Fix post-merge regressions: DOI module, CladeCumulus API, and route type stability

src/core/doi.jl

@@ -16,6 +16,8 @@
 #   * Durable write-ahead journal; immutable DOI/provenance receipts
 #   * DOI insertion never rewrites scientific objects
 
+module DOI
+
 using Dates, SHA, HTTP, JSON3, Logging
 
 export DOIConfig, Deposition, PublicationReceipt,

src/pipeline/phylogeny.jl

@@ -34,6 +34,7 @@ export REFERENCE_STEPS, PLACEMENT_STEPS, Step, placement_settings, run_workflow,
     using ..PipelineLog
     using ..Validation
     using ..Tools: tool_bin, _sq, _run_logged, _safe_optional_args, _num
+    import ..Tools
     using ..RemoteExec: run_remote, checked_target
     import ..Provenance
 

src/server/routes/clade_cumulus.jl

@@ -64,7 +64,9 @@ function _probe_optional_phylo_tool(tool_key::String, fallbacks::Vector{String})
     end
 end
 
-function _load_run_table_df(study::String, run::String, table::String; group::Union{String,Nothing}=nothing)
+function _load_run_table_df(study::String, run::String, table::AbstractString;
+                            group::Union{String,Nothing}=nothing)
+    table = String(table)
     dir = _require_duckdb(study, run; group)
     isnothing(dir) && return (nothing, nothing, json_error(404, "no_results",
         "No results for run '$run' - run the pipeline first"))
@@ -92,9 +94,9 @@ function _resolve_tree_inputs_from_request(
     body,
     source_digests::OrderedDict{String,String},
 )
-    tree_source = lowercase(strip(string(get(body, :treeSource, "auto"))))
-    tree_file = strip(string(get(body, :treeFile, "")))
-    inline_newick = strip(string(get(body, :newick, "")))
+    tree_source = String(lowercase(strip(string(get(body, :treeSource, "auto")))))
+    tree_file = String(strip(string(get(body, :treeFile, ""))))
+    inline_newick = String(strip(string(get(body, :newick, ""))))
 
     if tree_source == "study_tree" || (!isempty(tree_file) && tree_source == "auto")
         _valid_tree_file(tree_file) || return (nothing, nothing, :auto,
@@ -145,19 +147,27 @@ end
             names_df = DataFrame(DBInterface.execute(con, "SHOW TABLES"))
             tlist = sort(String[string(r.name) for r in eachrow(names_df)])
             for t in tlist
-                cols = _duckdb_columns(con, t)
-                scols = _sample_count_columns(con, t)
-                isempty(scols) && continue
-                nrows = Int(only(DataFrame(DBInterface.execute(con, "SELECT COUNT(*) AS n FROM \"$t\""))).n)
-                has_seq = any(c -> c in ("Sequence", "sequence", "seq", "DNA"), cols)
-                ranks = [r for r in MetaManifold.CladeCumulus.DEFAULT_TAXONOMIC_RANKS if r in cols]
-                push!(tables_info, OrderedDict{String,Any}(
-                    "table"        => t,
-                    "row_count"    => nrows,
-                    "sample_count" => length(scols),
-                    "has_sequence" => has_seq,
-                    "ranks"        => ranks,
-                ))
+                # `SHOW TABLES` includes views; a view backed by a DuckDB
+                # replacement scan is bound to the connection that registered it
+                # and cannot be queried from a new connection.
+                try
+                    cols = _duckdb_columns(con, t)
+                    scols = _sample_count_columns(con, t)
+                    isempty(scols) && continue
+                    nrows = Int(only(DataFrame(DBInterface.execute(con, "SELECT COUNT(*) AS n FROM \"$t\""))).n)
+                    has_seq = any(c -> c in ("Sequence", "sequence", "seq", "DNA"), cols)
+                    ranks = [r for r in MetaManifold.CladeCumulus.DEFAULT_TAXONOMIC_RANKS if r in cols]
+                    push!(tables_info, OrderedDict{String,Any}(
+                        "table"        => t,
+                        "row_count"    => nrows,
+                        "sample_count" => length(scols),
+                        "has_sequence" => has_seq,
+                        "ranks"        => ranks,
+                    ))
+                catch err
+                    err isa InterruptException && rethrow()
+                    @warn "clade-cumulus sources: skipping unreadable DuckDB object" object=t exception=err
+                end
             end
         finally
             DBInterface.close!(con)
@@ -200,10 +210,10 @@ end
         return json_error(400, "invalid_json", "Request body must be valid JSON")
     end
 
-    table = strip(string(get(body, :table, "merged")))
+    table = String(strip(string(get(body, :table, "merged"))))
     _valid_name(table) || return json_error(400, "invalid_table", "Invalid table name '$table'")
 
-    mode_str = lowercase(strip(string(get(body, :mode, "combined"))))
+    mode_str = String(lowercase(strip(string(get(body, :mode, "combined")))))
     mode_str in ("phylogenetic", "taxonomic", "combined") ||
         return json_error(400, "invalid_mode", "mode must be 'phylogenetic', 'taxonomic', or 'combined'")
     mode_sym = Symbol(mode_str)
@@ -253,6 +263,7 @@ end
     # Compute Faith's PD + Unweighted & Weighted UniFrac when a phylogenetic tree is present,
     # including split `.jplace` query placements (`<qname>@edge<N>#<k>`).
     diversity_payload = nothing
+    try
     if cc_res.phylo_root !== nothing && !isempty(meta.sample_cols)
         tip_list = sort!(collect(MetaManifold.CladeCumulus._collect_tree_tips!(Set{String}(), cc_res.phylo_root)))
         id_col = MetaManifold.CladeCumulus._detect_id_col(df)
@@ -268,13 +279,13 @@ end
             jd_div = MetaManifold.CladeCumulus.parse_jplace(jplace_str)
             for q in jd_div.queries
                 q.status === :valid && !isempty(q.candidates) || continue
-                tw = sum((c.weight for c in q.candidates); init = 0.0)
+                tw = sum((c.like_weight for c in q.candidates); init = 0.0)
                 tw > 0.0 || continue
                 multi = length(q.candidates) > 1
                 for (qname, _) in q.names
                     for (ci, cand) in enumerate(q.candidates)
                         tid = multi ? string(qname, "@edge", cand.edge_num, "#", ci) : qname
-                        tip_weights[tid] = cand.weight / tw
+                        tip_weights[tid] = cand.like_weight / tw
                     end
                 end
             end
@@ -328,6 +339,9 @@ end
                 "top_branch_contributions"    => top_branches,
             )
         end
+    catch e
+        @error "clade-cumulus diversity computation failed" exception=(e, catch_backtrace())
+        return json_error(500, "clade_cumulus_diversity_failed", sprint(showerror, e))
     end
 
     receipt = MetaManifold.Epistemic.create_receipt(;
@@ -386,15 +400,15 @@ end
         return json_error(400, "invalid_json", "Request body must be valid JSON")
     end
 
-    source_id = strip(string(get(body, :sourceId, "")))
-    target_id = strip(string(get(body, :targetId, "")))
+    source_id = String(strip(string(get(body, :sourceId, ""))))
+    target_id = String(strip(string(get(body, :targetId, ""))))
     (isempty(source_id) || isempty(target_id)) &&
         return json_error(400, "missing_clade_ids", "Both sourceId and targetId are required")
 
-    table = strip(string(get(body, :table, "merged")))
+    table = String(strip(string(get(body, :table, "merged"))))
     _valid_name(table) || return json_error(400, "invalid_table", "Invalid table name '$table'")
 
-    mode_str = lowercase(strip(string(get(body, :mode, "combined"))))
+    mode_str = String(lowercase(strip(string(get(body, :mode, "combined")))))
     mode_str in ("phylogenetic", "taxonomic", "combined") ||
         return json_error(400, "invalid_mode", "mode must be 'phylogenetic', 'taxonomic', or 'combined'")
     mode_sym = Symbol(mode_str)

src/server/routes/cladistics.jl

@@ -205,7 +205,7 @@ function _cc_compute(study::String, id::String)
     isnothing(doc) && error("The Cladistics source document is unreadable")
     counts, tips, samples, counts_doc = _cc_read_counts(study, id)
     tree_text = read(_clad_files(study, id)["reference.treefile"], String)
-    tree = CC.parse_newick(tree_text)
+    tree = CC.parse_phylogenetic_tree(tree_text)
     Set(keys(tree.tips)) == Set(tips) ||
         error("The inferred tree tips do not exactly match the saved ASV count columns")
     analysed = CC.analyse_phylogeny(tree, counts, tips, samples)

src/server/routes/trees.jl

@@ -17,9 +17,9 @@ 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")
 
-_tree_format(file::String) = endswith(lowercase(file), ".jplace") ? "jplace" : "newick"
+_tree_format(file::AbstractString) = endswith(lowercase(file), ".jplace") ? "jplace" : "newick"
 
-function _valid_tree_file(file::String)::Bool
+function _valid_tree_file(file::AbstractString)::Bool
     _valid_name(file) && any(ext -> endswith(lowercase(file), ext), _TREE_EXTENSIONS)
 end
 

src/server/server.jl

@@ -118,7 +118,6 @@ module Server
     include(joinpath(@__DIR__, "routes", "phylogeny.jl"))
     include(joinpath(@__DIR__, "routes", "cladistics.jl"))
     include(joinpath(@__DIR__, "routes", "clade_cumulus.jl"))
-    include(joinpath(@__DIR__, "routes", "cladistics.jl"))
 
     ## Bad request middleware
     # Helpers deep in a route (e.g. `_req_group`) throw this to reject a request.

test/unit/test_clade_cumulus.jl

@@ -252,8 +252,8 @@ done
 echo "(MMTIP_000001:0.05,(MMTIP_000002:0.03,MMTIP_000003:0.04)0.910:0.12,MMTIP_000004:0.08);" > "$OUT"
 """)
             chmod(mock_ft, 0o755)
-            old_ft = get(PH.Tools._tools, "fasttree", nothing)
-            PH.Tools._tools["fasttree"] = mock_ft
+            old_ft = get(MetaManifold.Tools._tools, "fasttree", nothing)
+            MetaManifold.Tools._tools["fasttree"] = mock_ft
             try
                 s4 = [
                     "ASV_1" => "ACGTACGTACGTACGTACGT",
@@ -267,9 +267,9 @@ echo "(MMTIP_000001:0.05,(MMTIP_000002:0.03,MMTIP_000003:0.04)0.910:0.12,MMTIP_0
                                r["sha256"] == bytes2hex(open(sha256, mock_ft)), ft_res.tool_records)
             finally
                 if old_ft === nothing
-                    delete!(PH.Tools._tools, "fasttree")
+                    delete!(MetaManifold.Tools._tools, "fasttree")
                 else
-                    PH.Tools._tools["fasttree"] = old_ft
+                    MetaManifold.Tools._tools["fasttree"] = old_ft
                 end
             end
         end