From 340054d01ea4174e5000955199fb0993b99e7be9 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sat, 25 May 2024 15:26:51 -0400 Subject: [PATCH] Edited web endpoint/controllers descriptions --- src/main/java/cpath/web/ApiControllerV1.java | 16 ++++++++-------- src/main/java/cpath/web/ApiControllerV2.java | 12 ++++++------ 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/main/java/cpath/web/ApiControllerV1.java b/src/main/java/cpath/web/ApiControllerV1.java index 767bbca4..9c9dfcac 100644 --- a/src/main/java/cpath/web/ApiControllerV1.java +++ b/src/main/java/cpath/web/ApiControllerV1.java @@ -35,7 +35,7 @@ public class ApiControllerV1 extends BasicController { @GetMapping(path = "get", produces = {"application/vnd.biopax.rdf+xml", "application/ld+json", "application/json", "application/xml", "text/plain"}) @Operation( - summary = "Fetch a BioPAX sub-model by URIs/IDs and optionally convert to another output format (query parameters must be URL-encoded and not too many).", + summary = "Fetch a BioPAX sub-model by URIs/IDs and optionally convert to another output format (query parameters must be URL-encoded and not too many)", description = "Retrieve BioPAX pathways, interactions, physical entities from the db by URIs; " + "optionally, convert the result to other output formats." ) @@ -73,7 +73,7 @@ public void fetchQuery(@Valid Fetch args, BindingResult bindingResult, @GetMapping(path = "top_pathways", produces = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE}) @Operation( - summary = "HTTP GET, search for top pathways.", + summary = "Search for top-level bio pathways", description = "Find root/parent Pathway objects, i.e, ones that are neither 'controlled' " + "nor a 'pathwayComponent' of another biological process; trivial pathways are excluded from the results;" + " can filter by datasource and organism." @@ -88,7 +88,7 @@ public SearchResponse topPathwaysQueryGet(@Valid TopPathways args, BindingResult consumes = {APPLICATION_FORM_URLENCODED_VALUE}, produces = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE}) @Operation( - summary = "Search for top-level bio pathways.", + summary = "Search for top-level bio pathways", description = "Find root/parent Pathway objects that are neither controlled " + "nor a pathwayComponent of another biological process; trivial pathways are excluded from the results;" + " can filter by datasource and organism." @@ -117,7 +117,7 @@ public SearchResponse topPathwaysQuery(@Valid TopPathways args, BindingResult bi @GetMapping(path = "traverse", produces = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE}) @Operation( - summary = "Access properties of BioPAX elements using graph path expressions", + summary = "Access properties of BioPAX elements using graph path expressions (xpath-like)", description = "To collect specific BioPAX property values, use the following path accessor format: " + "InitialClass/property[:filterClass]/[property][:filterClass]... A \"*\" sign after the property " + "instructs the path accessor to transitively traverse that property. For example, the following " + @@ -140,7 +140,7 @@ public TraverseResponse traverseQueryGet(@Valid Traverse args, BindingResult bin consumes = {APPLICATION_FORM_URLENCODED_VALUE}, produces = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE}) @Operation( - summary = "Access properties of BioPAX elements using graph path expressions (xpath-like).", + summary = "Access properties of BioPAX elements using graph path expressions (xpath-like)", description = "To collect specific BioPAX property values, use the following path accessor format: " + "InitialClass/property[:filterClass]/[property][:filterClass]... A \"*\" sign after the property " + "instructs the path accessor to transitively traverse that property. For example, the following " + @@ -177,7 +177,7 @@ public TraverseResponse traverseQuery(@Valid Traverse args, BindingResult bindin @GetMapping(path = "graph", produces = {"application/vnd.biopax.rdf+xml", "application/ld+json", "application/json", "application/xml", "text/plain"}) @Operation( - summary = "BioPAX Graph Query and optional converter to another output format (parameters must be URL-encoded and not too many).", + summary = "A BioPAX graph query and optional converter to another output formats (parameters must be URL-encoded and not too many)", description = "Find connections of bio network elements, such as the shortest path between " + "two proteins or the neighborhood for a particular protein state or all states. " + "Optionally, convert the result to other output formats." + @@ -195,7 +195,7 @@ public void graphQueryGet(@Valid Graph args, BindingResult bindingResult, consumes = {APPLICATION_FORM_URLENCODED_VALUE}, produces = {"application/vnd.biopax.rdf+xml", "application/ld+json", "application/json", "application/xml", "text/plain"}) @Operation( - summary = "A BioPAX graph query and optional converter to another output format.", + summary = "A BioPAX graph query and optional converter to another output formats", description = "Find connections of bio network elements, such as the shortest path between " + "two proteins or the neighborhood for a particular protein state or all states. " + "Optionally, convert the result to other output formats." + @@ -249,7 +249,7 @@ public void graphQuery(@Valid Graph args, BindingResult bindingResult, @GetMapping(path = "search", produces = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE}) @Operation( - summary = "Full-text search in the BioPAX database with Lucene query syntax", + summary = "Full-text search in the BioPAX model using Lucene query syntax", description = """

The index field names are: uri, keyword, name, pathway, xrefid, datasource, organism. diff --git a/src/main/java/cpath/web/ApiControllerV2.java b/src/main/java/cpath/web/ApiControllerV2.java index 81d57236..c00a36ad 100644 --- a/src/main/java/cpath/web/ApiControllerV2.java +++ b/src/main/java/cpath/web/ApiControllerV2.java @@ -63,7 +63,7 @@ public void fetchQuery(@Valid @RequestBody Fetch args, BindingResult bindingResu @PostMapping(path = "top_pathways", produces = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE}) @Operation( - summary = "Search for top-level bio pathways.", + summary = "Search for top-level bio pathways", description = "Find root/parent Pathway objects that are neither controlled " + "nor a pathwayComponent of another biological process; trivial pathways are excluded from the results;" + " can filter by datasource and organism." @@ -92,7 +92,7 @@ public SearchResponse topPathwaysQuery(@Valid @RequestBody TopPathways args, Bin @PostMapping(path = "traverse", produces = {APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE}) @Operation( - summary = "Access properties of BioPAX elements using graph path expressions (xpath-like).", + summary = "Access properties of BioPAX elements using graph path expressions (xpath-like)", description = "To collect specific BioPAX property values, use the following path accessor format: " + "InitialClass/property[:filterClass]/[property][:filterClass]... A \"*\" sign after the property " + "instructs the path accessor to transitively traverse that property. For example, the following " + @@ -173,7 +173,7 @@ public SearchResponse searchQuery(@Valid @RequestBody Search args, BindingResult @PostMapping(path = "neighborhood", produces = {"application/vnd.biopax.rdf+xml", "application/ld+json", "application/json", "application/xml", "text/plain"}) @Operation( - summary = "BioPAX Neighborhood graph query and optional converter to another output format.", + summary = "BioPAX Neighborhood graph query and optional converter to another output format", description = "Find the neighborhood network given the source bio entity URIs/IDs. " + "Optionally, convert the result to other output formats." ) @@ -198,7 +198,7 @@ public void neighborhoodQuery(@Valid @RequestBody Neighborhood args, BindingResu @PostMapping(path = "pathsbetween", produces = {"application/vnd.biopax.rdf+xml", "application/ld+json", "application/json", "application/xml", "text/plain"}) @Operation( - summary = "BioPAX PathsBetween graph query and optional converter to another output format.", + summary = "BioPAX PathsBetween graph query and optional converter to another output format", description = "Find the BioPAX subnetwork that includes all paths between given source bio entities (URIs/IDs). " + "Optionally, convert the result to other output formats." ) @@ -223,7 +223,7 @@ public void pathsbetweenQuery(@Valid @RequestBody PathsBetween args, BindingResu @PostMapping(path = "pathsfromto", produces = {"application/vnd.biopax.rdf+xml", "application/ld+json", "application/json", "application/xml", "text/plain"}) @Operation( - summary = "BioPAX PathsFromTo graph query and optional converter to another output format.", + summary = "BioPAX PathsFromTo graph query and optional converter to another output format", description = "Find a subnetwork that includes entities on the paths from the source bio " + "entities (URIs/IDs) to the targets (if empty array, then PathsBetween algorithm is used). " + "Optionally, convert the result to other output formats." @@ -249,7 +249,7 @@ public void pathsfromtoQuery(@Valid @RequestBody PathsFromTo args, BindingResult @PostMapping(path = "commonstream", produces = {"application/vnd.biopax.rdf+xml", "application/ld+json", "application/json", "application/xml", "text/plain"}) @Operation( - summary = "BioPAX CommonStream graph query and optional converter to another output format.", + summary = "BioPAX CommonStream graph query and optional converter to another output format", description = "Find a BioPAX common stream subnetwork from the source bio entities (URIs/IDs). " + "Optionally, convert the result to other output formats." )