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MRG: adjust Signature::name() to return Option<String> instead of filename() and md5sum() #3434

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merged 19 commits into from
Dec 18, 2024
Merged

MRG: adjust Signature::name() to return Option<String> instead of filename() and md5sum() #3434

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2e63b1b
WIP: fix intersect_manifest on empty names
ctb Dec 15, 2024
5cf7c72
fix compile
ctb Dec 15, 2024
f1b889c
more debug
ctb Dec 15, 2024
3cc41a1
even more debug
ctb Dec 15, 2024
1dccd2c
avoid defaulting name() to filename()
ctb Dec 15, 2024
f5974ef
default to empty string
ctb Dec 15, 2024
8a9d657
isolate changes
ctb Dec 15, 2024
c84565c
add test
ctb Dec 17, 2024
11db611
fix name
ctb Dec 17, 2024
d2300b7
fix test
ctb Dec 17, 2024
c0165bd
Merge branch 'latest' of github.com:sourmash-bio/sourmash into fix_in…
ctb Dec 17, 2024
0f006e1
Merge branch 'latest' into fix_intersect_manifest
ctb Dec 17, 2024
34dba54
change Signature::name() to Option<String>
ctb Dec 17, 2024
6ad32c1
switch to using name_str
ctb Dec 17, 2024
0ed80c1
cleanup
ctb Dec 17, 2024
2c7a070
cargo fmt
ctb Dec 17, 2024
e910e7c
fix clippy
ctb Dec 17, 2024
6b6df75
wow, ok
ctb Dec 17, 2024
9f0702d
update to docstring
ctb Dec 18, 2024
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10 changes: 9 additions & 1 deletion src/core/src/index/revindex/disk_revindex.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -351,7 +351,15 @@ impl RevIndexOps for RevIndex {
.collection
.record_for_dataset(dataset_id)
.expect("dataset not found");
Some((row.name().into(), size))

let mut name = row.name();
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This is ugly - is there an idiomatic way to do this??

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yuck: https://stackoverflow.com/questions/45343320/how-can-i-return-the-first-non-empty-string

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@luizirber luizirber Dec 17, 2024 •
edited
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maybe?

let name = [row.name(), row.filename(), row.md5()]
    .into_iter()
    .skip_while(|v| v.is_empty())
    .next()
    .unwrap();  // guaranteed to succeed because `md5` always exists

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yeh.... :)

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in 0ed80c1

if name == "" {
name = row.filename();
}
if name == "" {
name = row.md5();
}
Some((name.into(), size))
} else {
None
}
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2 changes: 1 addition & 1 deletion src/core/src/index/revindex/mod.rs
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Expand Up @@ -558,7 +558,7 @@ mod test {
)?;

assert_eq!(matches.len(), 1);
assert_eq!(matches[0].name(), "../genome-s10.fa.gz");
assert_eq!(matches[0].name(), ""); // signature name is empty
assert_eq!(matches[0].f_match(), 1.0);

Ok(())
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6 changes: 3 additions & 3 deletions src/core/src/signature.rs
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Expand Up @@ -448,10 +448,8 @@ impl Signature {
pub fn name(&self) -> String {
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since r0.18.0 is not released yet, do we want to make this
pub fn name(&self) -> Option<String> {
instead? This wil change calls around in other places, but seems to communicate better that the name exists or not instead of getting a .name() call that might return ""

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ooh, I like it! let me give it a try 🙇

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34dba54

if let Some(name) = &self.name {
name.clone()
} else if let Some(filename) = &self.filename {
filename.clone()
} else {
self.md5sum()
"".into()
}
}

Expand Down Expand Up @@ -982,6 +980,8 @@ mod test {
assert_eq!(sig.signatures[0].size(), 3);
assert_eq!(sig.signatures[1].size(), 2);
assert_eq!(sig.signatures[2].size(), 1);

assert_eq!(sig.name(), "");
}

#[test]
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