Panic when adding a node to a child

[simonpenel]

Hi, I just start to learn Rust, so I apologize if my question is stupid!
I encounter a problem when building a tree by adding nodes to the root then adding nodes its children:

let mut arbrevide = taxonomy::GeneralTaxonomy::default();
arbrevide.add(0,"Gauche").expect("Impossible d'ajouter un noeud");
arbrevide.add(0,"Droite").expect("Impossible d'ajouter un noeud");
// arbrevide.remove(1).expect("Impossible de supprimer un noeud"); // a remettre
println!("ARBRE VIDE = {:?}",arbrevide);
println!(">>>TAXIDS = {:?}",arbrevide.tax_ids);
println!(">>>LONGUEUR = {}",arbrevide.tax_ids.len());
arbrevide.add(1,"Super").expect("Impossible d'ajouter un noeud");

There is a panic signal when I try to add a node to the node with an internal_taxid equal to 1
Note that if the line
arbrevide.remove(1).expect("Impossible de supprimer un noeud");
is uncommented, it works fine....

I understand that there is a problem at the children_lookup level...

What is the correct way to build a tree then?

thanks for your help

all the best
Simon

[Keats]

So it looks like we don't actually check if the parent exists before trying to add the new node. This should return an error instead of a out of bound panics. I'll fix it soonish

[simonpenel]

Thanks a lot!!
( It seems to me that the parent exists in my code? Maybe I missed something)
all the best,
Simon

[Keats]

It's in the children_lookup that we are not inserting it when calling with GeneralTaxonomy::default(). We don't really use that method at all in our code except in one test so I guess it was easy to miss. We mostly load existing ones via https://github.com/onecodex/taxonomy#loading-a-taxonomy

[audy]

I ran into this as well:

In [3]: tax = taxonomy.Taxonomy.from_ncbi('ncbi_taxonomy/nodes.dmp', 'ncbi_taxonomy/names.dmp')

In [4]: parent = tax['2']

In [5]: parent
Out[5]: <TaxonomyNode (id=2 rank="superkingdom" name="Bacteria"))>

In [6]: tax.add_node
Out[6]: Taxonomy.add_node  # built-in bound method

In [7]: tax.add_node?
Docstring: Add a new node to the tree at the parent provided.
Type:      builtin_function_or_method

In [8]: tax.add_node('2', '10000000001')

In [9]: tax['10000000001']
Out[9]: <TaxonomyNode (id=10000000001 rank="no rank" name=""))>

In [10]: tax.add_node('2', '10000000002')

In [11]: tax['10000000002']
Out[11]: <TaxonomyNode (id=10000000002 rank="no rank" name=""))>

In [12]: tax.add_node('10000000002', '10000000003')
thread '<unnamed>' panicked at 'index out of bounds: the len is 2423674 but the index is 2423675', src/base.rs:252:9
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
---------------------------------------------------------------------------
PanicException                            Traceback (most recent call last)
<ipython-input-12-248cb6e8e221> in <module>
----> 1 tax.add_node('10000000002', '10000000003')

PanicException: index out of bounds: the len is 2423674 but the index is 2423675

In [13]: tax.children('10000000002')
thread '<unnamed>' panicked at 'index out of bounds: the len is 2423674 but the index is 2423675', src/base.rs:339:9

[Keats]

With #39 ?

[audy]

@Keats yep, from fixes:

In [1]: import taxonomy

In [2]: tax =taxonomy.Taxonomy.from_ncbi("ncbi_taxonomy")

In [3]: tax.add_node('2', '10000000001')

In [4]: tax.add_node('10000000001', '10000000002')
thread '<unnamed>' panicked at 'index out of bounds: the len is 2423674 but the index is 2423674', src/base.rs:209:9
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

[Keats]

This should be fixed in the fixes branch