From 6b1d1bb9a4af461f2bd428287989f35429ecb45b Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Wed, 21 Aug 2024 06:39:18 -0700
Subject: [PATCH 01/42] make error catchable

---
 src/core/src/index/revindex/mod.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/core/src/index/revindex/mod.rs b/src/core/src/index/revindex/mod.rs
index aac0d47c14..3345424fdf 100644
--- a/src/core/src/index/revindex/mod.rs
+++ b/src/core/src/index/revindex/mod.rs
@@ -186,7 +186,7 @@ impl RevIndex {
 
     pub fn open<P: AsRef<Path>>(index: P, read_only: bool, spec: Option<&str>) -> Result<Self> {
         let opts = db_options();
-        let cfs = DB::list_cf(&opts, index.as_ref()).unwrap();
+        let cfs = DB::list_cf(&opts, index.as_ref())?;
 
         if cfs.into_iter().any(|c| c == COLORS) {
             // TODO: ColorRevIndex can't be read-only for now,

From 7e73e8ffd9caabb29085e192740d5d8761a1b38c Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Wed, 21 Aug 2024 07:03:04 -0700
Subject: [PATCH 02/42] flag another problematic unwrap

---
 src/core/src/storage/mod.rs | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index 12f456fc22..6791b7219b 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -657,7 +657,8 @@ impl Storage for MemStorage {
     }
 
     fn load_sig(&self, path: &str) -> Result<SigStore> {
-        Ok(self.sigs.read().unwrap().get(path).unwrap().clone())
+        let x = self.sigs.read().unwrap(); // @CTB this is causing a problem
+        Ok(x.get(path).unwrap().clone())
     }
 
     fn save_sig(&self, path: &str, sig: Signature) -> Result<String> {

From 2896c496231801f2d53a525e914396be529b256f Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Wed, 21 Aug 2024 07:11:14 -0700
Subject: [PATCH 03/42] more

---
 src/core/src/storage/mod.rs | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index 6791b7219b..714fb63162 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -657,8 +657,11 @@ impl Storage for MemStorage {
     }
 
     fn load_sig(&self, path: &str) -> Result<SigStore> {
-        let x = self.sigs.read().unwrap(); // @CTB this is causing a problem
-        Ok(x.get(path).unwrap().clone())
+        let x = self.sigs.read().unwrap();
+        match x.get(path) {
+            Some(path) => Ok(path.clone()),
+            None => panic!("cannot get path")
+        }
     }
 
     fn save_sig(&self, path: &str, sig: Signature) -> Result<String> {

From 45b1a8ff2f24e4742c9457bc388b5e9a1fd637f9 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Wed, 21 Aug 2024 07:12:58 -0700
Subject: [PATCH 04/42] more

---
 src/core/src/storage/mod.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index 714fb63162..856f8ff210 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -660,7 +660,7 @@ impl Storage for MemStorage {
         let x = self.sigs.read().unwrap();
         match x.get(path) {
             Some(path) => Ok(path.clone()),
-            None => panic!("cannot get path")
+            None => panic!("cannot get path '{path}'")
         }
     }
 

From e8d79994745186b3be01c86fbf3a9a2e1e953aa6 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Wed, 21 Aug 2024 07:43:29 -0700
Subject: [PATCH 05/42] upd log message

---
 src/core/src/index/revindex/disk_revindex.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/core/src/index/revindex/disk_revindex.rs b/src/core/src/index/revindex/disk_revindex.rs
index 511bdbcc4c..ac36c5b626 100644
--- a/src/core/src/index/revindex/disk_revindex.rs
+++ b/src/core/src/index/revindex/disk_revindex.rs
@@ -114,7 +114,7 @@ impl RevIndex {
 
         info!("Compact SSTs");
         index.compact();
-        info!("Processed {} reference sigs", processed_sigs.into_inner());
+        info!("Done! Processed {} reference sigs", processed_sigs.into_inner());
 
         Ok(module::RevIndex::Plain(index))
     }

From 53bcf0274f4b7bdec81077b44591af3a932a0270 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Wed, 21 Aug 2024 08:10:04 -0700
Subject: [PATCH 06/42] provide correct error

---
 src/core/src/collection.rs | 3 +--
 src/core/src/errors.rs     | 5 +++++
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index bc03274c41..38312f6de1 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -121,8 +121,7 @@ impl Collection {
             .zip(other.iter())
             .all(|((id1, rec1), (id2, rec2))| id1 == id2 && rec1 == rec2)
             .then(|| self.len())
-            // TODO: right error here
-            .ok_or(Error::MismatchKSizes)
+            .ok_or(Error::CollectionNotSuperset)
     }
 
     pub fn from_zipfile<P: AsRef<Path>>(zipfile: P) -> Result<Self> {
diff --git a/src/core/src/errors.rs b/src/core/src/errors.rs
index 90c028eb38..1a61a07041 100644
--- a/src/core/src/errors.rs
+++ b/src/core/src/errors.rs
@@ -49,6 +49,9 @@ pub enum SourmashError {
     #[error("error while calculating ANI confidence intervals: {message}")]
     ANIEstimationError { message: String },
 
+    #[error("collection is not a superset")]
+    CollectionNotSuperset,
+
     #[error(transparent)]
     ReadDataError(#[from] ReadDataError),
 
@@ -104,6 +107,7 @@ pub enum SourmashErrorCode {
     NonEmptyMinHash = 1_06,
     MismatchNum = 1_07,
     NeedsAbundanceTracking = 1_08,
+    CollectionNotSuperset = 1_09,
     // Input sequence errors
     InvalidDNA = 11_01,
     InvalidProt = 11_02,
@@ -155,6 +159,7 @@ impl SourmashErrorCode {
             SourmashError::NifflerError { .. } => SourmashErrorCode::NifflerError,
             SourmashError::Utf8Error { .. } => SourmashErrorCode::Utf8Error,
             SourmashError::CsvError { .. } => SourmashErrorCode::CsvError,
+            SourmashError::CollectionNotSuperset { .. } => SourmashErrorCode::CollectionNotSuperset,
 
             #[cfg(not(target_arch = "wasm32"))]
             #[cfg(feature = "branchwater")]

From d467d9f16a75134d5b3d9c0683ebc52df5659690 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Thu, 22 Aug 2024 08:28:36 -0700
Subject: [PATCH 07/42] switch Manifest from paths to TryFrom

---
 src/core/src/collection.rs |  4 +++-
 src/core/src/manifest.rs   | 29 ++++++++++++++++++++---------
 2 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 38312f6de1..5d72f5b619 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -177,8 +177,10 @@ impl Collection {
         // TODO:
         // - figure out if there is a common path between sigs for FSStorage?
 
+        let manifest: Manifest = paths.try_into()?;
+
         Ok(Self {
-            manifest: paths.into(),
+            manifest,
             storage: InnerStorage::new(
                 FSStorage::builder()
                     .fullpath("".into())
diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index 0a84a3e495..b79308a67c 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -288,8 +288,10 @@ impl From<Vec<Record>> for Manifest {
     }
 }
 
-impl From<&[PathBuf]> for Manifest {
-    fn from(paths: &[PathBuf]) -> Self {
+impl TryFrom<&[PathBuf]> for Manifest {
+    type Error = crate::Error;
+
+    fn try_from(paths: &[PathBuf]) -> Result<Self> {
         #[cfg(feature = "parallel")]
         let iter = paths.par_iter();
 
@@ -298,21 +300,30 @@ impl From<&[PathBuf]> for Manifest {
 
         let records: Vec<Record> = iter
             .flat_map(|p| {
-                let recs: Vec<Record> = Signature::from_path(p)
-                    .unwrap_or_else(|_| panic!("Error processing {:?}", p))
-                    .into_iter()
+                let sigs: Result<Vec<Signature>> = Signature::from_path(p);
+                // @CTB need to get this error out :think:
+                let sigs: Vec<Signature> = sigs.unwrap();
+                let recs: Vec<Record> = sigs
+                    .iter()
                     .flat_map(|v| Record::from_sig(&v, p.as_str()))
                     .collect();
                 recs
             })
             .collect();
 
-        Manifest { records }
+        let records: Result<Vec<Record>> = Ok(records);
+
+        match records {
+            Ok(records) => Ok(Manifest { records }),
+            Err(x) => Err(crate::Error::MismatchKSizes)
+        }
     }
 }
 
-impl From<&PathBuf> for Manifest {
-    fn from(pathlist: &PathBuf) -> Self {
+impl TryFrom<&PathBuf> for Manifest {
+    type Error = crate::Error;
+
+    fn try_from(pathlist: &PathBuf) -> Result<Self> {
         let file = File::open(pathlist).unwrap_or_else(|_| panic!("Failed to open {:?}", pathlist));
         let reader = BufReader::new(file);
 
@@ -322,7 +333,7 @@ impl From<&PathBuf> for Manifest {
             .map(PathBuf::from)
             .collect();
 
-        paths.as_slice().into()
+        paths.as_slice().try_into()
     }
 }
 

From 5f1eef619ddaede316a1b809fa767c47e0c23d89 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Thu, 22 Aug 2024 09:30:15 -0700
Subject: [PATCH 08/42] Revert "provide correct error"

This reverts commit 53bcf0274f4b7bdec81077b44591af3a932a0270.
---
 src/core/src/collection.rs | 3 ++-
 src/core/src/errors.rs     | 5 -----
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 5d72f5b619..cf73cdc8d3 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -121,7 +121,8 @@ impl Collection {
             .zip(other.iter())
             .all(|((id1, rec1), (id2, rec2))| id1 == id2 && rec1 == rec2)
             .then(|| self.len())
-            .ok_or(Error::CollectionNotSuperset)
+            // TODO: right error here
+            .ok_or(Error::MismatchKSizes)
     }
 
     pub fn from_zipfile<P: AsRef<Path>>(zipfile: P) -> Result<Self> {
diff --git a/src/core/src/errors.rs b/src/core/src/errors.rs
index 1a61a07041..90c028eb38 100644
--- a/src/core/src/errors.rs
+++ b/src/core/src/errors.rs
@@ -49,9 +49,6 @@ pub enum SourmashError {
     #[error("error while calculating ANI confidence intervals: {message}")]
     ANIEstimationError { message: String },
 
-    #[error("collection is not a superset")]
-    CollectionNotSuperset,
-
     #[error(transparent)]
     ReadDataError(#[from] ReadDataError),
 
@@ -107,7 +104,6 @@ pub enum SourmashErrorCode {
     NonEmptyMinHash = 1_06,
     MismatchNum = 1_07,
     NeedsAbundanceTracking = 1_08,
-    CollectionNotSuperset = 1_09,
     // Input sequence errors
     InvalidDNA = 11_01,
     InvalidProt = 11_02,
@@ -159,7 +155,6 @@ impl SourmashErrorCode {
             SourmashError::NifflerError { .. } => SourmashErrorCode::NifflerError,
             SourmashError::Utf8Error { .. } => SourmashErrorCode::Utf8Error,
             SourmashError::CsvError { .. } => SourmashErrorCode::CsvError,
-            SourmashError::CollectionNotSuperset { .. } => SourmashErrorCode::CollectionNotSuperset,
 
             #[cfg(not(target_arch = "wasm32"))]
             #[cfg(feature = "branchwater")]

From eb46ecde66d5d6b6e6802f54bf99fff72c143038 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Thu, 22 Aug 2024 09:32:40 -0700
Subject: [PATCH 09/42] Revert "switch Manifest from paths to TryFrom"

This reverts commit d467d9f16a75134d5b3d9c0683ebc52df5659690.
---
 src/core/src/collection.rs |  4 +---
 src/core/src/manifest.rs   | 29 +++++++++--------------------
 2 files changed, 10 insertions(+), 23 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index cf73cdc8d3..bc03274c41 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -178,10 +178,8 @@ impl Collection {
         // TODO:
         // - figure out if there is a common path between sigs for FSStorage?
 
-        let manifest: Manifest = paths.try_into()?;
-
         Ok(Self {
-            manifest,
+            manifest: paths.into(),
             storage: InnerStorage::new(
                 FSStorage::builder()
                     .fullpath("".into())
diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index b79308a67c..0a84a3e495 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -288,10 +288,8 @@ impl From<Vec<Record>> for Manifest {
     }
 }
 
-impl TryFrom<&[PathBuf]> for Manifest {
-    type Error = crate::Error;
-
-    fn try_from(paths: &[PathBuf]) -> Result<Self> {
+impl From<&[PathBuf]> for Manifest {
+    fn from(paths: &[PathBuf]) -> Self {
         #[cfg(feature = "parallel")]
         let iter = paths.par_iter();
 
@@ -300,30 +298,21 @@ impl TryFrom<&[PathBuf]> for Manifest {
 
         let records: Vec<Record> = iter
             .flat_map(|p| {
-                let sigs: Result<Vec<Signature>> = Signature::from_path(p);
-                // @CTB need to get this error out :think:
-                let sigs: Vec<Signature> = sigs.unwrap();
-                let recs: Vec<Record> = sigs
-                    .iter()
+                let recs: Vec<Record> = Signature::from_path(p)
+                    .unwrap_or_else(|_| panic!("Error processing {:?}", p))
+                    .into_iter()
                     .flat_map(|v| Record::from_sig(&v, p.as_str()))
                     .collect();
                 recs
             })
             .collect();
 
-        let records: Result<Vec<Record>> = Ok(records);
-
-        match records {
-            Ok(records) => Ok(Manifest { records }),
-            Err(x) => Err(crate::Error::MismatchKSizes)
-        }
+        Manifest { records }
     }
 }
 
-impl TryFrom<&PathBuf> for Manifest {
-    type Error = crate::Error;
-
-    fn try_from(pathlist: &PathBuf) -> Result<Self> {
+impl From<&PathBuf> for Manifest {
+    fn from(pathlist: &PathBuf) -> Self {
         let file = File::open(pathlist).unwrap_or_else(|_| panic!("Failed to open {:?}", pathlist));
         let reader = BufReader::new(file);
 
@@ -333,7 +322,7 @@ impl TryFrom<&PathBuf> for Manifest {
             .map(PathBuf::from)
             .collect();
 
-        paths.as_slice().try_into()
+        paths.as_slice().into()
     }
 }
 

From 923af44f713b0d7f61449de1df0911035e9d129c Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Fri, 23 Aug 2024 15:07:56 -0700
Subject: [PATCH 10/42] poor person's picklist?

---
 src/core/src/manifest.rs | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index 0a84a3e495..e09c178e4b 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -8,6 +8,7 @@ use getset::{CopyGetters, Getters, Setters};
 use rayon::prelude::*;
 use serde::de;
 use serde::{Deserialize, Serialize};
+use std::collections::HashSet;
 
 use crate::encodings::HashFunctions;
 use crate::prelude::*;
@@ -209,6 +210,18 @@ impl Manifest {
     pub fn iter(&self) -> impl Iterator<Item = &Record> {
         self.records.iter()
     }
+
+    pub fn len(&self) -> usize {
+        self.records.len()
+    }
+
+    pub fn match_picklist(self, pick: HashSet<(&str, &str)>) -> Result<Self> {
+        let rows = self.records.iter().filter(|row| {
+            pick.contains((row.name().as_str(), row.md5().as_str()))
+        }).collect();
+        
+        Ok(Self { rows })    
+    }
 }
 
 impl Select for Manifest {

From 315dfffe25720dda387116574cd58feb66c9afa6 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Fri, 23 Aug 2024 15:17:53 -0700
Subject: [PATCH 11/42] add picklist select

---
 src/core/src/collection.rs |  7 +++++++
 src/core/src/manifest.rs   | 10 +++++-----
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index bc03274c41..ef37fe3ced 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -2,6 +2,7 @@ use std::ops::{Deref, DerefMut};
 
 use camino::Utf8Path as Path;
 use camino::Utf8PathBuf as PathBuf;
+use std::collections::HashSet;
 
 use crate::encodings::Idx;
 use crate::manifest::{Manifest, Record};
@@ -215,6 +216,12 @@ impl Collection {
         assert_eq!(sig.signatures.len(), 1);
         Ok(sig)
     }
+
+    pub fn select_picklist(&self, pick: HashSet<(&str, &str)>) -> Self {
+        // @CTB: why do we need this clone here?
+        let manifest = self.manifest.clone().select_picklist(pick);
+        Self { manifest, storage: self.storage.clone() }
+    }
 }
 
 impl Select for Collection {
diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index e09c178e4b..eea5fd5bbf 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -215,12 +215,12 @@ impl Manifest {
         self.records.len()
     }
 
-    pub fn match_picklist(self, pick: HashSet<(&str, &str)>) -> Result<Self> {
-        let rows = self.records.iter().filter(|row| {
-            pick.contains((row.name().as_str(), row.md5().as_str()))
-        }).collect();
+    pub fn select_picklist(self, pick: HashSet<(&str, &str)>) -> Self {
+        let records = self.records.iter().filter(|row| {
+            pick.contains(&(row.name().as_str(), row.md5().as_str()))
+        }).cloned().collect();
         
-        Ok(Self { rows })    
+        Self { records }
     }
 }
 

From 1fb658a04b4ddf143a63507443d1e8c014bc8ee0 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Fri, 23 Aug 2024 15:38:52 -0700
Subject: [PATCH 12/42] ok

---
 src/core/src/collection.rs | 2 +-
 src/core/src/manifest.rs   | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index ef37fe3ced..b897624423 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -217,7 +217,7 @@ impl Collection {
         Ok(sig)
     }
 
-    pub fn select_picklist(&self, pick: HashSet<(&str, &str)>) -> Self {
+    pub fn select_picklist(&self, pick: HashSet<(String, String)>) -> Self {
         // @CTB: why do we need this clone here?
         let manifest = self.manifest.clone().select_picklist(pick);
         Self { manifest, storage: self.storage.clone() }
diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index eea5fd5bbf..9a52396ce3 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -215,9 +215,9 @@ impl Manifest {
         self.records.len()
     }
 
-    pub fn select_picklist(self, pick: HashSet<(&str, &str)>) -> Self {
+    pub fn select_picklist(self, pick: HashSet<(String, String)>) -> Self {
         let records = self.records.iter().filter(|row| {
-            pick.contains(&(row.name().as_str(), row.md5().as_str()))
+            pick.contains(&(row.name().clone(), row.md5().clone()))
         }).cloned().collect();
         
         Self { records }

From a1229825c121fe69d75925cf569620e0e56425ab Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Fri, 23 Aug 2024 15:48:33 -0700
Subject: [PATCH 13/42] picklist by ref

---
 src/core/src/collection.rs | 2 +-
 src/core/src/manifest.rs   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index b897624423..06e0f7f37f 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -217,7 +217,7 @@ impl Collection {
         Ok(sig)
     }
 
-    pub fn select_picklist(&self, pick: HashSet<(String, String)>) -> Self {
+    pub fn select_picklist(&self, pick: &HashSet<(String, String)>) -> Self {
         // @CTB: why do we need this clone here?
         let manifest = self.manifest.clone().select_picklist(pick);
         Self { manifest, storage: self.storage.clone() }
diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index 9a52396ce3..d32254fae2 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -215,7 +215,7 @@ impl Manifest {
         self.records.len()
     }
 
-    pub fn select_picklist(self, pick: HashSet<(String, String)>) -> Self {
+    pub fn select_picklist(self, pick: &HashSet<(String, String)>) -> Self {
         let records = self.records.iter().filter(|row| {
             pick.contains(&(row.name().clone(), row.md5().clone()))
         }).cloned().collect();

From 39816ab87ad3d7df7452312a3900e169488aab40 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Fri, 23 Aug 2024 16:21:11 -0700
Subject: [PATCH 14/42] add manifest.is_empty()

---
 src/core/src/manifest.rs | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index d32254fae2..4756f924be 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -215,6 +215,10 @@ impl Manifest {
         self.records.len()
     }
 
+    pub fn is_empty(&self) -> bool {
+        self.records.len() == 0
+    }
+
     pub fn select_picklist(self, pick: &HashSet<(String, String)>) -> Self {
         let records = self.records.iter().filter(|row| {
             pick.contains(&(row.name().clone(), row.md5().clone()))

From 61416fb2d81bef3c00d2185913b9f7290a110904 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sat, 24 Aug 2024 06:16:47 -0700
Subject: [PATCH 15/42] update revindex indexing message

---
 src/core/src/index/revindex/disk_revindex.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/core/src/index/revindex/disk_revindex.rs b/src/core/src/index/revindex/disk_revindex.rs
index 511bdbcc4c..ac36c5b626 100644
--- a/src/core/src/index/revindex/disk_revindex.rs
+++ b/src/core/src/index/revindex/disk_revindex.rs
@@ -114,7 +114,7 @@ impl RevIndex {
 
         info!("Compact SSTs");
         index.compact();
-        info!("Processed {} reference sigs", processed_sigs.into_inner());
+        info!("Done! Processed {} reference sigs", processed_sigs.into_inner());
 
         Ok(module::RevIndex::Plain(index))
     }

From 3a7abe9484bce884f0f536c75c28c97fb683e265 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sat, 24 Aug 2024 06:43:35 -0700
Subject: [PATCH 16/42] propagate error on bad directory when opening RocksDB

---
 src/core/src/index/revindex/mod.rs | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/core/src/index/revindex/mod.rs b/src/core/src/index/revindex/mod.rs
index aac0d47c14..013c17081b 100644
--- a/src/core/src/index/revindex/mod.rs
+++ b/src/core/src/index/revindex/mod.rs
@@ -186,7 +186,7 @@ impl RevIndex {
 
     pub fn open<P: AsRef<Path>>(index: P, read_only: bool, spec: Option<&str>) -> Result<Self> {
         let opts = db_options();
-        let cfs = DB::list_cf(&opts, index.as_ref()).unwrap();
+        let cfs = DB::list_cf(&opts, index.as_ref())?;
 
         if cfs.into_iter().any(|c| c == COLORS) {
             // TODO: ColorRevIndex can't be read-only for now,
@@ -1020,4 +1020,14 @@ mod test {
 
         Ok(())
     }
+
+    #[test]
+    fn rocksdb_storage_fail_bad_directory() -> Result<()> {
+        let testdir = TempDir::new()?;
+
+        match RevIndex::open(testdir, true, None) {
+            Err(_) => Ok(()),
+            Ok(_) => panic!("test should not reach here"),
+        }
+    }
 }

From fe75c6cc762bb2d1edf26e936ae14b3725d807d7 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sat, 24 Aug 2024 06:59:11 -0700
Subject: [PATCH 17/42] do we not need len?

---
 src/core/src/manifest.rs | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index 4756f924be..276a89f46a 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -211,14 +211,14 @@ impl Manifest {
         self.records.iter()
     }
 
-    pub fn len(&self) -> usize {
+/*    pub fn len(&self) -> usize {
         self.records.len()
     }
 
     pub fn is_empty(&self) -> bool {
         self.records.len() == 0
     }
-
+*/
     pub fn select_picklist(self, pick: &HashSet<(String, String)>) -> Self {
         let records = self.records.iter().filter(|row| {
             pick.contains(&(row.name().clone(), row.md5().clone()))

From 5fb20fc84a8c0f25c2071e49d9c0728cf8f106b7 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sat, 24 Aug 2024 07:08:35 -0700
Subject: [PATCH 18/42] nope, don't need em

---
 src/core/src/manifest.rs | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index 276a89f46a..47e06be7a2 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -211,14 +211,6 @@ impl Manifest {
         self.records.iter()
     }
 
-/*    pub fn len(&self) -> usize {
-        self.records.len()
-    }
-
-    pub fn is_empty(&self) -> bool {
-        self.records.len() == 0
-    }
-*/
     pub fn select_picklist(self, pick: &HashSet<(String, String)>) -> Self {
         let records = self.records.iter().filter(|row| {
             pick.contains(&(row.name().clone(), row.md5().clone()))

From 2c590102f97b12284f40ce4cfbdfe8ef9bd54342 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sat, 24 Aug 2024 07:13:58 -0700
Subject: [PATCH 19/42] revert for now

---
 src/core/src/storage/mod.rs | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index 856f8ff210..12f456fc22 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -657,11 +657,7 @@ impl Storage for MemStorage {
     }
 
     fn load_sig(&self, path: &str) -> Result<SigStore> {
-        let x = self.sigs.read().unwrap();
-        match x.get(path) {
-            Some(path) => Ok(path.clone()),
-            None => panic!("cannot get path '{path}'")
-        }
+        Ok(self.sigs.read().unwrap().get(path).unwrap().clone())
     }
 
     fn save_sig(&self, path: &str, sig: Signature) -> Result<String> {

From 6fee40340e8eccb94a89c6d39412e4d88e974253 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 27 Aug 2024 06:33:35 -0700
Subject: [PATCH 20/42] adjust select_picklist per luiz

---
 src/core/src/collection.rs | 3 +--
 src/core/src/manifest.rs   | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 06e0f7f37f..53755f7e08 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -218,8 +218,7 @@ impl Collection {
     }
 
     pub fn select_picklist(&self, pick: &HashSet<(String, String)>) -> Self {
-        // @CTB: why do we need this clone here?
-        let manifest = self.manifest.clone().select_picklist(pick);
+        let manifest = self.manifest.select_picklist(pick);
         Self { manifest, storage: self.storage.clone() }
     }
 }
diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index 47e06be7a2..000717992d 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -211,7 +211,7 @@ impl Manifest {
         self.records.iter()
     }
 
-    pub fn select_picklist(self, pick: &HashSet<(String, String)>) -> Self {
+    pub fn select_picklist(&self, pick: &HashSet<(String, String)>) -> Self {
         let records = self.records.iter().filter(|row| {
             pick.contains(&(row.name().clone(), row.md5().clone()))
         }).cloned().collect();

From 06754027ef00170f6aab1655e9fc14df434a6806 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 27 Aug 2024 06:48:44 -0700
Subject: [PATCH 21/42] simplify and encapsulate

---
 src/core/src/collection.rs |  5 ++---
 src/core/src/manifest.rs   | 13 +++++++++++--
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 53755f7e08..843be43fe0 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -2,7 +2,6 @@ use std::ops::{Deref, DerefMut};
 
 use camino::Utf8Path as Path;
 use camino::Utf8PathBuf as PathBuf;
-use std::collections::HashSet;
 
 use crate::encodings::Idx;
 use crate::manifest::{Manifest, Record};
@@ -217,8 +216,8 @@ impl Collection {
         Ok(sig)
     }
 
-    pub fn select_picklist(&self, pick: &HashSet<(String, String)>) -> Self {
-        let manifest = self.manifest.select_picklist(pick);
+    pub fn intersect_manifest(&self, mf: &Manifest) -> Self {
+        let manifest = self.manifest.intersect_manifest(mf);
         Self { manifest, storage: self.storage.clone() }
     }
 }
diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index 000717992d..1fb22f83e5 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -211,9 +211,18 @@ impl Manifest {
         self.records.iter()
     }
 
-    pub fn select_picklist(&self, pick: &HashSet<(String, String)>) -> Self {
+    pub fn intersect_manifest(&self, other: &Manifest) -> Self {
+        // @CTB: do we want to key on other things, like ksize, moltype, hash?
+        // As long as we avoid internal_location we should be fine...
+
+        // extract tuples from other mf:
+        let pairs: HashSet<_> = other
+            .iter()
+            .map(|r| (r.name(), r.md5()))
+            .collect();
+
         let records = self.records.iter().filter(|row| {
-            pick.contains(&(row.name().clone(), row.md5().clone()))
+            pairs.contains(&(row.name(), row.md5()))
         }).cloned().collect();
         
         Self { records }

From 17f50efcf45f6b484d0c4e2f807a2bc2903538fd Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 27 Aug 2024 07:02:49 -0700
Subject: [PATCH 22/42] cargo fmt

---
 src/core/src/collection.rs |  5 ++++-
 src/core/src/manifest.rs   | 13 +++++++------
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 843be43fe0..f7168273b5 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -218,7 +218,10 @@ impl Collection {
 
     pub fn intersect_manifest(&self, mf: &Manifest) -> Self {
         let manifest = self.manifest.intersect_manifest(mf);
-        Self { manifest, storage: self.storage.clone() }
+        Self {
+            manifest,
+            storage: self.storage.clone(),
+        }
     }
 }
 
diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index 1fb22f83e5..147f8d63a0 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -216,15 +216,16 @@ impl Manifest {
         // As long as we avoid internal_location we should be fine...
 
         // extract tuples from other mf:
-        let pairs: HashSet<_> = other
+        let pairs: HashSet<_> = other.iter().map(|r| (r.name(), r.md5())).collect();
+
+        // @CTB use par_iter here, optionally?
+        let records = self
+            .records
             .iter()
-            .map(|r| (r.name(), r.md5()))
+            .filter(|row| pairs.contains(&(row.name(), row.md5())))
+            .cloned()
             .collect();
 
-        let records = self.records.iter().filter(|row| {
-            pairs.contains(&(row.name(), row.md5()))
-        }).cloned().collect();
-        
         Self { records }
     }
 }

From 39c140bf06ced4d0125eb283e6889fc88119ecbf Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 15 Sep 2024 10:03:32 -0700
Subject: [PATCH 23/42] add a test of intersect_manifest

---
 src/core/src/manifest.rs | 58 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)

diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index 147f8d63a0..ef7d7eec6a 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -540,4 +540,62 @@ mod test {
         let scaled100 = manifest.select(&selection).unwrap();
         assert_eq!(scaled100.len(), 6);
     }
+
+    #[test]
+    fn manifest_intersect() {
+        let temp_dir = TempDir::new().unwrap();
+        let utf8_output = PathBuf::from_path_buf(temp_dir.path().to_path_buf())
+            .expect("Path should be valid UTF-8");
+        let filename = utf8_output.join("sig-pathlist.txt");
+        // build sig filenames
+        let base_path = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
+        let test_sigs = vec![
+            "../../tests/test-data/47.fa.sig",
+            "../../tests/test-data/63.fa.sig",
+        ];
+
+        let full_paths: Vec<_> = test_sigs
+            .into_iter()
+            .map(|sig| base_path.join(sig))
+            .collect();
+
+        // write a file in test directory with a filename on each line
+        let mut pathfile = File::create(&filename).unwrap();
+        for sigfile in &full_paths {
+            writeln!(pathfile, "{}", sigfile).unwrap();
+        }
+
+        // load into manifest
+        let manifest = Manifest::from(&filename);
+        assert_eq!(manifest.len(), 2);
+
+        // now do just one sketch -
+        let test_sigs2 = vec![
+            "../../tests/test-data/63.fa.sig",
+        ];
+
+        let filename2 = utf8_output.join("sig-pathlist-single.txt");
+
+        let full_paths: Vec<_> = test_sigs2
+            .into_iter()
+            .map(|sig| base_path.join(sig))
+            .collect();
+
+        let mut pathfile2 = File::create(&filename2).unwrap();
+        for sigfile in &full_paths {
+            writeln!(pathfile2, "{}", sigfile).unwrap();
+        }
+
+        // load into another manifest
+        let manifest2 = Manifest::from(&filename2);
+        assert_eq!(manifest2.len(), 1);
+
+        // intersect with itself => same.
+        let new_mf = manifest2.intersect_manifest(&manifest);
+        assert_eq!(new_mf.len(), 1);
+
+        // intersect with other => single.
+        let new_mf = manifest.intersect_manifest(&manifest2);
+        assert_eq!(new_mf.len(), 1);
+    }
 }

From 16f72c5b3eaca7e280b8df67061b7c021aba1a57 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 15 Sep 2024 10:43:10 -0700
Subject: [PATCH 24/42] impl PartialEq/Eq for Record, ignoring
 internal_location

---
 src/core/src/manifest.rs | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index ef7d7eec6a..bb13752bdb 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -18,7 +18,7 @@ use crate::Result;
 
 /// Individual manifest record, containing information about sketches.
 
-#[derive(Debug, Serialize, Deserialize, Clone, CopyGetters, Getters, Setters, PartialEq, Eq)]
+#[derive(Debug, Serialize, Deserialize, Clone, CopyGetters, Getters, Setters)]
 pub struct Record {
     #[getset(get = "pub", set = "pub")]
     internal_location: PathBuf,
@@ -177,6 +177,21 @@ impl Record {
     }
 }
 
+impl PartialEq for Record {
+    // match everything but internal_location
+    fn eq(&self, other: &Self) -> bool {
+        self.md5 == other.md5 &&
+            self.ksize == other.ksize &&
+            self.scaled == other.scaled &&
+            self.n_hashes == other.n_hashes &&
+            self.with_abundance == other.with_abundance &&
+            self.name == other.name &&
+            self.filename == other.filename
+    }
+}
+
+impl Eq for Record {}
+
 impl Manifest {
     pub fn from_reader<R: Read>(rdr: R) -> Result<Self> {
         let mut records = vec![];

From 2146f307f239705146a5f9e8860653e6f9d551a9 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 15 Sep 2024 17:18:04 -0700
Subject: [PATCH 25/42] switch to using full Record for intersect_manifest

---
 src/core/src/manifest.rs | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index bb13752bdb..edc1edae6b 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -1,6 +1,8 @@
 use std::fs::File;
 use std::io::{BufRead, BufReader, Read, Write};
 use std::ops::Deref;
+use std::collections::HashSet;
+use std::hash::{Hash, Hasher};
 
 use camino::Utf8PathBuf as PathBuf;
 use getset::{CopyGetters, Getters, Setters};
@@ -8,7 +10,6 @@ use getset::{CopyGetters, Getters, Setters};
 use rayon::prelude::*;
 use serde::de;
 use serde::{Deserialize, Serialize};
-use std::collections::HashSet;
 
 use crate::encodings::HashFunctions;
 use crate::prelude::*;
@@ -192,6 +193,16 @@ impl PartialEq for Record {
 
 impl Eq for Record {}
 
+impl Hash for Record { // @CTB moltype, other things? test compare empty.
+    fn hash<H: Hasher>(&self, state: &mut H) {
+        self.md5.hash(state);
+        self.scaled.hash(state);
+        self.with_abundance.hash(state);
+        self.name.hash(state);
+        self.filename.hash(state);
+    }
+}
+
 impl Manifest {
     pub fn from_reader<R: Read>(rdr: R) -> Result<Self> {
         let mut records = vec![];
@@ -227,17 +238,14 @@ impl Manifest {
     }
 
     pub fn intersect_manifest(&self, other: &Manifest) -> Self {
-        // @CTB: do we want to key on other things, like ksize, moltype, hash?
-        // As long as we avoid internal_location we should be fine...
-
         // extract tuples from other mf:
-        let pairs: HashSet<_> = other.iter().map(|r| (r.name(), r.md5())).collect();
+        let pairs: HashSet<_> = other.iter().map(|r| r).collect();
 
         // @CTB use par_iter here, optionally?
         let records = self
             .records
             .iter()
-            .filter(|row| pairs.contains(&(row.name(), row.md5())))
+            .filter(|row| pairs.contains(row))
             .cloned()
             .collect();
 

From 32839ae5a5ee35442abc6002728b25454d965c70 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 15 Sep 2024 18:05:59 -0700
Subject: [PATCH 26/42] round out comparison & hashing for Record

---
 src/core/src/manifest.rs | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index edc1edae6b..ee95415e2d 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -183,7 +183,9 @@ impl PartialEq for Record {
     fn eq(&self, other: &Self) -> bool {
         self.md5 == other.md5 &&
             self.ksize == other.ksize &&
+            self.moltype == other.moltype &&
             self.scaled == other.scaled &&
+            self.num == other.num &&
             self.n_hashes == other.n_hashes &&
             self.with_abundance == other.with_abundance &&
             self.name == other.name &&
@@ -193,10 +195,14 @@ impl PartialEq for Record {
 
 impl Eq for Record {}
 
-impl Hash for Record { // @CTB moltype, other things? test compare empty.
+impl Hash for Record {
     fn hash<H: Hasher>(&self, state: &mut H) {
         self.md5.hash(state);
+        self.ksize.hash(state);
+        self.moltype.hash(state);
         self.scaled.hash(state);
+        self.num.hash(state);
+        self.n_hashes.hash(state);
         self.with_abundance.hash(state);
         self.name.hash(state);
         self.filename.hash(state);
@@ -241,7 +247,6 @@ impl Manifest {
         // extract tuples from other mf:
         let pairs: HashSet<_> = other.iter().map(|r| r).collect();
 
-        // @CTB use par_iter here, optionally?
         let records = self
             .records
             .iter()

From 43ee757212d18934d9caf79ab1f0b823067b051e Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 15 Sep 2024 18:18:33 -0700
Subject: [PATCH 27/42] cargo fmt

---
 src/core/src/manifest.rs | 26 ++++++++++++--------------
 1 file changed, 12 insertions(+), 14 deletions(-)

diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index ee95415e2d..cb1f47487d 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -1,8 +1,8 @@
+use std::collections::HashSet;
 use std::fs::File;
+use std::hash::{Hash, Hasher};
 use std::io::{BufRead, BufReader, Read, Write};
 use std::ops::Deref;
-use std::collections::HashSet;
-use std::hash::{Hash, Hasher};
 
 use camino::Utf8PathBuf as PathBuf;
 use getset::{CopyGetters, Getters, Setters};
@@ -181,15 +181,15 @@ impl Record {
 impl PartialEq for Record {
     // match everything but internal_location
     fn eq(&self, other: &Self) -> bool {
-        self.md5 == other.md5 &&
-            self.ksize == other.ksize &&
-            self.moltype == other.moltype &&
-            self.scaled == other.scaled &&
-            self.num == other.num &&
-            self.n_hashes == other.n_hashes &&
-            self.with_abundance == other.with_abundance &&
-            self.name == other.name &&
-            self.filename == other.filename
+        self.md5 == other.md5
+            && self.ksize == other.ksize
+            && self.moltype == other.moltype
+            && self.scaled == other.scaled
+            && self.num == other.num
+            && self.n_hashes == other.n_hashes
+            && self.with_abundance == other.with_abundance
+            && self.name == other.name
+            && self.filename == other.filename
     }
 }
 
@@ -598,9 +598,7 @@ mod test {
         assert_eq!(manifest.len(), 2);
 
         // now do just one sketch -
-        let test_sigs2 = vec![
-            "../../tests/test-data/63.fa.sig",
-        ];
+        let test_sigs2 = vec!["../../tests/test-data/63.fa.sig"];
 
         let filename2 = utf8_output.join("sig-pathlist-single.txt");
 

From 1594dc48929acbfa6be5a43ed04e57cce8cdb65f Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Mon, 16 Sep 2024 09:34:30 -0700
Subject: [PATCH 28/42] remove identity closure

---
 src/core/src/manifest.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/core/src/manifest.rs b/src/core/src/manifest.rs
index cb1f47487d..2f1eca7e0f 100644
--- a/src/core/src/manifest.rs
+++ b/src/core/src/manifest.rs
@@ -245,7 +245,7 @@ impl Manifest {
 
     pub fn intersect_manifest(&self, other: &Manifest) -> Self {
         // extract tuples from other mf:
-        let pairs: HashSet<_> = other.iter().map(|r| r).collect();
+        let pairs: HashSet<_> = other.iter().collect();
 
         let records = self
             .records

From 2465c02198f251c923c10d51fbfaae1967f44b0d Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Mon, 16 Sep 2024 14:22:51 -0700
Subject: [PATCH 29/42] add in a print for debugging

---
 src/core/src/storage/mod.rs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index 12f456fc22..f25ffdc596 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -469,6 +469,7 @@ impl Select for SigStore {
     fn select(mut self, selection: &Selection) -> Result<Self> {
         // TODO: find better error
         let sig = self.data.take().ok_or(Error::MismatchKSizes)?;
+        eprintln!("YYY {:?}", sig);
         self.data = OnceCell::with_value(sig.select(selection)?);
         Ok(self)
     }

From 5af5f4566cdba5f79f1cb26385554f392995a6da Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Mon, 16 Sep 2024 14:24:57 -0700
Subject: [PATCH 30/42] more print

---
 src/core/src/signature.rs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/core/src/signature.rs b/src/core/src/signature.rs
index 0ab8190f98..a8975c762a 100644
--- a/src/core/src/signature.rs
+++ b/src/core/src/signature.rs
@@ -795,6 +795,7 @@ impl ToWriter for Signature {
 
 impl Select for Signature {
     fn select(mut self, selection: &Selection) -> Result<Self, Error> {
+        eprintln!("ZZZ: {}", self.signatures.len());
         self.signatures.retain(|s| {
             let mut valid = true;
             valid = if let Some(ksize) = selection.ksize() {

From b46565d67478be53854f15a68176981f1ba91100 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Mon, 16 Sep 2024 14:28:26 -0700
Subject: [PATCH 31/42] remove prints

---
 src/core/src/signature.rs   | 1 -
 src/core/src/storage/mod.rs | 1 -
 2 files changed, 2 deletions(-)

diff --git a/src/core/src/signature.rs b/src/core/src/signature.rs
index a8975c762a..0ab8190f98 100644
--- a/src/core/src/signature.rs
+++ b/src/core/src/signature.rs
@@ -795,7 +795,6 @@ impl ToWriter for Signature {
 
 impl Select for Signature {
     fn select(mut self, selection: &Selection) -> Result<Self, Error> {
-        eprintln!("ZZZ: {}", self.signatures.len());
         self.signatures.retain(|s| {
             let mut valid = true;
             valid = if let Some(ksize) = selection.ksize() {
diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index f25ffdc596..12f456fc22 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -469,7 +469,6 @@ impl Select for SigStore {
     fn select(mut self, selection: &Selection) -> Result<Self> {
         // TODO: find better error
         let sig = self.data.take().ok_or(Error::MismatchKSizes)?;
-        eprintln!("YYY {:?}", sig);
         self.data = OnceCell::with_value(sig.select(selection)?);
         Ok(self)
     }

From 9c267528977fab0bb04dc1da86c47290bff68bf8 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 17 Sep 2024 08:34:15 -0700
Subject: [PATCH 32/42] add a test for Collection::intersect_manifest

---
 src/core/src/collection.rs | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index f7168273b5..fdd47a1f58 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -245,6 +245,7 @@ mod test {
     use crate::selection::Selection;
     use crate::signature::Signature;
     use crate::Result;
+    use crate::manifest::Manifest;
 
     #[test]
     fn sigstore_selection_with_downsample() {
@@ -366,6 +367,33 @@ mod test {
         assert_eq!(cl.len(), 0);
     }
 
+    #[test]
+    fn collection_intersect_manifest() {
+        // load test sigs
+        let mut filename = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
+        // four num=500 sigs
+        filename.push("../../tests/test-data/genome-s11.fa.gz.sig");
+        let file = File::open(filename).unwrap();
+        let reader = BufReader::new(file);
+        let sigs: Vec<Signature> = serde_json::from_reader(reader).expect("Loading error");
+        assert_eq!(sigs.len(), 4);
+        // load sigs into collection + select compatible signatures
+        let cl = Collection::from_sigs(sigs)
+            .unwrap();
+        // all sigs should remain
+        assert_eq!(cl.len(), 4);
+
+        // grab first record
+        let manifest = cl.manifest();
+        let record = manifest.iter().next().unwrap().clone();
+        let vr = vec![record];
+
+        // now intersect:
+        let manifest2 = Manifest::from(vr);
+        let cl2 = cl.intersect_manifest(&manifest2);
+        assert_eq!(cl2.len(), 1);
+    }
+
     #[test]
     fn sigstore_sig_from_record() {
         // load test sigs

From 63df7a828f5a1cd909db650bebaae937ca74f561 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 17 Sep 2024 12:22:58 -0700
Subject: [PATCH 33/42] panic in bad circumstances

---
 src/core/src/storage/mod.rs | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index 12f456fc22..38bfdd507d 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -298,9 +298,10 @@ impl Storage for FSStorage {
 
     fn load_sig(&self, path: &str) -> Result<SigStore> {
         let raw = self.load(path)?;
-        let sig = Signature::from_reader(&mut &raw[..])?
-            // TODO: select the right sig?
-            .swap_remove(0);
+
+        let mut vs = Signature::from_reader(&mut &raw[..])?;
+        if vs.len() > 1 { panic!("more than one sig."); }
+        let sig = vs.swap_remove(0);
 
         Ok(sig.into())
     }

From 4c29e9ec221241d94602493e26c304cbc5ab917c Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 24 Sep 2024 07:15:13 -0700
Subject: [PATCH 34/42] add unimplemented when there are multiple Signatures

---
 src/core/src/collection.rs  |  2 +-
 src/core/src/storage/mod.rs | 20 +++++++++++++-------
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 2493f313fc..66f3311dff 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -238,11 +238,11 @@ mod test {
 
     use crate::encodings::HashFunctions;
     use crate::manifest::Manifest;
+    use crate::manifest::Manifest;
     use crate::prelude::Select;
     use crate::selection::Selection;
     use crate::signature::Signature;
     use crate::Result;
-    use crate::manifest::Manifest;
 
     #[test]
     fn sigstore_selection_with_downsample() {
diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index 38bfdd507d..bae75c3b6a 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -33,9 +33,11 @@ pub trait Storage {
     /// Load signature from internal path
     fn load_sig(&self, path: &str) -> Result<SigStore> {
         let raw = self.load(path)?;
-        let sig = Signature::from_reader(&mut &raw[..])?
-            // TODO: select the right sig?
-            .swap_remove(0);
+        let mut vs = Signature::from_reader(&mut &raw[..])?;
+        if vs.len() > 1 {
+            unimplemented!("only one Signature currently allowed");
+        }
+        let sig = vs.swap_remove(0);
 
         Ok(sig.into())
     }
@@ -300,7 +302,9 @@ impl Storage for FSStorage {
         let raw = self.load(path)?;
 
         let mut vs = Signature::from_reader(&mut &raw[..])?;
-        if vs.len() > 1 { panic!("more than one sig."); }
+        if vs.len() > 1 {
+            unimplemented!("only one Signature currently allowed");
+        }
         let sig = vs.swap_remove(0);
 
         Ok(sig.into())
@@ -369,9 +373,11 @@ impl Storage for ZipStorage {
 
     fn load_sig(&self, path: &str) -> Result<SigStore> {
         let raw = self.load(path)?;
-        let sig = Signature::from_reader(&mut &raw[..])?
-            // TODO: select the right sig?
-            .swap_remove(0);
+        let mut vs = Signature::from_reader(&mut &raw[..])?;
+        if vs.len() > 1 {
+            unimplemented!("only one Signature currently allowed");
+        }
+        let sig = vs.swap_remove(0);
 
         Ok(sig.into())
     }

From 70b1c5dbaf8dacdd6e52a22a5b7b627e6fb54f45 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 24 Sep 2024 07:26:57 -0700
Subject: [PATCH 35/42] upd

---
 src/core/src/collection.rs | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 66f3311dff..669e7d5588 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -237,8 +237,6 @@ mod test {
     use super::Collection;
 
     use crate::encodings::HashFunctions;
-    use crate::manifest::Manifest;
-    use crate::manifest::Manifest;
     use crate::prelude::Select;
     use crate::selection::Selection;
     use crate::signature::Signature;

From b95ea9a9ca422833cd2f7420977015171a2399c0 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 24 Sep 2024 07:36:42 -0700
Subject: [PATCH 36/42] ??

---
 src/core/src/collection.rs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 669e7d5588..aa8e33e6e8 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -237,6 +237,7 @@ mod test {
     use super::Collection;
 
     use crate::encodings::HashFunctions;
+    use crate::manifest::Manifest;
     use crate::prelude::Select;
     use crate::selection::Selection;
     use crate::signature::Signature;

From c5b2d4d368f90232a20d8fabb8d555b8e5b7b37a Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 27 Oct 2024 07:35:30 -0700
Subject: [PATCH 37/42] document InnerStorage a bit

---
 src/core/src/storage/mod.rs | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index 47ef9d14a7..7e5914fe71 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -72,6 +72,15 @@ pub enum StorageError {
     MissingFeature(String, String),
 }
 
+/// InnerStorage: a catch-all type that allows using any Storage in
+/// parallel contexts.
+///
+/// Arc allows ref counting to share it between threads;
+/// RwLock makes sure there is only one writer possible (and a lot of readers);
+/// dyn Storage so we can init with anything that implements the Storage trait;
+/// Send + Sync + 'static is kind of a cheat to avoid lifetimes issues: we
+///    should get rid of that 'static if possible... -- Luiz.
+
 #[derive(Clone)]
 pub struct InnerStorage(Arc<RwLock<dyn Storage + Send + Sync + 'static>>);
 

From f370ed78aa419eb9bcfbbe48fee5b0e632be9ea7 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 27 Oct 2024 09:19:40 -0700
Subject: [PATCH 38/42] document InnerStorage a bit

---
 src/core/src/storage/mod.rs | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index 7e5914fe71..97b676d370 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -77,9 +77,10 @@ pub enum StorageError {
 ///
 /// Arc allows ref counting to share it between threads;
 /// RwLock makes sure there is only one writer possible (and a lot of readers);
-/// dyn Storage so we can init with anything that implements the Storage trait;
-/// Send + Sync + 'static is kind of a cheat to avoid lifetimes issues: we
-///    should get rid of that 'static if possible... -- Luiz.
+/// dyn Storage so we can init with anything that implements the Storage trait.
+
+// Send + Sync + 'static is kind of a cheat to avoid lifetimes issues: we
+//    should get rid of that 'static if possible... -- Luiz.
 
 #[derive(Clone)]
 pub struct InnerStorage(Arc<RwLock<dyn Storage + Send + Sync + 'static>>);

From 874a9a8542bed339819eacf6854337a22457b459 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 27 Oct 2024 09:47:16 -0700
Subject: [PATCH 39/42] finally, a test that works (well, fails appropriately)

---
 src/core/src/collection.rs | 46 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 9ad2d891bc..ade03d9623 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -416,6 +416,52 @@ mod test {
         }
     }
 
+    // this test could probably be simpler
+    #[test]
+    fn sigstore_sig_from_record_2() {
+        use crate::manifest::Record;
+        use crate::storage::{ FSStorage, InnerStorage };
+        use crate::selection::Selection;
+
+        // load test sigs
+        let mut filename = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
+        filename.push("../../tests/test-data/short.sig");
+
+        // CTB: this could probably be improved somehow...
+        let filename: String = filename.into();
+        let filename_ref = filename.as_str();
+
+        // load signatures
+        let sigs = Signature::from_path(filename.clone()).expect("error loading");
+
+        // convert to records
+        let records: Vec<Record> = sigs
+            .into_iter()
+            .flat_map(|v| Record::from_sig(&v, filename_ref))
+            .collect();
+
+        eprintln!("{:?}", records);
+
+        // build a new collection using this manifest
+        let manifest: Manifest = records.into();
+        let collection = Collection::new(manifest,
+                                         InnerStorage::new(
+                                             FSStorage::builder()
+                                                 .fullpath("../../tests/test-data/".into())
+                                                 .subdir("".into())
+                                                 .build())
+        );
+
+        let selection = Selection::builder().build();
+
+        for (_idx, rec) in collection.iter() {
+            // need to pass select again here so we actually downsample
+            let this_sig = collection.sig_from_record(rec).unwrap().select(&selection).unwrap();
+            let this_mh = this_sig.minhash().unwrap();
+            assert_eq!(this_mh.scaled(), 2000);
+        }
+    }
+
     #[test]
     fn sigstore_selection_moltype_zip() {
         // load test sigs

From 0745990ab6f022cebba84b1a5b0ac43b768020c4 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 27 Oct 2024 11:00:23 -0700
Subject: [PATCH 40/42] cleanup

---
 src/core/src/collection.rs   |  35 +++++++++++++++++------------------
 src/core/src/storage/mod.rs  |   2 +-
 tests/test-data/short.sig.gz | Bin 0 -> 10995 bytes
 3 files changed, 18 insertions(+), 19 deletions(-)
 create mode 100644 tests/test-data/short.sig.gz

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index ade03d9623..25803d6de2 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -420,21 +420,19 @@ mod test {
     #[test]
     fn sigstore_sig_from_record_2() {
         use crate::manifest::Record;
-        use crate::storage::{ FSStorage, InnerStorage };
         use crate::selection::Selection;
+        use crate::storage::{FSStorage, InnerStorage};
 
         // load test sigs
         let mut filename = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
-        filename.push("../../tests/test-data/short.sig");
-
-        // CTB: this could probably be improved somehow...
+        filename.push("../../tests/test-data/short.sig.gz");
         let filename: String = filename.into();
         let filename_ref = filename.as_str();
 
         // load signatures
         let sigs = Signature::from_path(filename.clone()).expect("error loading");
 
-        // convert to records
+        // convert to records, loaded from 'short.sig.gz'.
         let records: Vec<Record> = sigs
             .into_iter()
             .flat_map(|v| Record::from_sig(&v, filename_ref))
@@ -444,22 +442,23 @@ mod test {
 
         // build a new collection using this manifest
         let manifest: Manifest = records.into();
-        let collection = Collection::new(manifest,
-                                         InnerStorage::new(
-                                             FSStorage::builder()
-                                                 .fullpath("../../tests/test-data/".into())
-                                                 .subdir("".into())
-                                                 .build())
+        let collection = Collection::new(
+            manifest,
+            InnerStorage::new(
+                FSStorage::builder()
+                    .fullpath("../../tests/test-data/".into())
+                    .subdir("".into())
+                    .build(),
+            ),
         );
 
-        let selection = Selection::builder().build();
+        // pull off first record
+        let v: Vec<_> = collection.iter().collect();
+        let (_idx, rec) = v.first().expect("no records in collection?!");
 
-        for (_idx, rec) in collection.iter() {
-            // need to pass select again here so we actually downsample
-            let this_sig = collection.sig_from_record(rec).unwrap().select(&selection).unwrap();
-            let this_mh = this_sig.minhash().unwrap();
-            assert_eq!(this_mh.scaled(), 2000);
-        }
+        // this will panic with "unimplemented" because there are two
+        // sketches and that is not supported.
+        let _first_sig = collection.sig_from_record(rec).expect("no sig!?");
     }
 
     #[test]
diff --git a/src/core/src/storage/mod.rs b/src/core/src/storage/mod.rs
index 97b676d370..e098f58eba 100644
--- a/src/core/src/storage/mod.rs
+++ b/src/core/src/storage/mod.rs
@@ -314,7 +314,7 @@ impl Storage for FSStorage {
 
         let mut vs = Signature::from_reader(&mut &raw[..])?;
         if vs.len() > 1 {
-            unimplemented!("only one Signature currently allowed");
+            unimplemented!("only one Signature currently allowed when using 'load_sig'");
         }
         let sig = vs.swap_remove(0);
 
diff --git a/tests/test-data/short.sig.gz b/tests/test-data/short.sig.gz
new file mode 100644
index 0000000000000000000000000000000000000000..84047034dc965758f24d9889e8f54b813fe40ef5
GIT binary patch
literal 10995
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HcmV?d00001


From d68d8d4144c838f4c855b4cac8029713ee84ecbe Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 27 Oct 2024 11:04:11 -0700
Subject: [PATCH 41/42] a much cleaner test

---
 src/core/src/collection.rs | 34 +++-------------------------------
 1 file changed, 3 insertions(+), 31 deletions(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 25803d6de2..440770f60f 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -416,41 +416,13 @@ mod test {
         }
     }
 
-    // this test could probably be simpler
     #[test]
+    #[should_panic]              // for now...
     fn sigstore_sig_from_record_2() {
-        use crate::manifest::Record;
-        use crate::selection::Selection;
-        use crate::storage::{FSStorage, InnerStorage};
-
-        // load test sigs
         let mut filename = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
         filename.push("../../tests/test-data/short.sig.gz");
-        let filename: String = filename.into();
-        let filename_ref = filename.as_str();
-
-        // load signatures
-        let sigs = Signature::from_path(filename.clone()).expect("error loading");
-
-        // convert to records, loaded from 'short.sig.gz'.
-        let records: Vec<Record> = sigs
-            .into_iter()
-            .flat_map(|v| Record::from_sig(&v, filename_ref))
-            .collect();
-
-        eprintln!("{:?}", records);
-
-        // build a new collection using this manifest
-        let manifest: Manifest = records.into();
-        let collection = Collection::new(
-            manifest,
-            InnerStorage::new(
-                FSStorage::builder()
-                    .fullpath("../../tests/test-data/".into())
-                    .subdir("".into())
-                    .build(),
-            ),
-        );
+        let v = [filename];
+        let collection = Collection::from_paths(&v).expect("no sigs!?");
 
         // pull off first record
         let v: Vec<_> = collection.iter().collect();

From abc01c168de7d13d1f36d1c3efe055586e47f875 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 27 Oct 2024 11:06:13 -0700
Subject: [PATCH 42/42] cargo fmt

---
 src/core/src/collection.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/core/src/collection.rs b/src/core/src/collection.rs
index 440770f60f..28659df05f 100644
--- a/src/core/src/collection.rs
+++ b/src/core/src/collection.rs
@@ -417,7 +417,7 @@ mod test {
     }
 
     #[test]
-    #[should_panic]              // for now...
+    #[should_panic] // for now...
     fn sigstore_sig_from_record_2() {
         let mut filename = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
         filename.push("../../tests/test-data/short.sig.gz");