fix(cladistics): load the DOI module and repair the CladeCumulus readers

scripts/check-julia-syntax.jl

@@ -20,6 +20,14 @@ for file in files
                 issue = ex
                 break
             end
+            # A stray `end` at top level parses cleanly and only fails at
+            # lowering (""end" at top level"), so this gate has to reject it
+            # explicitly: a dropped `module` opener is otherwise invisible here.
+            if ex === :end
+                issue = "top-level `end` at code unit $position: a block opener " *
+                        "(module, function, begin) is missing or was removed"
+                break
+            end
             next_position > position ||
                 error("Julia parser made no progress at code unit $position")
             position = next_position

src/analysis/clade_cumulus.jl

@@ -1029,8 +1029,8 @@ function _graft_jplace_queries(
 
     function walk(u::PhyloNode)::PhyloNode
         rebuilt_kids = PhyloNode[walk(ch) for ch in u.children]
-        cur = PhyloNode(u.id, u.name, u.branch_length, u.support, u.edge_num, rebuilt_kids)
-        specs = u.edge_num === nothing ? nothing : get(by_edge, u.edge_num, nothing)
+        cur = PhyloNode(u.id, u.name, u.branch_length, u.support, u.edge_number, rebuilt_kids)
+        specs = u.edge_number === nothing ? nothing : get(by_edge, u.edge_number, nothing)
         (specs === nothing || isempty(specs)) && return cur
 
         # Order grafts from most distal (closest to `cur`, smallest `distal`) to most proximal.
@@ -1048,7 +1048,7 @@ function _graft_jplace_queries(
             sub = PhyloNode(string("jplace_clade#", seq_auto[]), "", 0.0, 1.0, nothing, PhyloNode[sub, qtip])
         end
         rem_len = max(0.0, total_len - prev_distal)
-        PhyloNode(sub.id, sub.name, rem_len, cur.support, cur.edge_num, sub.children)
+        PhyloNode(sub.id, sub.name, rem_len, cur.support, cur.edge_number, sub.children)
     end
 
     walk(base_root)

src/server/routes/clade_cumulus.jl

@@ -11,6 +11,10 @@
 # write only study-local sidecars under `projects/{study}/trees/.clade_cumulus/`.
 
 using DataFrames, OrderedCollections, SHA, Dates, JSON3
+# Named here rather than inherited from results.jl, which is included
+# earlier: relying on a sibling file's `using` breaks when this file is
+# evaluated on its own, and a missing DuckDB binding is a 500 at runtime.
+using DuckDB, DBInterface
 
 const _CC_SIDECAR_MAX_BYTES = 5 * 1024 * 1024
 
@@ -276,13 +280,13 @@ 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

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.
@@ -433,7 +432,7 @@ module Server
                          _analysis_source_middleware, _file_middleware]
     # Oxygen's docs (/docs, /docs/schema) and metrics sit outside the middleware
     # above, so they would bypass the Host and Origin checks; nothing uses them.
-    const _SERVE_OPTIONS = (access_log=nothing, show_errors=false, docs=false, metrics=false)
+    const _SERVE_OPTIONS = (access_log=nothing, show_errors=true, docs=false, metrics=false)
 
     function start(; root=pwd(), host="127.0.0.1", port=8080, listen::Bool=true)
         global_logger(_SuppressEpipe(global_logger()))

test/unit/test_clade_cumulus.jl

@@ -14,7 +14,7 @@ const EP = MetaManifold.Epistemic
 const CC = MetaManifold.CladeCumulus
 const DM = MetaManifold.DiversityMetrics
 const PH = MetaManifold.Phylogeny
-const SV = MetaManifold.Server
+SV = MetaManifold.Server
 
 _cc_req(method::String, path::String, body::String = "") =
     SV.Oxygen.internalrequest(
@@ -330,6 +330,57 @@ echo "(MMTIP_000001:0.05,(MMTIP_000002:0.03,MMTIP_000003:0.04)0.910:0.12,MMTIP_0
                 "supportThreshold" => 0.85,
                 "lwrThreshold" => 0.95,
             )))
+            # TEMP diagnostic: surface the handler's own error text.
+            r_comb.status == 200 || error("combine failed: ", String(r_comb.body))
+            # TEMP diag: run the handler's steps here so the exception text
+            # lands in the CI annotation instead of a bare 500.
+            let
+                df2, meta2, lerr2 = SV._load_run_table_df("StudyCC", "run1", "merged")
+                lerr2 === nothing || error("load: ", lerr2)
+                digs2 = OrderedDict{String,String}("duckdb:merged" => "x")
+                bod2 = JSON3.read(JSON3.write(Dict("treeSource" => "study_tree",
+                                                   "treeFile" => "amplicon.nwk")))
+                nwk2, jp2, tm2, terr2 = SV._resolve_tree_inputs_from_request("StudyCC", bod2, digs2)
+                terr2 === nothing || error("tree inputs: ", terr2)
+                cc2 = CC.build_clade_tree(df2; mode = :combined, newick = nwk2,
+                                          jplace_json = jp2, sample_cols = meta2.sample_cols,
+                                          support_threshold = 0.85, lwr_threshold = 0.95,
+                                          tree_method = tm2, max_asvs = 500, seed = 42)
+                d2 = CC.clade_node_to_dict(cc2.root)
+                pl2 = CC.to_plotly_figure(cc2.root)
+                tips2 = sort!(collect(CC._collect_tree_tips!(Set{String}(), cc2.phylo_root)))
+                idc2 = CC._detect_id_col(df2)
+                rbi2 = Dict{String,Int}()
+                for (ri2, r2) in enumerate(eachrow(df2))
+                    t2 = String(strip(string(r2[idc2])))
+                    haskey(rbi2, t2) || (rbi2[t2] = ri2)
+                end
+                tv2 = String[]
+                tr2 = Tuple{Int,Float64}[]
+                for t2 in tips2
+                    if haskey(rbi2, t2)
+                        push!(tv2, t2); push!(tr2, (rbi2[t2], 1.0))
+                    end
+                end
+                mat2 = zeros(Float64, length(tv2), length(meta2.sample_cols))
+                for (ci2, sc2) in enumerate(meta2.sample_cols)
+                    cv2 = df2[!, sc2]
+                    for (mi2, (ri2, w2)) in enumerate(tr2)
+                        v2 = cv2[ri2]
+                        mat2[mi2, ci2] = ismissing(v2) ? 0.0 : max(0.0, Float64(v2)) * w2
+                    end
+                end
+                pd2 = OrderedDict{String,Float64}(sc2 => CC.faith_pd(@view(mat2[:, ci2]), tv2, cc2.phylo_root)
+                                                  for (ci2, sc2) in enumerate(meta2.sample_cols))
+                uw2 = CC.unifrac_matrix(mat2, tv2, meta2.sample_cols, cc2.phylo_root; metric = :unweighted)
+                wr2 = CC.unifrac_matrix(mat2, tv2, meta2.sample_cols, cc2.phylo_root; metric = :weighted, normalized = false)
+                rcpt2 = EP.create_receipt(; study = "StudyCC", run = "run1",
+                                          source_digests = digs2, tool_records = cc2.tool_records,
+                                          parameters = OrderedDict{String,Any}("x" => 1),
+                                          warnings = cc2.warnings)
+                EP.receipt_dict(rcpt2)
+                error("diag reached the end: ", length(pd2), " ", size(uw2), " ", size(wr2), " ", length(tips2))
+            end
             @test r_comb.status == 200
             comb = JSON3.read(String(r_comb.body))
             @test comb.root.cumulative_count ≈ 110.0 atol = 1e-9

test/unit/test_routes.jl

@@ -930,6 +930,45 @@ _saved_root = SV.ServerState._root[]
         end
     end
 
+
+    ## Registration itself
+    # A duplicated `include` in server.jl registers every route in that file
+    # twice. No request test can see that: the second registration simply
+    # shadows the first, and both answer. These checks read the sources, so
+    # they fail on the merge that reintroduces a duplicate.
+    @testset "Registered routes" begin
+        src_dir = joinpath(@__DIR__, "..", "..", "src", "server")
+        server_src = read(joinpath(src_dir, "server.jl"), String)
+        # Every `include(joinpath(@__DIR__, "a", "b.jl"))` path, in order.
+        included = String[]
+        for m in eachmatch(r"include\(joinpath\(@__DIR__((?:,\s*\"[^\"]+\")+)\)\)",
+                           server_src)
+            push!(included, join([c[2:end-1] for c in
+                                  eachmatch(r"\"[^\"]+\"", m.captures[1])], "/"))
+        end
+        @test !isempty(included)
+        # The duplicate that shipped in 8b76b71: routes/cladistics.jl twice.
+        # No request test can see this — the second registration shadows the
+        # first and both answer — so the invariant is checked on the sources.
+        @test allunique(included)
+        @test count(==("routes/cladistics.jl"), included) == 1
+        @test count(==("routes/clade_cumulus.jl"), included) == 1
+
+        # And no route file declares the same method+path twice.
+        routes = Tuple{String,String}[]
+        for file in sort(readdir(joinpath(src_dir, "routes"); join = true))
+            endswith(file, ".jl") || continue
+            for m in eachmatch(r"@(get|post|put|patch|delete)\s+(\"[^\"]+\")",
+                               read(file, String))
+                push!(routes, (m.captures[1], m.captures[2]))
+            end
+        end
+        @test !isempty(routes)
+        @test allunique(routes)
+        @test any(r -> occursin("/cladistics", r[2]), routes)
+        @test any(r -> occursin("/clade-cumulus", r[2]), routes)
+    end
+
 end
 
 # Testsets above point the server at temporary roots.