refactor: update field name and tests

Ebedthan · Jun 25, 2024 · fdb92d5 · fdb92d5
1 parent cd9e64b
commit fdb92d5
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Showing 6 changed files with 15 additions and 49 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "xgt"
-version = "0.3.0"
+version = "0.4.0"
 edition = "2021"
 authors = ["Anicet Ebou <anicet.ebou@gmail.com>"]
 description = "xgt enables efficient querying and parsing of GTDB data"

diff --git a/README.md b/README.md
@@ -26,10 +26,10 @@ xgt -h
 ```
 # Search subcommand: search GTDB
 ## Search all Escherichia (genus) genomes
-xgt search Escherichia
+xgt search g__Escherichia
 
-## Search all genomes with genus name containing escherichia
-xgt search --partial escherichia
+## Search all genomes with genus name containing Escherichia
+xgt search --partial g__Escherichia -o output.json
 
 ## Search from a list
 xgt search -f list.txt
@@ -63,8 +63,6 @@ Full help is available from `xgt --help`.
 To tell `xgt` to _not_ verify the peer, use the `-k/--insecure` option.
 Currently (as of Apr 28, 2024), you should add this option to your command to get the desired result as GTDB API's server has a certificate issue.
 
-
-
 ## Minimum supported Rust version
 `xgt` minimum [Rust](https://www.rust-lang.org/) version is 1.70.0.
 

diff --git a/src/app.rs b/src/app.rs
@@ -21,41 +21,30 @@ pub fn build_app() -> Command {
                         .short('c')
                         .long("count")
                         .action(ArgAction::SetTrue)
-                        .help("Count the number of genomes"),
+                        .help("count the number of genomes"),
                 )
                 .arg(
                     Arg::new("id")
                         .short('i')
                         .long("id")
                         .action(ArgAction::SetTrue)
-                        .help("Print only genome ID"),
+                        .help("only print genome id"),
                 )
                 .arg(
                     Arg::new("field")
                         .short('F')
                         .long("field")
                         .value_name("STR")
-                        .default_value("gtdb_tax")
-                        .value_parser(["all", "gtdb_tax", "ncbi_tax", "ncbi_org", "ncbi_id"])
-                        .help("Search field"),
+                        .default_value("gtdb")
+                        .value_parser(["gtdb", "ncbi"])
+                        .help("which taxonomy to search"),
                 )
                 .arg(
                     Arg::new("file")
                         .short('f')
                         .long("file")
                         .value_name("FILE")
-                        .help("Search from name in FILE"),
-                )
-                .arg(
-                    Arg::new("level")
-                        .short('l')
-                        .long("level")
-                        .value_name("STR")
-                        .help("Taxon level to search")
-                        .default_value("genus")
-                        .value_parser([
-                            "species", "genus", "family", "order", "class", "phylum", "domain",
-                        ]),
+                        .help("search from name in FILE"),
                 )
                 .arg(
                     Arg::new("out")
@@ -267,20 +256,14 @@ mod tests {
     fn test_app() {
         std::env::set_var("NO_COLOR", "true");
         let app = build_app();
-        let args = vec![
-            "xgt", "search", "p__taxon", "-l", "class", "--count", "--raw",
-        ];
+        let args = vec!["xgt", "search", "p__taxon", "--count", "--raw"];
         let matches = app.get_matches_from(args);
         assert_eq!(matches.subcommand_name(), Some("search"));
         let submatches = matches.subcommand_matches("search").unwrap();
         assert_eq!(
             submatches.get_one::<String>("name"),
             Some(&"p__taxon".to_owned())
         );
-        assert_eq!(
-            submatches.get_one::<String>("level"),
-            Some(&"class".to_owned())
-        );
         assert!(submatches.get_flag("count"));
         assert!(submatches.get_flag("raw"));
     }
@@ -291,16 +274,14 @@ mod tests {
             "xgt",
             "search",
             "p__taxon",
-            "-l",
-            "class",
             "--count",
             "--raw",
             "--id",
             "--partial",
             "--rep",
             "--type",
             "--field",
-            "ncbi_tax",
+            "ncbi",
         ]);
         let subcommand_parser = arg_parser.subcommand_matches("search").unwrap();
         assert!(subcommand_parser.get_flag("count"));
@@ -313,13 +294,9 @@ mod tests {
             subcommand_parser.get_one::<String>("name"),
             Some(&"p__taxon".to_owned())
         );
-        assert_eq!(
-            subcommand_parser.get_one::<String>("level"),
-            Some(&"class".to_owned())
-        );
         assert_eq!(
             subcommand_parser.get_one::<String>("field"),
-            Some(&"ncbi_tax".to_owned())
+            Some(&"ncbi".to_owned())
         );
     }
 

diff --git a/src/main.rs b/src/main.rs
@@ -52,16 +52,13 @@ fn handle_taxon_command(sub_matches: &clap::ArgMatches) -> Result<()> {
     Ok(())
 }
 
-/*
 #[cfg(test)]
 mod tests {
     use super::*;
     use std::ffi::OsString;
 
     #[test]
     fn test_search_command() {
-        let needle = vec!["Aminobacter".to_string(), "Rhizobium".to_string()];
-        let level = "phylum".to_string();
         let id = true;
         let count = true;
         let raw = true;
@@ -73,8 +70,6 @@ mod tests {
             OsString::from("search"),
             OsString::from("--file"),
             OsString::from("test/test.txt"),
-            OsString::from("--level"),
-            OsString::from(level.clone()),
             OsString::from("--id"),
             OsString::from("--partial"),
             OsString::from("--count"),
@@ -88,8 +83,6 @@ mod tests {
         let args =
             utils::SearchArgs::from_arg_matches(matches.subcommand_matches("search").unwrap());
 
-        assert_eq!(args.get_needle(), needle);
-        assert_eq!(args.get_level(), level);
         assert_eq!(args.get_gid(), id);
         assert_eq!(args.get_count(), count);
         assert_eq!(args.get_raw(), raw);
@@ -115,4 +108,3 @@ mod tests {
         assert_eq!(args.output, Some(String::from("met.json")));
     }
 }
-*/
diff --git a/test/test.txt b/test/test.txt
@@ -1,2 +1 @@
-Aminobacter
-Rhizobium
+g__Aminobacter