Merge branch 'master' into development

OpenTreeOfLife · Sep 15, 2024 · 4babd22 · 4babd22
2 parents 2d65260 + 49aeedb
commit 4babd22
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diff --git a/data/synth-setups/synth-2/expectedws/subtree-2/expected.json b/data/synth-setups/synth-2/expectedws/subtree-2/expected.json
@@ -1,6 +1,6 @@
 {
-  "newick": "((((((((((Magnoliophyta_ott99252,eudicotyledons_ott431495)Mesangiospermae_ott5298374)Liliopsida_ott1058517)Petrosaviidae_ott5308424)Asparagales_ott557124)Amaryllidaceae_ott258473)Amaryllidoideae_ott267867,Glaucophyta_ott664970,Rhodophyta_ott878953)Archaeplastida_ott5268475,Amaryllis_carrascoi_ott4671788),((((((((Dipnotetrapodomorpha_ott4940726)Sarcopterygii_ott458402)Euteleostomi_ott114654)Teleostomi_ott114656)'Gnathostomata (superclass in phylum Chordata) ott278114')'Vertebrata (subphylum in Opisthokonta) ott801601')'Craniata (subphylum in Deuterostomia) ott947318')Chordata_ott125642)Deuterostomia_ott147604,(((Rhynchonellata_ott107877)Rhynchonelliformea_ott681832)Brachiopoda_ott826261,Platyhelminthes_ott555379,Annelida_ott941620,Mollusca_ott802117)Lophotrochozoa_ott155737,Haptophyta_ott151014,Choanoflagellida_ott202765,(('Ciliophora (phylum in subkingdom SAR) ott302424')Alveolata_ott266751,((Foraminifera_ott936399)Retaria_ott4972641)Rhizaria_ott6929,(Bacillariophyta_ott5342311)Stramenopiles_ott266745)SAR_ott5246039,Nematoda_ott395057,(((((Ascomycota_ott439373,Basidiomycota_ott634628)Dikarya_ott656316)'h2007-1 ott5584405')'h2007-2 ott5576447')Fungi_ott352914)Nucletmycea_ott5246132,(Arachnida_ott511967)Chelicerata_ott1041457,Cnidaria_ott641033,Centrohelida_ott755852,(Insecta_ott1062253)Hexapoda_ott568991,Amoebozoa_ott1064655,Excavata_ott2927065,Amaryllis_brevicornis_ott4671798)Eukaryota_ott304358,Bacteria_ott844192,'Archaea (domain silva:D37982/#1) ott996421')cellular_organisms_ott93302;",
+  "newick": "((((((((((Magnoliophyta_ott99252,eudicotyledons_ott431495)Mesangiospermae_ott5298374)Liliopsida_ott1058517)Petrosaviidae_ott5308424)Asparagales_ott557124)Amaryllidaceae_ott258473)Amaryllidoideae_ott267867,Glaucophyta_ott664970,Rhodophyta_ott878953)Archaeplastida_ott5268475,Amaryllis_carrascoi_ott4671788)mrcaott56601ott4671788,((((((((Dipnotetrapodomorpha_ott4940726)Sarcopterygii_ott458402)Euteleostomi_ott114654)Teleostomi_ott114656)'Gnathostomata (superclass in phylum Chordata) ott278114')'Vertebrata (subphylum in Opisthokonta) ott801601')'Craniata (subphylum in Deuterostomia) ott947318')Chordata_ott125642)Deuterostomia_ott147604,(((Rhynchonellata_ott107877)Rhynchonelliformea_ott681832)Brachiopoda_ott826261,Platyhelminthes_ott555379,Annelida_ott941620,Mollusca_ott802117)Lophotrochozoa_ott155737,Haptophyta_ott151014,Choanoflagellida_ott202765,(('Ciliophora (phylum in subkingdom SAR) ott302424')Alveolata_ott266751,((Foraminifera_ott936399)Retaria_ott4972641)Rhizaria_ott6929,(Bacillariophyta_ott5342311)Stramenopiles_ott266745)SAR_ott5246039,Nematoda_ott395057,(((((Ascomycota_ott439373,Basidiomycota_ott634628)Dikarya_ott656316)'h2007-1 ott5584405')'h2007-2 ott5576447')Fungi_ott352914)Nucletmycea_ott5246132,(Arachnida_ott511967)Chelicerata_ott1041457,Cnidaria_ott641033,Centrohelida_ott755852,(Insecta_ott1062253)Hexapoda_ott568991,Amoebozoa_ott1064655,Excavata_ott2927065,Amaryllis_brevicornis_ott4671798)Eukaryota_ott304358,Bacteria_ott844192,'Archaea (domain silva:D37982/#1) ott996421')cellular_organisms_ott93302;",
   "supporting_studies": [
     "xx_2@Tree1"
   ]
-}
+}
diff --git a/expectedws/subtree/expected.json b/expectedws/subtree/expected.json
@@ -1,5 +1,5 @@
 {
-  "newick": "((A1_ott1,A2_ott2,A3_ott3)A_ott100,(B1_ott11,B2_ott12,B3_ott13)B_ott200);",
+  "newick": "((A1_ott1,A2_ott2,A3_ott3)A_ott100,(B1_ott11,B2_ott12,B3_ott13)B_ott200)mrcaott1ott11;",
   "supporting_studies": [
     "xx_1@t1"
   ]

diff --git a/ws/tolwsbooting.cpp b/ws/tolwsbooting.cpp
@@ -241,7 +241,7 @@ std::string process_subtree(const json& parsedargs) {
     int height_limit = extract_argument_or_default<int>(parsedargs, "height_limit", (format == "arguson")? 3 : -1);
     const SummaryTreeAnnotation * sta = get_annotations(tts, synth_id);
     const SummaryTree_t * treeptr = get_summary_tree(tts, synth_id);
-    bool all_node_labels = extract_argument_or_default<bool>(parsedargs, "include_all_node_labels", false);
+    bool all_node_labels = extract_argument_or_default<bool>(parsedargs, "include_all_node_labels", true);
     if (format == "newick") {
         return newick_subtree_ws_method(tts, treeptr, node_id, nns, all_node_labels, height_limit);
     } else {