appears to export taxonomy, but not synonyms

Author: mtholder

tools/taxonomy-parser.cpp

@@ -335,7 +335,8 @@ void write_meta_xml(const std::string ofn) {
 "    <field term=\"http://rs.tdwg.org/dwc/terms/class\" index=\"6\"/>\n"
 "    <field term=\"http://rs.tdwg.org/dwc/terms/order\" index=\"7\"/>\n"
 "    <field term=\"http://rs.tdwg.org/dwc/terms/family\" index=\"8\"/>\n"
-"    <field term=\"http://rs.tdwg.org/dwc/terms/genus\" index=\"8\"/>\n"
+"    <field term=\"http://rs.tdwg.org/dwc/terms/genus\" index=\"9\"/>\n"
+"    <field term=\"http://rs.tdwg.org/dwc/terms/species\" index=\"10\"/>\n"
 "  </core>\n"
 "</archive>\n";
     std::ofstream tf (ofn);
@@ -344,7 +345,18 @@ void write_meta_xml(const std::string ofn) {
 }
 
 std::unordered_map<TaxonomicRank, int> g_rank2num;
-
+const char dwca_sep = ',';
+string escape_for_dwca(const string & ins) {
+    if (ins.find(dwca_sep) == string::npos) {
+        return ins;
+    }
+    string estr;
+    estr.reserve(2 + ins.length());
+    estr.append(1, '\"');
+    estr.append(ins);
+    estr.append(1, '\"');
+    return estr;
+}
 void ini_global_rank_num() {
     g_rank2num[TaxonomicRank::RANK_SPECIES] = 5;
     g_rank2num[TaxonomicRank::RANK_GENUS] = 4;
@@ -357,45 +369,81 @@ void ini_global_rank_num() {
 
 void write_ranks(std::ostream & out,
     const Tree_t::node_type & node,
-    const TaxonomyRecord & rec 
+    const TaxonomyRecord & rec,
+    const Taxonomy & taxonomy
     ) {
-    string kingdom_s; // 0
-    string phylum_s;  // 1
-    string class_s;   // 2
-    string order_s;   // 3
-    string family_s;  // 4
-    string genus_s;   // 5
-    string species_s; // 6
     int ini_looking_for = 6;
     int looking_for = ini_looking_for;
     std::vector<std::string> n_rank_names;
     n_rank_names.resize(1 + looking_for);
     auto tr = string_to_rank(rec.rank, true);
-    if (tr == TaxonomicRank::RANK_NO_RANK
-        || tr == TaxonomicRank::RANK_NO_RANK_TERMINAL) {
-        // pass
-    } else {
-        auto to_num_it = g_rank2num.find(tr);
-        if (to_num_it != g_rank2num.end()) {
-            looking_for = to_num_it->second;
-            n_rank_names.at(1 + looking_for) = rec.name;
+    auto to_num_it = g_rank2num.find(tr);
+    if (to_num_it != g_rank2num.end()) {
+        looking_for = to_num_it->second;
+        n_rank_names.at(1 + looking_for) = rec.name;
+    }
+    auto * curr_nd = &node;
+    while (looking_for >= 0) {
+        curr_nd = curr_nd->get_parent();
+        if (curr_nd == nullptr) {
+            break;
         }
+        assert(curr_nd->has_ott_id());
+        auto ott_id = curr_nd->get_ott_id();
+        const auto & curr_rec = taxonomy.record_from_id(ott_id);
+        auto ctr = string_to_rank(curr_rec.rank, true);
+        auto cto_num_it = g_rank2num.find(ctr);
+        if (cto_num_it != g_rank2num.end()) {
+            looking_for = cto_num_it->second;
+            n_rank_names.at(1 + looking_for) = curr_rec.name;
+        }   
+    }
+    for (auto nm : n_rank_names) {
+        out << dwca_sep << escape_for_dwca(nm);
     }
 }
 
 void write_taxa_txt(const std::string ofn,
         const Taxonomy & taxonomy,
         const Tree_t & the_tree ) {
     std::ofstream tf (ofn);
-    std::ostream * osp = &cout;
+    // std::ostream * osp = &cout;
+    std::ostream * osp = &tf;
+    *osp << "taxonId"
+         << dwca_sep << "parentNameUsageID"
+         << dwca_sep << "scientificName"
+         << dwca_sep << "taxonRank"
+         << dwca_sep << "kingdom"
+         << dwca_sep << "phylum"
+         << dwca_sep << "class"
+         << dwca_sep << "order"
+         << dwca_sep << "family"
+         << dwca_sep << "genus"
+         << dwca_sep << "species" << '\n';
     for (auto nd : iter_pre_const(the_tree)) {
         assert(nd->has_ott_id());
         auto ott_id = nd->get_ott_id();
         const auto & rec = taxonomy.record_from_id(ott_id);
-        *osp << ott_id
-        << '\t' << rec.name 
-        << '\t' << rec.rank;
-        write_ranks(*osp, *nd, rec);
+        *osp << ott_id << dwca_sep;
+        auto par = nd->get_parent();
+        if (par != nullptr) {
+            *osp << par->get_ott_id();
+        }
+        
+        std::ostringstream rnss;
+        rnss << rec.name;
+        string rn = rnss.str();
+        *osp << dwca_sep << escape_for_dwca(rn)
+             << dwca_sep ;
+        auto tr = string_to_rank(rec.rank);
+        if (tr != TaxonomicRank::RANK_NO_RANK
+            && tr != TaxonomicRank::RANK_NO_RANK_TERMINAL
+            && tr != TaxonomicRank::RANK_INFRASPECIFICNAME) {
+            *osp << rec.rank;
+        } else {
+            // pass
+        }
+        write_ranks(*osp, *nd, rec, taxonomy);
         *osp << "\n";
     }
     tf.close();