address code review

protos/mehari/txs.proto

@@ -17,30 +17,38 @@ message SequenceDb {
     repeated string seqs = 3;
 }
 
+// Indicates the reference assembly of the transcript database.
 enum Assembly {
+    // Unknown.
     ASSEMBLY_UNKNOWN = 0;
+    // GRCh37.
     ASSEMBLY_GRCH37 = 1;
+    // GRCh38.
     ASSEMBLY_GRCH38 = 2;
 }
 
+// Indicates the transcript source.
 enum Source {
+    // Unknown.
     SOURCE_UNKNOWN = 0;
+    // RefSeq.
     SOURCE_REFSEQ = 1;
+    // Ensembl.
     SOURCE_ENSEMBL = 2;
 }
 
 message SourceVersion {
-    // Version of mehari used to build the database
+    // Version of mehari used to build the database.
     string mehari_version = 1;
-    // Assembly used, either GRCh37 or GRCh38 (or Unknown)
+    // Assembly used, either GRCh37 or GRCh38 (or Unknown).
     Assembly assembly = 2;
-    // Version of the assembly, optional
+    // Version of the assembly, optional.
     optional string assembly_version = 3;
-    // Source, either RefSeq or Ensembl (or Unknown)
-    Source source = 4;
-    // Version of the source, e.g. 112 for Ensembl
+    // Source, either RefSeq or Ensembl (or Unknown).
+    Source source_name = 4;
+    // Version of the source, e.g. 112 for Ensembl.
     string source_version = 5;
-    // Version of cdot
+    // Version of cdot.
     string cdot_version = 6;
 }
 
@@ -182,8 +190,6 @@ message TxSeqDatabase {
     SequenceDb seq_db = 2;
     // The version of the database.
     optional string version = 3;
-//    // The reference assembly that this database refers to. Removed in favour of source_version
-//    optional string genome_release = 4;
     // Version information; allow repeated here to be able to keep track of information when merging databases
     repeated SourceVersion source_version = 5;
 }

src/db/create/mod.rs

@@ -58,6 +58,7 @@ pub struct Args {
     pub transcript_source_version: Option<String>,
 
     /// Version of cdot data.
+    #[arg(long)]
     pub cdot_version: String,
 
     /// Path to output protobuf file to write to.
@@ -91,10 +92,14 @@ pub struct Args {
     pub threads: usize,
 }
 
+/// Source of the transcripts.
 #[derive(Debug, Clone, Copy, ValueEnum)]
 pub enum TxSource {
+    /// RefSeq.
     RefSeq,
+    /// Ensembl.
     Ensembl,
+    /// Other.
     Other,
 }
 
@@ -1759,7 +1764,7 @@ pub fn run(common: &crate::common::Args, args: &Args) -> Result<(), Error> {
 
         let assembly_version = args.assembly_version.clone();
 
-        let source = match args.transcript_source {
+        let source_name = match args.transcript_source {
             TxSource::RefSeq => Source::Refseq,
             TxSource::Ensembl => Source::Ensembl,
             TxSource::Other => Source::Unknown,
@@ -1772,7 +1777,7 @@ pub fn run(common: &crate::common::Args, args: &Args) -> Result<(), Error> {
             mehari_version: crate::common::version().to_string(),
             assembly: i32::from(assembly),
             assembly_version,
-            source: i32::from(source),
+            source_name: i32::from(source_name),
             source_version,
             cdot_version,
         }

src/db/merge.rs

@@ -31,8 +31,7 @@ pub fn merge_transcript_databases(
         assert!(first.source_version.iter().map(|v| v.assembly).all_equal());
         let assembly = first
             .source_version
-            .iter()
-            .next()
+            .first()
             .expect("At least one source_version entry expected")
             .assembly;
         assert!(others