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Merge pull request #248 from geneontology/add-result-count-search-api…
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…-issue235

adding result count request parameter #235 and #230
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@goodb
goodb committed Oct 1, 2019
2 parents e161fb6 + 034edd3 commit 751befa
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Showing 2 changed files with 72 additions and 52 deletions.
120 changes: 70 additions & 50 deletions minerva-server/src/main/java/org/geneontology/minerva/server/handler/ModelSearchHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -94,25 +94,27 @@ public ModelSearchResult searchGet(
@QueryParam("group") Set<String> group,
@QueryParam("date") String date,
@QueryParam("offset") int offset,
@QueryParam("limit") int limit
@QueryParam("limit") int limit,
@QueryParam("count") String count
){
ModelSearchResult result = new ModelSearchResult();
result = search(gene_product_class_uris, goterms, pmids, title, state, contributor, group, date, offset, limit);
return result;
result = search(gene_product_class_uris, goterms, pmids, title, state, contributor, group, date, offset, limit, count);
return result;
}
//TODO make junit tests out of these.
//examples
//http://127.0.0.1:6800/search/?
//?gene_product_class_uri=http://identifiers.org/mgi/MGI:1328355
//&gene_product_class_uri=http://identifiers.org/mgi/MGI:87986
//?gp=http://identifiers.org/mgi/MGI:1328355
//&gp=http://identifiers.org/mgi/MGI:87986
//&goterm=http://purl.obolibrary.org/obo/GO_0030968
//&title=mouse
//&pmid=PMID:19911006
//&state=development&state=review {development, production, closed, review, delete} or operator
//&count
public ModelSearchResult search(
Set<String> gene_product_ids, Set<String> goterms, Set<String>pmids,
String title_search,Set<String> state_search, Set<String> contributor_search, Set<String> group_search, String date_search,
int offset, int limit) {
int offset, int limit, String count) {
ModelSearchResult r = new ModelSearchResult();
Set<String> type_ids = new HashSet<String>();
if(gene_product_ids!=null) {
Expand Down Expand Up @@ -226,7 +228,18 @@ public ModelSearchResult search(
if(offset==0&&limit==0) {
limit_constraint = "LIMIT 1000\n";
}

//default group by
String group_by_constraint = "GROUP BY ?id ?date ?title ?cam ?state <ind_return_list> ";
//default return block
String return_block = "?cam ?id ?date ?title ?state <ind_return_list> (GROUP_CONCAT(?contributor;separator=\";\") AS ?contributors) (GROUP_CONCAT(?group;separator=\";\") AS ?groups)";
if(count!=null) {
return_block = "(count(distinct ?cam) as ?count)";
limit_constraint = "";
offset_constraint = "";
group_by_constraint = "";
}
sparql = sparql.replaceAll("<return_block>", return_block);
sparql = sparql.replaceAll("<group_by_constraint>", group_by_constraint);
sparql = sparql.replaceAll("<ind_return_list>", ind_return_list);
sparql = sparql.replaceAll("<types>", types);
sparql = sparql.replaceAll("<pmid_constraints>", pmid_constraints);
Expand Down Expand Up @@ -254,62 +267,69 @@ public ModelSearchResult search(
e.printStackTrace();
return r;
}

String n_count = null;
try {
while(result.hasNext()) {
BindingSet bs = result.next();
//model meta
String id = bs.getBinding("id").getValue().stringValue();
String date = bs.getBinding("date").getValue().stringValue();
String title = bs.getBinding("title").getValue().stringValue();
String contribs = bs.getBinding("contributors").getValue().stringValue();
//optional values (some are empty)
Binding state_binding = bs.getBinding("state");
String state = "";
if(state_binding!=null) {
state = state_binding.getValue().stringValue();
}
Binding group_binding = bs.getBinding("groups");
String groups_ = "";
if(group_binding!=null) {
groups_ = group_binding.getValue().stringValue();
}
Set<String> contributors = new HashSet<String>();
if(contributors!=null) {
for(String c : contribs.split(";")) {
contributors.add(c);
if(count!=null) {
n_count = bs.getBinding("count").getValue().stringValue();
}else {
//model meta
String id = bs.getBinding("id").getValue().stringValue();
String date = bs.getBinding("date").getValue().stringValue();
String title = bs.getBinding("title").getValue().stringValue();
String contribs = bs.getBinding("contributors").getValue().stringValue();
//optional values (some are empty)
Binding state_binding = bs.getBinding("state");
String state = "";
if(state_binding!=null) {
state = state_binding.getValue().stringValue();
}
}
Set<String> groups = new HashSet<String>();
if(groups_!=null) {
for(String c : groups_.split(";")) {
groups.add(c);
Binding group_binding = bs.getBinding("groups");
String groups_ = "";
if(group_binding!=null) {
groups_ = group_binding.getValue().stringValue();
}
Set<String> contributors = new HashSet<String>();
if(contributors!=null) {
for(String c : contribs.split(";")) {
contributors.add(c);
}
}
}
ModelMeta mm = id_model.get(id);
if(mm==null) {
mm = new ModelMeta(id, date, title, state, contributors, groups);
}
//matching
for(String ind : ind_return.keySet()) {
String ind_class_match = bs.getBinding(ind.replace("?", "")).getValue().stringValue();
Set<String> matching_inds = mm.query_match.get(ind_return.get(ind));
if(matching_inds==null) {
matching_inds = new HashSet<String>();
Set<String> groups = new HashSet<String>();
if(groups_!=null) {
for(String c : groups_.split(";")) {
groups.add(c);
}
}
ModelMeta mm = id_model.get(id);
if(mm==null) {
mm = new ModelMeta(id, date, title, state, contributors, groups);
}
//matching
for(String ind : ind_return.keySet()) {
String ind_class_match = bs.getBinding(ind.replace("?", "")).getValue().stringValue();
Set<String> matching_inds = mm.query_match.get(ind_return.get(ind));
if(matching_inds==null) {
matching_inds = new HashSet<String>();
}
matching_inds.add(ind_class_match);
mm.query_match.put(ind_return.get(ind), matching_inds);
}
matching_inds.add(ind_class_match);
mm.query_match.put(ind_return.get(ind), matching_inds);
id_model.put(id, mm);
}
id_model.put(id, mm);
}
} catch (QueryEvaluationException e) {
r.message = "Query Evaluation Problem - probably a time out";
r.error = e.getMessage();
e.printStackTrace();
return r;
}
r.n = id_model.size();
r.models = new HashSet<ModelMeta>(id_model.values());
} if(n_count!=null) {
r.n = Integer.parseInt(n_count);
}else {
r.n = id_model.size();
r.models = new HashSet<ModelMeta>(id_model.values());
}
try {
result.close();
} catch (QueryEvaluationException e) {
Expand Down
4 changes: 2 additions & 2 deletions minerva-server/src/main/resources/ModelSearchQueryTemplate.rq
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ PREFIX causally_upstream_of: <http://purl.obolibrary.org/obo/RO_0002411>
PREFIX provides_direct_input_for: <http://purl.obolibrary.org/obo/RO_0002413>
PREFIX directly_positively_regulates: <http://purl.obolibrary.org/obo/RO_0002629>

SELECT ?cam ?id ?date ?title ?state <ind_return_list> (GROUP_CONCAT(?contributor;separator=";") AS ?contributors) (GROUP_CONCAT(?group;separator=";") AS ?groups)
SELECT <return_block>
WHERE {
GRAPH ?cam {
?cam <http://purl.org/dc/elements/1.1/title> ?title ;
Expand All @@ -31,7 +31,7 @@ WHERE {
<title_constraint>
}
}
GROUP BY ?id ?date ?title ?cam ?state <ind_return_list>
<group_by_constraint>
ORDER BY desc(?date)
<limit_constraint>
<offset_constraint>
Expand Down

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