Skip to content

Fix CladeCumulus graft edge field and tree-file validation type #229

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
hyperpolymath merged 11 commits into from
Oct 23, 2026
Merged

Fix CladeCumulus graft edge field and tree-file validation type #229

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
b6ab932
fix(clade-cumulus): repair field names, NHX support capture, LWR tole…
hyperpolymath Oct 23, 2026
0e409ed
fix(doi): restore missing module DOI opener
hyperpolymath Oct 23, 2026
238598e
fix(clade-cumulus): PhyloNode edge field is edge_number; widen _valid…
hyperpolymath Oct 23, 2026
6f052cc
fix(clade-cumulus): structured 500 for unhandled route errors; remain…
hyperpolymath Oct 23, 2026
6644ff5
fix(trees): accept AbstractString in tree-file helpers
hyperpolymath Oct 23, 2026
45eafa0
fix(clade-cumulus): stem-inclusive subtree PD after drag-drop; const …
hyperpolymath Oct 23, 2026
8502ffa
test: drop const from SV alias so test files can share one Main session
hyperpolymath Oct 23, 2026
f7b2996
fix(compositional): implement compositional_erfc locally; fix multino…
hyperpolymath Oct 23, 2026
bba6044
ci: retrigger (previous push produced no CI run)
hyperpolymath Oct 23, 2026
56d149d
merge: origin/main (#222, #226) into session branch
hyperpolymath Oct 23, 2026
49466a3
Merge branch 'main' into arena/86bcd6f5-metamanifold-webui
hyperpolymath Oct 23, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 9 additions & 0 deletions src/server/routes/clade_cumulus.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -190,6 +190,15 @@ end
end

@post "/api/v1/studies/{study}/runs/{run}/clade-cumulus" function(req::HTTP.Request, study::String, run::String)
try
return _clade_cumulus_post_impl(req, study, run)
catch e
@error "clade-cumulus request failed" exception = (e, catch_backtrace())
return json_error(500, "clade_cumulus_failed", sprint(showerror, e))
end
end

function _clade_cumulus_post_impl(req::HTTP.Request, study::String, run::String)
group = _req_group(req)
err = _validate_run_request(study, run)
!isnothing(err) && return err
Expand Down
10 changes: 5 additions & 5 deletions src/server/routes/trees.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,29 +14,29 @@ const _TREE_MAX_BYTES = 50 * 1024 * 1024
const _VIEW_MAX_BYTES = 5 * 1024 * 1024
const _tree_view_lock = ReentrantLock()

_trees_dir(study::String) = joinpath(ServerState.projects_dir(), study, "trees")
_tree_view_path(study::String, file::String) = joinpath(_trees_dir(study), ".views", file * ".json")
_trees_dir(study::AbstractString) = joinpath(ServerState.projects_dir(), study, "trees")
_tree_view_path(study::AbstractString, file::AbstractString) = joinpath(_trees_dir(study), ".views", file * ".json")

_tree_format(file::AbstractString) = endswith(lowercase(file), ".jplace") ? "jplace" : "newick"

function _valid_tree_file(file::AbstractString)::Bool

@chatgpt-codex-connector chatgpt-codex-connector Bot Oct 23, 2026

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

P1 Badge Normalize the tree filename before calling _tree_format

When treeFile comes from the JSON request, _resolve_tree_inputs_from_request obtains a SubString from strip; widening this validator lets that value pass, but the same path then calls the still-String-only _tree_format(tree_file) at src/server/routes/clade_cumulus.jl:113. Thus every treeSource: "study_tree" POST reaches a MethodError before the analysis try/catch and returns 500; convert tree_file to String at the request boundary or widen _tree_format too.

Useful? React with 👍 / 👎.

_valid_name(file) && any(ext -> endswith(lowercase(file), ext), _TREE_EXTENSIONS)
end

function _study_exists(study::String)::Bool
function _study_exists(study::AbstractString)::Bool
_valid_name(study) &&
(isdir(joinpath(ServerState.projects_dir(), study)) || study in _study_names())
end

function _tree_request_error(study::String, file::Union{String,Nothing}=nothing)
function _tree_request_error(study::AbstractString, file::Union{AbstractString,Nothing}=nothing)
_study_exists(study) || return json_error(404, "study_not_found", "Study '$study' not found")
isnothing(file) && return nothing
_valid_tree_file(file) || return json_error(400, "invalid_name",
"Tree files need a plain name ending in one of: $(join(_TREE_EXTENSIONS, ", "))")
nothing
end

function _tree_listing(study::String)
function _tree_listing(study::AbstractString)
dir = _trees_dir(study)
isdir(dir) || return NamedTuple[]
files = sort(filter(f -> _valid_tree_file(f) && isfile(joinpath(dir, f)), readdir(dir)))
Expand Down
Loading