feat: add -k option and some optimizations

Ebedthan · Apr 28, 2024 · bd086be · bd086be
1 parent 128a185
commit bd086be
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Showing 9 changed files with 401 additions and 137 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 = "0.1.0"
+version = "0.3.0"
 edition = "2021"
 authors = ["Anicet Ebou <anicet.ebou@gmail.com>"]
 description = "xgt enables efficient querying and parsing of GTDB data"
@@ -14,7 +14,8 @@ anyhow = "1.0.69"
 clap = "4.1.8"
 serde = { version ="1.0.153", features = ["derive"] }
 serde_json = "1.0.94"
-ureq = { version = "2.6.2", features = ["json"] }
+ureq = { version = "2.6.2", features = ["json", "native-tls"] }
+native-tls = "0.2"
 
 [dev-dependencies]
 mockito = "1.0.2"

diff --git a/README.md b/README.md
@@ -57,6 +57,12 @@ xgt taxon --search --partial g__Escherichia
 
 Full help is available from `xgt --help`.
 
+## Certificate verification
+
+`xgt` through `ureq` performs peer SSL certificate verification by default. 
+To tell `xgt` to _not_ verify the peer, use `-k/--insecure` option.
+Currently (as of Apr 28, 2024), you should add this options to your command to get the desired result as the GTDB API have 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
@@ -85,6 +85,13 @@ pub fn build_app() -> Command {
                         .long("type")
                         .action(ArgAction::SetTrue)
                         .help("Search NCBI type material only"),
+                )
+                .arg(
+                    Arg::new("insecure")
+                        .short('k')
+                        .long("insecure")
+                        .help("Disable SSL certificate verification")
+                        .action(ArgAction::SetTrue),
                 ),
         )
         .subcommand(
@@ -131,6 +138,13 @@ pub fn build_app() -> Command {
                         .help("Output raw JSON")
                         .value_name("FILE")
                         .value_parser(is_existing),
+                )
+                .arg(
+                    Arg::new("insecure")
+                        .short('k')
+                        .long("insecure")
+                        .help("Disable SSL certificate verification")
+                        .action(ArgAction::SetTrue),
                 ),
         )
         .subcommand(
@@ -198,6 +212,13 @@ pub fn build_app() -> Command {
                         .long("reps")
                         .action(ArgAction::SetTrue)
                         .help("Set taxon V genomes search to lookup reps seqs only"),
+                )
+                .arg(
+                    Arg::new("insecure")
+                        .short('k')
+                        .long("insecure")
+                        .help("Disable SSL certificate verification")
+                        .action(ArgAction::SetTrue),
                 ),
         )
 }