Replace bibliography handling with bibliographix

Signed-off-by: trivernis <trivernis@protonmail.com>

Cargo.lock

@@ -52,6 +52,15 @@ name = "base64"
 version = "0.12.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 
+[[package]]
+name = "bibliographix"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "chrono 0.4.15 (registry+https://github.com/rust-lang/crates.io-index)",
+ "chrono-english 0.1.4 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
 [[package]]
 name = "bincode"
 version = "1.3.1"
@@ -98,7 +107,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 
 [[package]]
 name = "chrono"
-version = "0.4.13"
+version = "0.4.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 dependencies = [
  "num-integer 0.1.43 (registry+https://github.com/rust-lang/crates.io-index)",
@@ -106,6 +115,16 @@ dependencies = [
  "time 0.1.43 (registry+https://github.com/rust-lang/crates.io-index)",
 ]
 
+[[package]]
+name = "chrono-english"
+version = "0.1.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "chrono 0.4.15 (registry+https://github.com/rust-lang/crates.io-index)",
+ "scanlex 0.1.2 (registry+https://github.com/rust-lang/crates.io-index)",
+ "time 0.1.43 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
 [[package]]
 name = "clap"
 version = "2.33.2"
@@ -843,7 +862,7 @@ version = "1.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 dependencies = [
  "base64 0.12.3 (registry+https://github.com/rust-lang/crates.io-index)",
- "chrono 0.4.13 (registry+https://github.com/rust-lang/crates.io-index)",
+ "chrono 0.4.15 (registry+https://github.com/rust-lang/crates.io-index)",
  "indexmap 1.5.0 (registry+https://github.com/rust-lang/crates.io-index)",
  "line-wrap 0.1.1 (registry+https://github.com/rust-lang/crates.io-index)",
  "serde 1.0.114 (registry+https://github.com/rust-lang/crates.io-index)",
@@ -1034,6 +1053,11 @@ dependencies = [
  "winapi-util 0.1.5 (registry+https://github.com/rust-lang/crates.io-index)",
 ]
 
+[[package]]
+name = "scanlex"
+version = "0.1.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+
 [[package]]
 name = "schannel"
 version = "0.1.19"
@@ -1121,8 +1145,9 @@ version = "0.23.0"
 dependencies = [
  "asciimath-rs 0.5.7 (registry+https://github.com/rust-lang/crates.io-index)",
  "base64 0.12.3 (registry+https://github.com/rust-lang/crates.io-index)",
+ "bibliographix 0.2.0 (registry+https://github.com/rust-lang/crates.io-index)",
  "charred 0.3.3 (registry+https://github.com/rust-lang/crates.io-index)",
- "chrono 0.4.13 (registry+https://github.com/rust-lang/crates.io-index)",
+ "chrono 0.4.15 (registry+https://github.com/rust-lang/crates.io-index)",
  "colored 1.9.3 (registry+https://github.com/rust-lang/crates.io-index)",
  "crossbeam-utils 0.7.2 (registry+https://github.com/rust-lang/crates.io-index)",
  "gh-emoji 1.0.3 (registry+https://github.com/rust-lang/crates.io-index)",
@@ -1563,6 +1588,7 @@ dependencies = [
 "checksum atty 0.2.14 (registry+https://github.com/rust-lang/crates.io-index)" = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
 "checksum autocfg 1.0.0 (registry+https://github.com/rust-lang/crates.io-index)" = "f8aac770f1885fd7e387acedd76065302551364496e46b3dd00860b2f8359b9d"
 "checksum base64 0.12.3 (registry+https://github.com/rust-lang/crates.io-index)" = "3441f0f7b02788e948e47f457ca01f1d7e6d92c693bc132c22b087d3141c03ff"
+"checksum bibliographix 0.2.0 (registry+https://github.com/rust-lang/crates.io-index)" = "ba3bc8793948a3de7d106d5f855afb085b998585c5f407ae59cd5489d3ed97c8"
 "checksum bincode 1.3.1 (registry+https://github.com/rust-lang/crates.io-index)" = "f30d3a39baa26f9651f17b375061f3233dde33424a8b72b0dbe93a68a0bc896d"
 "checksum bitflags 1.2.1 (registry+https://github.com/rust-lang/crates.io-index)" = "cf1de2fe8c75bc145a2f577add951f8134889b4795d47466a54a5c846d691693"
 "checksum bumpalo 3.4.0 (registry+https://github.com/rust-lang/crates.io-index)" = "2e8c087f005730276d1096a652e92a8bacee2e2472bcc9715a74d2bec38b5820"
@@ -1571,7 +1597,8 @@ dependencies = [
 "checksum cc 1.0.58 (registry+https://github.com/rust-lang/crates.io-index)" = "f9a06fb2e53271d7c279ec1efea6ab691c35a2ae67ec0d91d7acec0caf13b518"
 "checksum cfg-if 0.1.10 (registry+https://github.com/rust-lang/crates.io-index)" = "4785bdd1c96b2a846b2bd7cc02e86b6b3dbf14e7e53446c4f54c92a361040822"
 "checksum charred 0.3.3 (registry+https://github.com/rust-lang/crates.io-index)" = "1e01302bf6a3d92a90baa965f84a735938520ab9fd896f0694a71e8dec5405ce"
-"checksum chrono 0.4.13 (registry+https://github.com/rust-lang/crates.io-index)" = "c74d84029116787153e02106bf53e66828452a4b325cc8652b788b5967c0a0b6"
+"checksum chrono 0.4.15 (registry+https://github.com/rust-lang/crates.io-index)" = "942f72db697d8767c22d46a598e01f2d3b475501ea43d0db4f16d90259182d0b"
+"checksum chrono-english 0.1.4 (registry+https://github.com/rust-lang/crates.io-index)" = "4233ee19352739cfdcb5d7c2085005b166f6170ef2845ed9eef27a8fa5f95206"
 "checksum clap 2.33.2 (registry+https://github.com/rust-lang/crates.io-index)" = "10040cdf04294b565d9e0319955430099ec3813a64c952b86a41200ad714ae48"
 "checksum colored 1.9.3 (registry+https://github.com/rust-lang/crates.io-index)" = "f4ffc801dacf156c5854b9df4f425a626539c3a6ef7893cc0c5084a23f0b6c59"
 "checksum core-foundation 0.7.0 (registry+https://github.com/rust-lang/crates.io-index)" = "57d24c7a13c43e870e37c1556b74555437870a04514f7685f5b354e090567171"
@@ -1678,6 +1705,7 @@ dependencies = [
 "checksum ryu 1.0.5 (registry+https://github.com/rust-lang/crates.io-index)" = "71d301d4193d031abdd79ff7e3dd721168a9572ef3fe51a1517aba235bd8f86e"
 "checksum safemem 0.3.3 (registry+https://github.com/rust-lang/crates.io-index)" = "ef703b7cb59335eae2eb93ceb664c0eb7ea6bf567079d843e09420219668e072"
 "checksum same-file 1.0.6 (registry+https://github.com/rust-lang/crates.io-index)" = "93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502"
+"checksum scanlex 0.1.2 (registry+https://github.com/rust-lang/crates.io-index)" = "e6a2c84b697bc9496978f7457b17039a22b5d89c674964e8a480de4d5ddd55dc"
 "checksum schannel 0.1.19 (registry+https://github.com/rust-lang/crates.io-index)" = "8f05ba609c234e60bee0d547fe94a4c7e9da733d1c962cf6e59efa4cd9c8bc75"
 "checksum scopeguard 1.1.0 (registry+https://github.com/rust-lang/crates.io-index)" = "d29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd"
 "checksum security-framework 0.4.4 (registry+https://github.com/rust-lang/crates.io-index)" = "64808902d7d99f78eaddd2b4e2509713babc3dc3c85ad6f4c447680f3c01e535"

Cargo.toml

@@ -18,6 +18,8 @@ path = "src/main.rs"
 
 [dependencies]
 charred = "0.3.3"
+asciimath-rs = "0.5.7"
+bibliographix = "0.2.0"
 crossbeam-utils = "0.7.2"
 structopt = "0.3.14"
 minify = "1.1.1"
@@ -32,9 +34,8 @@ notify = "4.0.12"
 toml = "0.5.6"
 serde ="1.0.111"
 serde_derive = "1.0.111"
-asciimath-rs = "0.5.7"
 reqwest = {version = "0.10", features=["blocking"]}
 mime_guess = "2.0.3"
 mime = "0.3.16"
 base64 = "0.12.3"
-rayon = "1.3.1"
+rayon = "1.3.1"

src/elements/mod.rs

@@ -1,15 +1,18 @@
 pub mod tokens;
 
-use crate::references::bibliography::{BibEntry, BibReference, Bibliography};
+use crate::format::PlaceholderTemplate;
-use crate::references::configuration::Configuration;
+use crate::references::configuration::{ConfigRefEntry, Configuration};
 use crate::references::placeholders::ProcessPlaceholders;
 use crate::references::templates::{Template, TemplateVariable};
 use asciimath_rs::elements::special::Expression;
+use bibliographix::bib_manager::BibManager;
+use bibliographix::bibliography::bibliography_entry::BibliographyEntryReference;
+use bibliographix::references::bib_reference::BibRefAnchor;
 use std::collections::HashMap;
 use std::fs::read;
 use std::path::PathBuf;
 use std::sync::atomic::{AtomicBool, Ordering};
-use std::sync::{Arc, RwLock};
+use std::sync::{Arc, Mutex, RwLock};
 
 pub const SECTION: &str = "section";
 pub const PARAGRAPH: &str = "paragraph";
@@ -56,7 +59,7 @@ pub enum Line {
     Ruler(Ruler),
     Anchor(Anchor),
     Centered(Centered),
-    BibEntry(Arc<RwLock<BibEntry>>),
+    BibEntry(BibEntry),
 }
 
 #[derive(Clone, Debug)]
@@ -66,7 +69,7 @@ pub struct Document {
     pub(crate) path: Option<String>,
     pub(crate) placeholders: Vec<Arc<RwLock<Placeholder>>>,
     pub config: Configuration,
-    pub bibliography: Bibliography,
+    pub bibliography: BibManager,
     pub stylesheets: Vec<String>,
 }
 
@@ -284,7 +287,19 @@ impl Document {
             path: None,
             placeholders: Vec::new(),
             config: Configuration::default(),
-            bibliography: Bibliography::new(),
+            bibliography: BibManager::new(),
+            stylesheets: Vec::new(),
+        }
+    }
+
+    pub fn new_with_manager(is_root: bool, bibliography: BibManager) -> Self {
+        Self {
+            elements: Vec::new(),
+            is_root,
+            path: None,
+            placeholders: Vec::new(),
+            config: Configuration::default(),
+            bibliography,
             stylesheets: Vec::new(),
         }
     }
@@ -352,7 +367,6 @@ impl Document {
 
                     if let Some(doc) = &mut anchor.document {
                         self.placeholders.append(&mut doc.placeholders);
-                        self.bibliography.combine(&mut doc.bibliography);
                         doc.elements.reverse();
                         self.elements.append(&mut doc.elements);
                         anchor.document = None;
@@ -381,7 +395,7 @@ impl Document {
         self.postprocess_imports();
         if self.is_root {
             self.process_definitions();
-            self.bibliography.assign_entry_data();
+            self.bibliography.assign_entries_to_references();
             self.process_placeholders();
         }
     }
@@ -604,6 +618,7 @@ impl Placeholder {
 pub trait Metadata {
     fn get_bool(&self, key: &str) -> bool;
     fn get_string(&self, key: &str) -> Option<String>;
+    fn get_string_map(&self) -> HashMap<String, String>;
 }
 
 impl Metadata for InlineMetadata {
@@ -622,6 +637,21 @@ impl Metadata for InlineMetadata {
             None
         }
     }
+
+    fn get_string_map(&self) -> HashMap<String, String> {
+        let mut string_map = HashMap::new();
+        for (k, v) in &self.data {
+            match v {
+                MetadataValue::String(s) => string_map.insert(k.clone(), s.clone()),
+                MetadataValue::Bool(b) => string_map.insert(k.clone(), b.to_string()),
+                MetadataValue::Float(f) => string_map.insert(k.clone(), f.to_string()),
+                MetadataValue::Integer(i) => string_map.insert(k.clone(), i.to_string()),
+                _ => None,
+            };
+        }
+
+        string_map
+    }
 }
 
 impl Image {
@@ -650,3 +680,47 @@ impl Image {
         }
     }
 }
+
+#[derive(Clone, Debug)]
+pub struct BibEntry {
+    pub key: String,
+    pub entry: BibliographyEntryReference,
+}
+
+#[derive(Clone, Debug)]
+pub struct BibReference {
+    pub(crate) key: String,
+    pub(crate) entry_anchor: Arc<Mutex<BibRefAnchor>>,
+    pub(crate) display: Option<ConfigRefEntry>,
+}
+
+impl BibReference {
+    pub fn new(
+        key: String,
+        display: Option<ConfigRefEntry>,
+        anchor: Arc<Mutex<BibRefAnchor>>,
+    ) -> Self {
+        Self {
+            key: key.to_string(),
+            display,
+            entry_anchor: anchor,
+        }
+    }
+
+    pub(crate) fn get_formatted(&self) -> String {
+        if let Some(entry) = &self.entry_anchor.lock().unwrap().entry {
+            let entry = entry.lock().unwrap();
+            if let Some(display) = &self.display {
+                let display = display.read().unwrap();
+                let mut template = PlaceholderTemplate::new(display.get().as_string());
+                let mut value_map = HashMap::new();
+                value_map.insert("key".to_string(), entry.key());
+                template.set_replacements(value_map);
+                return template.render();
+            }
+            return format!("{}", entry.key());
+        }
+
+        return "citation needed".to_string();
+    }
+}

src/format/html.rs

@@ -1,7 +1,5 @@
 use crate::elements::*;
 use crate::format::PlaceholderTemplate;
-use crate::references::bibliography::{BibEntry, BibReference};
-use crate::references::configuration::Value;
 use crate::references::templates::{Template, TemplateVariable};
 use asciimath_rs::format::mathml::ToMathML;
 use htmlescape::{encode_attribute, encode_minimal};
@@ -43,7 +41,7 @@ impl ToHtml for Line {
             Line::Ruler(ruler) => ruler.to_html(),
             Line::Anchor(anchor) => anchor.to_html(),
             Line::Centered(centered) => centered.to_html(),
-            Line::BibEntry(bib) => bib.read().unwrap().to_html(),
+            Line::BibEntry(_) => "".to_string(),
         }
     }
 }
@@ -569,55 +567,6 @@ impl ToHtml for BibReference {
     }
 }
 
-impl ToHtml for BibEntry {
-    fn to_html(&self) -> String {
-        if !self.is_visible() {
-            return "".to_string();
-        }
-        if let Some(display) = &self.display {
-            let display = display.read().unwrap();
-            if let Value::Template(template) = display.get() {
-                let replacements = self
-                    .as_map()
-                    .iter()
-                    .map(|(k, v)| {
-                        (
-                            k.clone(),
-                            Element::Inline(Box::new(Inline::Plain(PlainText {
-                                value: v.clone(),
-                            }))),
-                        )
-                    })
-                    .collect();
-                return template
-                    .render(replacements)
-                    .iter()
-                    .fold("".to_string(), |a, b| format!("{}{}", a, b.to_html()));
-            }
-            let mut template = PlaceholderTemplate::new(display.get().as_string());
-            template.set_replacements(self.as_map());
-            format!(
-                "<span id='{}'>{}</span>",
-                encode_attribute(self.key.as_str()),
-                encode_minimal(template.render().as_str())
-            )
-        } else {
-            if let Some(url) = &self.url {
-                format!(
-                    "<a id={1} href='{0}'>{1}</a>",
-                    encode_attribute(url.as_str()),
-                    encode_minimal(self.key.as_str())
-                )
-            } else {
-                format!(
-                    "<span id='{0}'><u>{0}</u></span>",
-                    encode_attribute(self.key.as_str())
-                )
-            }
-        }
-    }
-}
-
 impl ToHtml for Template {
     fn to_html(&self) -> String {
         self.text

src/parser/inline.rs

@@ -1,11 +1,12 @@
 use super::{ParseError, ParseResult};
 use crate::elements::tokens::*;
+use crate::elements::BibReference;
 use crate::elements::*;
 use crate::parser::block::ParseBlock;
-use crate::references::bibliography::BibReference;
 use crate::references::configuration::keys::BIB_REF_DISPLAY;
 use crate::references::templates::{GetTemplateVariables, Template, TemplateVariable};
 use crate::Parser;
+use bibliographix::references::bib_reference::BibRef;
 use std::collections::HashMap;
 use std::sync::{Arc, RwLock};
 
@@ -301,13 +302,18 @@ impl ParseInline for Parser {
             self.ctm
                 .get_string_until_any_or_rewind(&[BIBREF_CLOSE], &[SPACE, LB], start_index)?;
         self.ctm.seek_one()?;
+        let bib_ref = BibRef::new(key.clone());
         let ref_entry = Arc::new(RwLock::new(BibReference::new(
             key,
             self.document.config.get_ref_entry(BIB_REF_DISPLAY),
+            bib_ref.anchor(),
         )));
         self.document
             .bibliography
-            .add_ref_entry(Arc::clone(&ref_entry));
+            .root_ref_anchor()
+            .lock()
+            .unwrap()
+            .insert(bib_ref);
 
         Ok(ref_entry)
     }

src/parser/line.rs

@@ -1,10 +1,13 @@
 use super::ParseResult;
 use crate::elements::tokens::*;
+use crate::elements::{BibEntry, Metadata};
 use crate::elements::{Cell, Centered, Header, Inline, Line, ListItem, Row, Ruler, TextLine};
 use crate::parser::inline::ParseInline;
-use crate::references::bibliography::BibEntry;
 use crate::Parser;
-use std::sync::{Arc, RwLock};
+use bibliographix::bibliography::bibliography_entry::BibliographyEntry;
+use bibliographix::bibliography::keys::{K_KEY, K_TYPE, K_URL, T_WEBSITE};
+use bibliographix::bibliography::FromHashMap;
+use std::collections::HashMap;
 
 pub(crate) trait ParseLine {
     fn parse_line(&mut self) -> ParseResult<Line>;
@@ -14,7 +17,7 @@ pub(crate) trait ParseLine {
     fn parse_centered(&mut self) -> ParseResult<Centered>;
     fn parse_ruler(&mut self) -> ParseResult<Ruler>;
     fn parse_text_line(&mut self) -> ParseResult<TextLine>;
-    fn parse_bib_entry(&mut self) -> ParseResult<Arc<RwLock<BibEntry>>>;
+    fn parse_bib_entry(&mut self) -> ParseResult<BibEntry>;
 }
 
 impl ParseLine for Parser {
@@ -174,7 +177,7 @@ impl ParseLine for Parser {
         }
     }
 
-    fn parse_bib_entry(&mut self) -> ParseResult<Arc<RwLock<BibEntry>>> {
+    fn parse_bib_entry(&mut self) -> ParseResult<BibEntry> {
         let start_index = self.ctm.get_index();
         self.ctm.seek_any(&INLINE_WHITESPACE)?;
         self.ctm.assert_char(&BIB_KEY_OPEN, Some(start_index))?;
@@ -188,18 +191,49 @@ impl ParseLine for Parser {
         self.ctm.seek_any(&INLINE_WHITESPACE)?;
 
         let entry = if let Ok(meta) = self.parse_inline_metadata() {
-            BibEntry::from_metadata(key, Box::new(meta), &self.document.config)
+            let mut string_map = meta.get_string_map();
+            string_map.insert(K_KEY.to_string(), key.clone());
+
+            if let Some(entry) = BibliographyEntry::from_hash_map(&string_map) {
+                *entry
+            } else {
+                eprintln!("Failed to parse bib entry with key {}", key);
+                return Err(self.ctm.rewind_with_error(start_index));
+            }
         } else {
             let url = self
                 .ctm
                 .get_string_until_any_or_rewind(&[LB], &[], start_index)?;
-            BibEntry::from_url(key, url, &self.document.config)
+            let mut map = HashMap::new();
+            map.insert(K_TYPE.to_string(), T_WEBSITE.to_string());
+            map.insert(K_URL.to_string(), url);
+            map.insert(K_KEY.to_string(), key.clone());
+
+            if let Some(entry) = BibliographyEntry::from_hash_map(&map) {
+                *entry
+            } else {
+                eprintln!("Failed to parse bib entry with key {}", key);
+                return Err(self.ctm.rewind_with_error(start_index));
+            }
         };
-        let entry_ref = Arc::new(RwLock::new(entry));
+
         self.document
             .bibliography
-            .add_bib_entry(Arc::clone(&entry_ref));
+            .entry_dictionary()
-
+            .lock()
-        Ok(entry_ref)
+            .unwrap()
+            .insert(entry);
+
+        Ok(BibEntry {
+            entry: self
+                .document
+                .bibliography
+                .entry_dictionary()
+                .lock()
+                .unwrap()
+                .get(&key)
+                .unwrap(),
+            key,
+        })
     }
 }

src/parser/mod.rs

@@ -5,6 +5,7 @@ pub(crate) mod line;
 use self::block::ParseBlock;
 use crate::elements::{Document, ImportAnchor};
 use crate::references::configuration::Configuration;
+use bibliographix::bib_manager::BibManager;
 use charred::tapemachine::{CharTapeMachine, TapeError, TapeResult};
 use colored::*;
 use crossbeam_utils::sync::WaitGroup;
@@ -42,6 +43,7 @@ impl Parser {
             Arc::new(Mutex::new(Vec::new())),
             false,
             Box::new(BufReader::new(f)),
+            BibManager::new(),
         ))
     }
 
@@ -58,17 +60,24 @@ impl Parser {
             Arc::new(Mutex::new(Vec::new())),
             false,
             Box::new(Cursor::new(text_bytes.to_vec())),
+            BibManager::new(),
         )
     }
 
     /// Creates a child parser from string text
-    pub fn child(text: String, path: PathBuf, paths: Arc<Mutex<Vec<PathBuf>>>) -> Self {
+    pub fn child(
+        text: String,
+        path: PathBuf,
+        paths: Arc<Mutex<Vec<PathBuf>>>,
+        bib_manager: BibManager,
+    ) -> Self {
         let text_bytes = text.as_bytes();
         Self::create(
             Some(PathBuf::from(path)),
             paths,
             true,
             Box::new(Cursor::new(text_bytes.to_vec())),
+            bib_manager,
         )
     }
 
@@ -76,6 +85,7 @@ impl Parser {
     pub fn child_from_file(
         path: PathBuf,
         paths: Arc<Mutex<Vec<PathBuf>>>,
+        bib_manager: BibManager,
     ) -> Result<Self, io::Error> {
         let f = File::open(&path)?;
         Ok(Self::create(
@@ -83,6 +93,7 @@ impl Parser {
             paths,
             true,
             Box::new(BufReader::new(f)),
+            bib_manager,
         ))
     }
 
@@ -91,6 +102,7 @@ impl Parser {
         paths: Arc<Mutex<Vec<PathBuf>>>,
         is_child: bool,
         mut reader: Box<dyn BufRead>,
+        bib_manager: BibManager,
     ) -> Self {
         if let Some(path) = path.clone() {
             paths.lock().unwrap().push(path.clone())
@@ -103,7 +115,7 @@ impl Parser {
             text.push('\n');
         }
 
-        let document = Document::new(!is_child);
+        let document = Document::new_with_manager(!is_child, bib_manager);
         Self {
             sections: Vec::new(),
             section_nesting: 0,
@@ -178,9 +190,10 @@ impl Parser {
         let wg = self.wg.clone();
         let paths = Arc::clone(&self.paths);
         let config = self.document.config.clone();
+        let bibliography = self.document.bibliography.create_child();
 
         let _ = thread::spawn(move || {
-            let mut parser = Parser::child_from_file(path, paths).unwrap();
+            let mut parser = Parser::child_from_file(path, paths, bibliography).unwrap();
             parser.set_config(config);
             let document = parser.parse();
             anchor_clone.write().unwrap().set_document(document);

src/references/bibliography.rs

@@ -1,200 +1 @@
-use crate::elements::Metadata;
-use crate::format::PlaceholderTemplate;
-use crate::references::configuration::keys::{BIB_DISPLAY, BIB_HIDE_UNUSED};
-use crate::references::configuration::{ConfigRefEntry, Configuration, Value};
-use std::collections::HashMap;
-use std::sync::{Arc, RwLock};
 
-const B_NUMBER: &str = "number";
-const B_AUTHOR: &str = "author";
-const B_DATE: &str = "date";
-const B_URL: &str = "url";
-const B_TITLE: &str = "title";
-const B_PUBLISHER: &str = "publisher";
-const B_NOTES: &str = "notes";
-
-#[derive(Clone, Debug)]
-pub struct BibEntry {
-    pub(crate) number: usize,
-    pub(crate) ref_count: usize,
-    pub key: String,
-    pub author: Option<String>,
-    pub date: Option<String>,
-    pub url: Option<String>,
-    pub title: Option<String>,
-    pub publisher: Option<String>,
-    pub notes: Option<String>,
-    pub display: Option<ConfigRefEntry>,
-    pub hide_unused: Option<ConfigRefEntry>,
-}
-
-#[derive(Clone, Debug)]
-pub struct BibReference {
-    pub(crate) key: String,
-    pub(crate) reference_entry: Option<Arc<RwLock<BibEntry>>>,
-    pub(crate) display: Option<ConfigRefEntry>,
-}
-
-#[derive(Clone, Debug)]
-pub struct Bibliography {
-    entries: HashMap<String, Arc<RwLock<BibEntry>>>,
-    references: Vec<Arc<RwLock<BibReference>>>,
-}
-
-impl BibEntry {
-    pub fn as_map(&self) -> HashMap<String, String> {
-        let mut map = HashMap::new();
-        map.insert(B_NUMBER.to_string(), format!("{}", self.number));
-        map.insert("key".to_string(), self.key.clone());
-        if let Some(author) = &self.author {
-            map.insert(B_AUTHOR.to_string(), author.clone());
-        }
-        if let Some(date) = &self.date {
-            map.insert(B_DATE.to_string(), date.clone());
-        }
-        if let Some(url) = &self.url {
-            map.insert(B_URL.to_string(), url.clone());
-        }
-        if let Some(title) = &self.title {
-            map.insert(B_TITLE.to_string(), title.clone());
-        }
-        if let Some(publisher) = &self.publisher {
-            map.insert(B_PUBLISHER.to_string(), publisher.clone());
-        }
-        if let Some(notes) = &self.notes {
-            map.insert(B_NOTES.to_string(), notes.clone());
-        }
-
-        map
-    }
-
-    pub fn from_metadata(key: String, data: Box<dyn Metadata>, config: &Configuration) -> Self {
-        BibEntry {
-            number: 0,
-            ref_count: 0,
-            key,
-            author: data.get_string(B_AUTHOR),
-            date: data.get_string(B_DATE),
-            url: data.get_string(B_URL),
-            title: data.get_string(B_TITLE),
-            publisher: data.get_string(B_PUBLISHER),
-            notes: data.get_string(B_NOTES),
-            display: config.get_ref_entry(BIB_DISPLAY),
-            hide_unused: config.get_ref_entry(BIB_HIDE_UNUSED),
-        }
-    }
-
-    pub fn from_url(key: String, url: String, config: &Configuration) -> Self {
-        BibEntry {
-            number: 0,
-            ref_count: 0,
-            key,
-            author: None,
-            date: None,
-            url: Some(url),
-            title: None,
-            publisher: None,
-            notes: None,
-            display: config.get_ref_entry(BIB_DISPLAY),
-            hide_unused: config.get_ref_entry(BIB_HIDE_UNUSED),
-        }
-    }
-
-    pub fn set_number(&mut self, number: usize) {
-        self.number = number
-    }
-
-    pub fn set_ref_count(&mut self, number: usize) {
-        self.ref_count = number
-    }
-
-    pub fn is_visible(&self) -> bool {
-        if let Some(hide_cfg) = &self.hide_unused {
-            let hide_cfg = hide_cfg.read().unwrap();
-            if let Value::Bool(b) = hide_cfg.get() {
-                if *b && self.ref_count == 0 {
-                    return false;
-                }
-            }
-        }
-
-        true
-    }
-}
-
-impl BibReference {
-    pub fn new(key: String, display: Option<ConfigRefEntry>) -> Self {
-        Self {
-            key: key.to_string(),
-            display,
-            reference_entry: None,
-        }
-    }
-
-    /// sets the reference to the bib entry
-    pub(crate) fn set_entry(&mut self, entry: Arc<RwLock<BibEntry>>) {
-        self.reference_entry = Some(entry)
-    }
-
-    pub(crate) fn get_formatted(&self) -> String {
-        if let Some(entry) = &self.reference_entry {
-            let entry = entry.read().unwrap();
-            if let Some(display) = &self.display {
-                let display = display.read().unwrap();
-                let mut template = PlaceholderTemplate::new(display.get().as_string());
-                template.set_replacements(entry.as_map());
-                return template.render();
-            }
-            return format!("{}", entry.number);
-        }
-
-        return "citation needed".to_string();
-    }
-}
-
-impl Bibliography {
-    pub fn new() -> Self {
-        Self {
-            entries: HashMap::new(),
-            references: Vec::new(),
-        }
-    }
-
-    pub(crate) fn assign_entry_data(&mut self) {
-        let mut count = 0;
-        self.references.iter().for_each(|e| {
-            let mut reference = e.write().unwrap();
-            if let Some(entry) = self.entries.get(&reference.key) {
-                {
-                    let mut entry_raw = entry.write().unwrap();
-                    let ref_count = entry_raw.ref_count;
-                    entry_raw.set_ref_count(ref_count + 1);
-                }
-                reference.set_entry(Arc::clone(entry));
-            }
-        });
-        self.entries.iter().for_each(|(_, e)| {
-            let mut entry = e.write().unwrap();
-            if entry.is_visible() {
-                count += 1;
-                entry.set_number(count)
-            }
-        });
-    }
-
-    pub fn add_ref_entry(&mut self, entry: Arc<RwLock<BibReference>>) {
-        self.references.push(entry)
-    }
-
-    pub fn add_bib_entry(&mut self, entry: Arc<RwLock<BibEntry>>) {
-        let key = entry.read().unwrap().key.clone();
-        self.entries.insert(key, entry);
-    }
-
-    pub fn combine(&mut self, other: &mut Bibliography) {
-        let other_entries = other.entries.clone();
-        other.entries = HashMap::new();
-        self.entries.extend(other_entries.into_iter());
-        self.references.append(&mut other.references);
-    }
-}

src/references/configuration/default.toml

@@ -1,4 +1,4 @@
 [bibliography]
 entry_display = "{{number}}: {{author}} - {{title}} - {{date}} - {{url}}"
-reference_display = "{{number}}"
+reference_display = "{{key}}"
 hide_unused = true