Initial edge updates #76
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src/models/accession.rs
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| @@ -1,4 +1,3 @@ | |||
| use crate::models::block_group::BlockGroup; | |||
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Just misc warning cleanup here and a few other places. It's work to pick through them to find legit compilation errors
| @@ -801,6 +802,41 @@ pub fn move_to(conn: &Connection, operation_conn: &Connection, operation: &Opera | |||
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| } | |||
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| pub fn start_operation<'a>( | |||
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Just some refactoring
dkhofer
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src/models/path.rs
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| @@ -146,6 +147,25 @@ impl Path { | |||
| rows.next().unwrap().unwrap() | |||
| } | |||
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| pub fn full_query(conn: &Connection, query: &str, params: impl Params) -> Vec<Path> { | |||
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What's the difference here and other queries? Does this version support carray?
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It does, but it turns out I don't need that for this PR. I'll put together a separate PR with this change for the places that need it
| } | ||
| } | ||
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| let new_name = format!( |
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i was thinking the fasta header should be part of the new name. So it would be like chr1-GFP, etc.
| }; | ||
| use crate::{calculate_hash, operation_management}; | ||
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| pub fn update_with_fasta( |
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Is this compatible as a branch off of #79 ? Where insert_bg_changes is the way to give updates? We're quickly moving to the multiple engineering round setups where this is still limited to 1 round. (e.g. we do one round of changes to insert a landing pad, and then another round to insert many genes into it. We can't refer to the landing pad region here).
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Let's say some fasta was imported by operation 1, and the region we want to replace with a landing pad is 10-20 on chr1.
gen update --fasta landing-pad.fa --start 10 --end 20 --contig-name chr1
Let's say that gets an operation ID of 2. This creates a new path for chr1 and adds the non-chr1 paths from operation 1, plus the new chr1, as entries in operation_paths associated with this operation 2. That means the current chr1 path (with landing pad) is what the next operation will reference for coordinates.
Let's say we want to integrate a gene to the landing pad starting at 12, going to 100. (No idea how biologically valid that is.)
gen update --fasta landing-pad.fa --start 12 --end 100 --contig-name chr1
That creates another new path, replacing the one that was created for operation 2. All the non-chr1 paths stay the same from operation 1.
Does that help explain my thinking?
…parameter is what matters
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src/updates/fasta.rs
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| Some(parent_sample_name), | ||
| ) | ||
| .unwrap(); | ||
| BlockGroup::clone(conn, block_group.id, new_bg_id); |
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what's the reason for the second clone?
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Oh, I didn't see that get_or_create_sample_block_group did the clone. Removed this line, thanks!
| panic!("No block group found with region name: {}", region_name); | ||
| } | ||
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| let path = BlockGroup::get_current_path(conn, new_block_group_id); |
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we should ensure the clone in blockgroup orders the newly created paths by order of id too so this actually returns the first path made in a cloned bg.
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Just made that change
src/updates/vcf.rs
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| @@ -243,7 +244,7 @@ pub fn update_with_vcf<'a>( | |||
| collection_name, | |||
| &fixed_sample, | |||
| seq_name.clone(), | |||
| coordinate_frame, | |||
| Some(""), | |||
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what's the reason for these? it should already be passing None
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Long story short, I was confused about our sample name conventions. I've reverted most of the changes to this file
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