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Merge pull request #103 from OpenTreeOfLife/forward-ottids
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Make the otcetera web services forward OTT ids in names like `ott12345`
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@bredelings
bredelings authored Nov 12, 2020
2 parents b14bf8e + 6e2120e commit 5b19cfb
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Showing 3 changed files with 45 additions and 25 deletions.
62 changes: 41 additions & 21 deletions otc/ws/tolws.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -313,7 +313,7 @@ bool is_ancestor_of(N* f, N* s)
return (sec_ind >= fdata->trav_enter and sec_ind <= fdata->trav_exit);
}

node_lookup_t find_node_by_id_str(const SummaryTree_t & tree, const string & node_id)
node_lookup_t find_node_by_id_str(const SummaryTree_t & tree, const RichTaxonomy& taxonomy, const string & node_id)
{
const auto & tree_data = tree.get_data();

Expand All @@ -323,24 +323,39 @@ node_lookup_t find_node_by_id_str(const SummaryTree_t & tree, const string & nod
// Get the OTT ID
long raw_ott_id = long_ott_id_from_name(node_id);

// Try to find the OTT ID in the summary tree.
if (raw_ott_id >= 0) {
OttId ott_id = check_ott_id_size(raw_ott_id);
auto i2nit = tree_data.id_to_node.find(ott_id);
if (i2nit != tree_data.id_to_node.end()) {
return {i2nit->second};
}
LOG(WARNING) << "not finding " << ott_id << " extracted from " << node_id;
// 1. Check that the ID is not negative
if (raw_ott_id < 0)
{
LOG(WARNING) << "OTT ID " << raw_ott_id << " (from '"<<node_id<<"') is negative!";
return {};
}

// 2. Try and forward the ID.
OttId ott_id = check_ott_id_size(raw_ott_id);
if (auto ott_id2 = taxonomy.get_unforwarded_id(ott_id))
ott_id = *ott_id2;
else
{
LOG(WARNING) << "OTT ID " << ott_id << " (from '"<<node_id<<"') is neither a current ID nor a forwarded ID.";
return {};
}

// We didn't find a summary tree node for this OTT ID. Is this node listed as broken?
// 3. Try to find the OTT ID in the summary tree.
auto i2nit = tree_data.id_to_node.find(ott_id);
if (i2nit != tree_data.id_to_node.end())
return {i2nit->second};

// 4. We didn't find a summary tree node for this OTT ID. Is this node listed as broken?
if (auto bt_it = tree_data.broken_taxa.find(node_id); bt_it != tree_data.broken_taxa.end())
{
// if found we return the MRCA pointer in the first slot of the pair.
// if found, we return the MRCA pointer in the first slot of the pair.
return broken_taxon(bt_it->second.first);
}
else
{
LOG(WARNING) << "OTT ID" << ott_id << " (from '"<<node_id<<"') is not in the synth tree, and is not listed as broken.";
return {};
}
}

if (std::regex_match(node_id, matches, mrca_id_pattern))
Expand All @@ -355,11 +370,11 @@ node_lookup_t find_node_by_id_str(const SummaryTree_t & tree, const string & nod
assert(matches.size() >= 2);
std::string first_id = matches[1];
std::string second_id = matches[2];
auto result1 = find_node_by_id_str(tree, first_id);
auto result1 = find_node_by_id_str(tree, taxonomy, first_id);
if (result1.node == nullptr) {
return result1;
}
auto result2 = find_node_by_id_str(tree, second_id);
auto result2 = find_node_by_id_str(tree, taxonomy, second_id);
if (result2.node == nullptr) {
return result2;
}
Expand All @@ -368,9 +383,9 @@ node_lookup_t find_node_by_id_str(const SummaryTree_t & tree, const string & nod
return {};
}

node_lookup_t find_required_node_by_id_str(const SummaryTree_t & tree, const string & node_id)
node_lookup_t find_required_node_by_id_str(const SummaryTree_t & tree, const RichTaxonomy& taxonomy, const string & node_id)
{
auto result = find_node_by_id_str(tree, node_id);
auto result = find_node_by_id_str(tree, taxonomy, node_id);
if (not result.node) {
throw OTCBadRequest() << "node_id '" << node_id << "' was not found!";
}
Expand Down Expand Up @@ -512,7 +527,9 @@ string node_info_ws_method(const TreesToServe & tts,
bool include_lineage) {
LOG(DEBUG)<<"Got to node_info_ws_method( )";

auto result = find_required_node_by_id_str(*tree_ptr, node_id);
auto locked_taxonomy = tts.get_readable_taxonomy();
const auto & taxonomy = locked_taxonomy.first;
auto result = find_required_node_by_id_str(*tree_ptr, taxonomy, node_id);

auto response = node_info_json(tts, sta, result.node, include_lineage);
response["query"] = node_id;
Expand All @@ -528,7 +545,7 @@ pair<vector<const SumTreeNode_t*>,json> find_nodes_for_id_strings(const RichTaxo
json broken = json::object();
optional<string> bad_node_id;
for (auto node_id : node_ids) {
auto result = find_node_by_id_str(*tree_ptr, node_id);
auto result = find_node_by_id_str(*tree_ptr, taxonomy, node_id);
if (not result.node or (result.was_broken and fail_broken)) {
// Possible statuses:
// - invalid (never minted id)
Expand Down Expand Up @@ -718,12 +735,13 @@ auto lookup(const Map& m, const Key& k)


const SumTreeNode_t * get_node_for_subtree(const SummaryTree_t * tree_ptr,
const string & node_id,
const string & node_id,
const RichTaxonomy& taxonomy,
int height_limit,
uint32_t tip_limit)
{
assert(tree_ptr != nullptr);
auto result = find_required_node_by_id_str(*tree_ptr, node_id);
auto result = find_required_node_by_id_str(*tree_ptr, taxonomy, node_id);
if (result.was_broken) {
json broken;
broken["mrca"] = get_synth_node_label(result.node);
Expand Down Expand Up @@ -849,9 +867,9 @@ string newick_subtree_ws_method(const TreesToServe & tts,
int height_limit)
{
const uint32_t NEWICK_TIP_LIMIT = 100000;
auto focal = get_node_for_subtree(tree_ptr, node_id, height_limit, NEWICK_TIP_LIMIT);
auto locked_taxonomy = tts.get_readable_taxonomy();
const auto & taxonomy = locked_taxonomy.first;
auto focal = get_node_for_subtree(tree_ptr, node_id, taxonomy, height_limit, NEWICK_TIP_LIMIT);
NodeNamerSupportedByStasher nnsbs(label_format, taxonomy, tts);
ostringstream out;
write_newick_generic<const SumTreeNode_t *, NodeNamerSupportedByStasher>(out, focal, nnsbs, include_all_node_labels, height_limit);
Expand Down Expand Up @@ -891,7 +909,9 @@ string arguson_subtree_ws_method(const TreesToServe & tts,
const string & node_id,
int height_limit) {
const uint32_t NEWICK_TIP_LIMIT = 25000;
auto focal = get_node_for_subtree(tree_ptr, node_id, height_limit, NEWICK_TIP_LIMIT);
auto locked_taxonomy = tts.get_readable_taxonomy();
const auto & taxonomy = locked_taxonomy.first;
auto focal = get_node_for_subtree(tree_ptr, node_id, taxonomy, height_limit, NEWICK_TIP_LIMIT);
json response;
response["synth_id"] = sta->synth_id;
set<string> usedSrcIds;
Expand Down
2 changes: 1 addition & 1 deletion otc/ws/tolws.h
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Original file line number Diff line number Diff line change
Expand Up @@ -257,7 +257,7 @@ struct node_lookup_t
node_lookup_t(const SumTreeNode_t* n):node(n) {}
};

node_lookup_t find_node_by_id_str(const SummaryTree_t & tree, const std::string & node_id);
node_lookup_t find_node_by_id_str(const SummaryTree_t & tree, const RichTaxonomy&, const std::string & node_id);

class TreesToServe;

Expand Down
6 changes: 3 additions & 3 deletions ws/tolwsbooting.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1208,7 +1208,7 @@ bool read_tree_and_annotations(const fs::path & config_path,
//const auto & n2n = sum_tree_data.name_to_node;
for (json::const_iterator nit = node_obj.begin(); nit != node_obj.end(); ++nit) {
string k = nit.key();
auto result = find_node_by_id_str(tree, k);
auto result = find_node_by_id_str(tree, taxonomy, k);
//auto stnit = n2n.find(k);
if (result.node == nullptr) {
throw OTCError() << "Node " << k << " from annotations not found in tree.";
Expand Down Expand Up @@ -1327,11 +1327,11 @@ bool read_tree_and_annotations(const fs::path & config_path,
for (json::const_iterator ai_it = attach_obj.begin(); ai_it != attach_obj.end(); ++ai_it) {
attach_id_list.push_back(ai_it.key());
}
auto mrca_result = find_node_by_id_str(tree, mrca_id);
auto mrca_result = find_node_by_id_str(tree, taxonomy, mrca_id);
vector<const SumTreeNode_t *> avec;
avec.reserve(attach_id_list.size());
for (auto attach_id : attach_id_list) {
auto [anptr, _] = find_node_by_id_str(tree, attach_id);
auto [anptr, _] = find_node_by_id_str(tree, taxonomy, attach_id);
assert(anptr != nullptr);
avec.push_back(anptr);
}
Expand Down

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