crate::utils::{ns, parse_rdf, serialize_rdf};
@@ -15,8 +15,7 @@ use serde::Serialize;
 use sophia::api::dataset::{Dataset, MutableDataset};
 use sophia::api::ns::{rdf, xsd, Namespace};
 use sophia::api::term::matcher::Any;
-use sophia::api::term::{SimpleTerm, Term};
-// use sophia::api::;
+use sophia::api::term::SimpleTerm;
 use sophia::inmem::dataset::LightDataset;
 use sophia::iri::{AsIriRef, Iri};
 use std::{fmt, str};
@@ -217,9 +216,6 @@ impl Nanopub {
         openssl_probe::init_ssl_cert_env_vars();
         let mut dataset = rdf.get_dataset()?;
 
-        let (priv_key, pubkey) = get_keys(&profile.private_key)?;
-        let pubkey_str = get_pubkey_str(&pubkey)?;
-
         // Extract graph URLs from the nanopub (fails if np not valid)
         let np_info = extract_np_info(&dataset, false)?;
 
@@ -231,7 +227,7 @@ impl Nanopub {
         dataset.insert(
             np_info.ns.get("sig")?,
             ns("npx").get("hasPublicKey")?,
-            &*pubkey_str,
+            &*profile.public_key,
             Some(&np_info.pubinfo),
         )?;
         dataset.insert(
@@ -247,9 +243,7 @@ impl Nanopub {
             Some(&np_info.pubinfo),
         )?;
 
-        // TODO: if not already set, automatically add the current date to pubinfo created
-        // But there is an error when trying to cast the string to xsd::dateTime
-        // np_uri dct:created "2023-11-17T14:13:52.560Z"^^xsd:dateTime ;
+        // If not already set, automatically add the current date to pubinfo created
         if dataset
             .quads_matching(
                 [
@@ -265,15 +259,13 @@ impl Nanopub {
         {
             let now = Utc::now();
             let datetime_str = now.format("%Y-%m-%dT%H:%M:%S%.3fZ").to_string();
-            // TODO: error when trying to convert to datetime
+            // TODO: there is an error when trying to cast the string to xsd::dateTime
             // let lit_date = "2019" * xsd::dateTime;
-            // let lit_date = datetime_str.as_str() * xsd::dateTime;
-            let lit_date = SimpleTerm::LiteralDatatype(datetime_str.into(), xsd::dateTime.iriref());
             dataset.insert(
                 np_info.ns.as_iri_ref(),
                 ns("dct").get("created")?,
-                lit_date,
-                // &*datetime_str * xsd::dateTime.iriref(),
+                SimpleTerm::LiteralDatatype(datetime_str.into(), xsd::dateTime.iriref()),
+                // datetime_str.as_str() * xsd::dateTime,
                 Some(&np_info.pubinfo),
             )?;
         }
@@ -315,7 +307,7 @@ impl Nanopub {
         // println!("NORMED QUADS sign before add signature\n{}", norm_quads);
 
         // Generate signature using the private key and normalized RDF
-        let signature_vec = priv_key.sign(
+        let signature_vec = profile.get_private_key()?.sign(
             Pkcs1v15Sign::new::<Sha256>(),
             &Sha256::digest(norm_quads.as_bytes()),
         )?;
@@ -348,7 +340,7 @@ impl Nanopub {
             rdf: rdf_str,
             trusty_hash,
             signature_hash,
-            public_key: pubkey_str,
+            public_key: profile.public_key.to_string(),
             orcid: profile.orcid_id.to_string(),
             published: false,
         })

lib/src/profile.rs

@@ -21,13 +21,16 @@ pub struct NpProfile {
 }
 
 impl NpProfile {
+    /// Create a new Nanopub profile
     pub fn new(
         orcid_id: &str,
         name: &str,
         private_key: &str,
         introduction_nanopub_uri: Option<&str>,
     ) -> Result<Self, NpError> {
-        let (_priv_key, pubkey) = get_keys(private_key)?;
+        let privkey =
+            RsaPrivateKey::from_pkcs8_der(&engine::general_purpose::STANDARD.decode(private_key)?)?;
+        let pubkey = RsaPublicKey::from(&privkey);
         Ok(Self {
             orcid_id: orcid_id.to_string(),
             name: name.to_string(),
@@ -37,7 +40,7 @@ impl NpProfile {
         })
     }
 
-    /// Extract profile from YAML file
+    /// Create a Nanopub profile from a YAML file
     pub fn from_file(filepath: &str) -> Result<Self, NpError> {
         let filepath = if filepath.is_empty() {
             // Default to home dir if nothing provided
@@ -59,6 +62,17 @@ impl NpProfile {
         profile.public_key = normalize_key(&fs::read_to_string(&profile.public_key)?)?;
         Ok(profile)
     }
+
+    /// Get the private key as `RsaPrivateKey` struct
+    pub fn get_private_key(&self) -> Result<RsaPrivateKey, NpError> {
+        Ok(RsaPrivateKey::from_pkcs8_der(
+            &engine::general_purpose::STANDARD.decode(&self.private_key)?,
+        )?)
+    }
+    /// Get the public key as `RsaPublicKey` struct
+    pub fn get_public_key(&self) -> Result<RsaPublicKey, NpError> {
+        Ok(RsaPublicKey::from(&self.get_private_key()?))
+    }
 }
 
 impl fmt::Display for NpProfile {
@@ -81,15 +95,7 @@ impl fmt::Display for NpProfile {
     }
 }
 
-/// Get `RsaPrivateKey` and `RsaPublicKey` given a private key string
-pub fn get_keys(private_key: &str) -> Result<(RsaPrivateKey, RsaPublicKey), NpError> {
-    let priv_key_bytes = engine::general_purpose::STANDARD.decode(private_key)?;
-    let priv_key = RsaPrivateKey::from_pkcs8_der(&priv_key_bytes)?;
-    let public_key = RsaPublicKey::from(&priv_key);
-    Ok((priv_key, public_key))
-}
-
-/// Normalize private/public keys (no prefix, no suffix, no newline)
+/// Normalize a private or public key string (remove prefix, suffix, newlines)
 pub fn normalize_key(key: &str) -> Result<String, NpError> {
     let mut normed_key = key.trim().to_string();
     let start_patterns = [

lib/src/publish.rs

@@ -11,8 +11,6 @@ pub async fn publish_np(server: &str, np: &str) -> Result<bool, NpError> {
         .header(reqwest::header::CONTENT_TYPE, "application/trig")
         .send()
         .await?;
-    // println!("DEBUG: publish resp: {:#?}", res);
-    // Ok(res.status() == 201)
     match res.status() {
         reqwest::StatusCode::CREATED => Ok(true),
         _ => {

lib/src/sign.rs

@@ -155,10 +155,6 @@ pub fn replace_ns_in_quads(
     new_ns: &str,
     new_uri: &str,
 ) -> Result<LightDataset, NpError> {
-    // println!(
-    //     "DEBUG: REPLACE_NS_IN_QUADS: Old ns: {} old_uri: {} new ns: {} new_uri: {}",
-    //     old_ns, old_uri, new_ns, new_uri
-    // );
     let mut new = LightDataset::new();
     for quad in dataset.quads() {
         let quad = quad?;
@@ -227,21 +223,10 @@ struct NormQuad {
 pub fn fix_normed_uri(uri: &str, separator: &str) -> String {
     if let Some(space_index) = uri.rfind(' ') {
         let last_frag = &uri[space_index + 1..];
-        // println!(
-        //     "DEBUG: last frag: '{}' URI: '{}' SEP: '{}'",
-        //     last_frag, uri, separator
-        // );
         if uri.ends_with(&format!(" {separator}")) || last_frag.is_empty() {
             uri.strip_suffix(separator).unwrap_or(uri).to_string()
         } else if last_frag.starts_with(separator) {
             uri.to_string()
-        // TODO: remove those checks, there are not useful anymore?
-        // } else if last_frag.starts_with('/') || last_frag.starts_with('.') {
-        //     format!(
-        //         "{} {separator}{}",
-        //         &uri[..space_index],
-        //         &uri[space_index + 2..]
-        //     )
         } else {
             format!("{} {separator}{}", &uri[..space_index], last_frag)
         }