check for file before grabbing json file from github

src/utils/af_utils.rs

@@ -167,12 +167,35 @@ pub fn add_chemistry_to_args_piscem(chem_str: &str, cmd: &mut std::process::Comm
 }
 
 pub fn get_permit_if_absent(af_home: &Path, chem: &Chemistry) -> Result<PermitListResult> {
+    // check if the file already exists
+    let odir = af_home.join("plist");
+    match chem {
+        Chemistry::TenxV2 => {
+            let chem_file = "10x_v2_permit.txt";
+            if odir.join(chem_file).exists() {
+                return Ok(PermitListResult::AlreadyPresent(odir.join(chem_file)));
+            }
+        }
+        Chemistry::TenxV3 => {
+            let chem_file = "10x_v3_permit.txt";
+            if odir.join(chem_file).exists() {
+                return Ok(PermitListResult::AlreadyPresent(odir.join(chem_file)));
+            }
+        }
+        _ => {
+            return Ok(PermitListResult::UnregisteredChemistry);
+        }
+    }
+
+    // the file doesn't exist, so get the json file that gives us
+    // the chemistry name to permit list URL mapping.
     let permit_dict_url = "https://raw.githubusercontent.com/COMBINE-lab/simpleaf/dev/resources/permit_list_info.json";
     let permit_dict: serde_json::Value = minreq::get(permit_dict_url)
         .send()?
         .json::<serde_json::Value>()?;
     let opt_chem_file: Option<String>;
     let opt_dl_url: Option<String>;
+    // parse the JSON appropriately based on the chemistry we have
     match chem {
         Chemistry::TenxV2 => {
             if let Some(d) = permit_dict.get("10xv2") {
@@ -219,8 +242,8 @@ pub fn get_permit_if_absent(af_home: &Path, chem: &Chemistry) -> Result<PermitLi
         }
     }
 
+    // actually download the permit list if we need it and don't have it.
     if let (Some(chem_file), Some(dl_url)) = (opt_chem_file, opt_dl_url) {
-        let odir = af_home.join("plist");
         if odir.join(&chem_file).exists() {
             Ok(PermitListResult::AlreadyPresent(odir.join(&chem_file)))
         } else {

src/utils/prog_utils.rs

@@ -7,7 +7,7 @@ use std::ffi::{OsStr, OsString};
 use std::path::{Path, PathBuf};
 use std::process::Command;
 use std::sync::Once;
-use tracing::{error, info};
+use tracing::{debug, error, info};
 use which::which;
 
 // The below functions are taken from the [`execute`](https://crates.io/crates/execute)
@@ -50,10 +50,20 @@ pub fn shell<S: AsRef<OsStr>>(cmd: S) -> Command {
 
 pub fn download_to_file<T: AsRef<str>>(url: T, filename: &str) -> Result<()> {
     let url = url.as_ref();
+
+    debug!(
+        "Downloading file from {} and writing to file {}",
+        url, filename
+    );
+
     let request = minreq::get(url).with_timeout(120).send()?;
     match request.status_code {
         200..=299 => {
             // success
+            debug!(
+                "Obtained status code {} from final url {}",
+                request.status_code, request.url
+            );
         }
         x => {
             bail!(