update entrypoint to match new server run cli

varfish-org · tedil · Jan 30, 2025 · Nov 28, 2024 · Dec 16, 2024 · Dec 16, 2024
commit f1c010fe8dd74330d1293c47153e38ba35b4cb78
diff --git a/utils/docker/entrypoint.sh b/utils/docker/entrypoint.sh
@@ -7,16 +7,23 @@ set -euo pipefail
 #
 #   PATH_DB         -- path to the database directory containing,
 #                      e.g., `grch3{7,8}/*.zst`.
-#                      default: /data/hpo
+#                      default: /data/mehari/db
 #   HTTP_HOST       -- host to listen on
 #                      default: 0.0.0.0
 #   HTTP_PORT       -- port
 #                      default: 8080
 
-PATH_DB=${PATH_DB-/data/mehari}
+PATH_DB=${PATH_DB-/data/mehari/db}
 HTTP_HOST=${HTTP_HOST-0.0.0.0}
 HTTP_PORT=${HTTP_PORT-8080}
 
+PATH_TRANSCRIPTS_37=$PATH_DB/grch37/seqvars/txs.bin.zst
+PATH_TRANSCRIPTS_38=$PATH_DB/grch38/seqvars/txs.bin.zst
+PATH_FREQUENCIES_37=$PATH_DB/grch37/seqvars/freqs
+PATH_FREQUENCIES_38=$PATH_DB/grch38/seqvars/freqs
+PATH_CLINVAR_37=$PATH_DB/grch37/seqvars/clinvar
+PATH_CLINVAR_38=$PATH_DB/grch38/seqvars/clinvar
+
 first=${1-}
 
 if [ "$first" == exec ]; then
@@ -26,7 +33,12 @@ else
   exec \
     mehari \
     server run \
-      --path-db "$PATH_DB" \
+      $(test -e "$PATH_TRANSCRIPTS_37" && echo --transcripts "$PATH_TRANSCRIPTS_37") \
+      $(test -e "$PATH_TRANSCRIPTS_38" && echo --transcripts "$PATH_TRANSCRIPTS_38") \
+      $(test -e "$PATH_FREQUENCIES_37" && echo --frequencies "$PATH_FREQUENCIES_37") \
+      $(test -e "$PATH_FREQUENCIES_38" && echo --frequencies "$PATH_FREQUENCIES_38") \
+      $(test -e "$PATH_CLINVAR_37" && echo --clinvar "$PATH_CLINVAR_37") \
+      $(test -e "$PATH_CLINVAR_38" && echo --clinvar "$PATH_CLINVAR_38") \
       --listen-host "$HTTP_HOST" \
       --listen-port "$HTTP_PORT"
 fi

diff --git a/src/verify/seqvars.rs b/src/verify/seqvars.rs
    /// Path to the input TSV file.
    #[arg(long)]
    pub path_input_tsv: String,
    /// Path to the reference FASTA file.

    #[arg(long)]
    pub path_reference_fasta: String,
    /// Path to output TSV file.

    #[arg(long)]
    pub path_output_tsv: String,

diff --git a/src/db/subset/mod.rs b/src/db/subset/mod.rs

 fn _extract_transcripts_by_txid(
    container_tx_db: &TranscriptDb,
    transcript_ids: &Vec<String>,
 ) -> (IndexSet<usize>, IndexSet<String>, IndexSet<String>) {
    let transcript_ids = IndexSet::<String>::from_iter(transcript_ids.iter().cloned());
    let (tx_idxs, gene_ids) = __extract_transcripts_from_db(container_tx_db, &transcript_ids);

 fn _extract_transcripts_by_hgnc_id(
    container_tx_db: &TranscriptDb,
    gene_symbols: &Vec<String>,
 ) -> Result<(IndexSet<usize>, IndexSet<String>, IndexSet<String>)> {
    let hgnc_ids = IndexSet::<String>::from_iter(gene_symbols.iter().cloned());
    let mut tx_idxs = Vec::new();
diff --git a/src/annotate/seqvars/mod.rs b/src/annotate/seqvars/mod.rs
 }

 pub(crate) fn load_transcript_dbs_for_assembly(
    tx_sources: &Vec<String>,
    assembly: Option<Assembly>,
 ) -> Result<Vec<TxSeqDatabase>, Error> {
    let pb_assembly = assembly.as_ref().and_then(proto_assembly_from);
	/// Path to the input TSV file.
	#[arg(long)]
	pub path_input_tsv: String,
	/// Path to the reference FASTA file.

Check warning on line 33 in src/verify/seqvars.rs GitHub Actions / clippy empty line after doc comment warning: empty line after doc comment --> src/verify/seqvars.rs:32:5 \| 32 \| / /// Path to the reference FASTA file. 33 \| \| \| \|_ \| = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#empty_line_after_doc_comments = note: `#[warn(clippy::empty_line_after_doc_comments)]` on by default = help: if the empty line is unintentional remove it
	#[arg(long)]
	pub path_reference_fasta: String,
	/// Path to output TSV file.

Check warning on line 37 in src/verify/seqvars.rs GitHub Actions / clippy empty line after doc comment `warning: empty line after doc comment --> src/verify/seqvars.rs:36:5 \| 36 \| / /// Path to output TSV file. 37 \| \| \| \|_ \| = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#empty_line_after_doc_comments = help: if the empty line is unintentional remove it`
	#[arg(long)]
	pub path_output_tsv: String,

	fn _extract_transcripts_by_txid(
	container_tx_db: &TranscriptDb,
	transcript_ids: &Vec<String>,
Check warning on line 228 in src/db/subset/mod.rs GitHub Actions / clippy writing `&Vec` instead of `&[_]` involves a new object where a slice will do warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do --> src/db/subset/mod.rs:228:21 \| 228 \| transcript_ids: &Vec<String>, \| ^^^^^^^^^^^^ help: change this to: `&[String]` \| = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
	) -> (IndexSet<usize>, IndexSet<String>, IndexSet<String>) {
	let transcript_ids = IndexSet::<String>::from_iter(transcript_ids.iter().cloned());
	let (tx_idxs, gene_ids) = __extract_transcripts_from_db(container_tx_db, &transcript_ids);

	fn _extract_transcripts_by_hgnc_id(
	container_tx_db: &TranscriptDb,
	gene_symbols: &Vec<String>,
Check warning on line 241 in src/db/subset/mod.rs GitHub Actions / clippy writing `&Vec` instead of `&[_]` involves a new object where a slice will do warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do --> src/db/subset/mod.rs:241:19 \| 241 \| gene_symbols: &Vec<String>, \| ^^^^^^^^^^^^ help: change this to: `&[String]` \| = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
	) -> Result<(IndexSet<usize>, IndexSet<String>, IndexSet<String>)> {
	let hgnc_ids = IndexSet::<String>::from_iter(gene_symbols.iter().cloned());
	let mut tx_idxs = Vec::new();
	}

	pub(crate) fn load_transcript_dbs_for_assembly(
	tx_sources: &Vec<String>,
Check warning on line 2119 in src/annotate/seqvars/mod.rs GitHub Actions / clippy writing `&Vec` instead of `&[_]` involves a new object where a slice will do warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do --> src/annotate/seqvars/mod.rs:2119:17 \| 2119 \| tx_sources: &Vec<String>, \| ^^^^^^^^^^^^ help: change this to: `&[String]` \| = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg = note: `#[warn(clippy::ptr_arg)]` on by default
	assembly: Option<Assembly>,
	) -> Result<Vec<TxSeqDatabase>, Error> {
	let pb_assembly = assembly.as_ref().and_then(proto_assembly_from);