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Use @NonNullApis annotations and fix numerous possible NPEs
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@arteymix
arteymix committed Apr 3, 2024
1 parent 98bd73b commit 1b14ea3
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Showing 61 changed files with 388 additions and 290 deletions.
28 changes: 15 additions & 13 deletions src/main/java/ubc/pavlab/rdp/controllers/AbstractSearchController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import org.apache.commons.lang3.tuple.Pair;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.MessageSource;
import org.springframework.lang.Nullable;
import org.springframework.validation.Errors;
import org.springframework.validation.Validator;
import org.springframework.web.bind.WebDataBinder;
Expand Down Expand Up @@ -60,14 +61,18 @@ public abstract class AbstractSearchController {
@Data
@NoArgsConstructor
@AllArgsConstructor(access = AccessLevel.PROTECTED)
protected static class SearchParams {
public static class SearchParams {
private boolean iSearch;
@Nullable
private Set<ResearcherPosition> researcherPositions;
@Nullable
private Set<ResearcherCategory> researcherCategories;
@Nullable
private Set<String> organUberonIds;
/**
* Order matters here because we want to preserve the UI rendering.
*/
@Nullable
private List<Integer> ontologyTermIds;

/**
Expand All @@ -81,14 +86,14 @@ public boolean isEmpty() {
@Data
@EqualsAndHashCode(callSuper = true)
@NoArgsConstructor
protected static class UserSearchParams extends SearchParams {
public static class UserSearchParams extends SearchParams {
@NotNull
private String nameLike;
private boolean prefix;
@NotNull
private String descriptionLike;

public UserSearchParams( String nameLike, boolean prefix, String descriptionLike, boolean iSearch, Set<ResearcherPosition> researcherPositions, Set<ResearcherCategory> researcherCategories, Set<String> organUberonIds, List<Integer> ontologyTermIds ) {
public UserSearchParams( String nameLike, boolean prefix, String descriptionLike, boolean iSearch, @Nullable Set<ResearcherPosition> researcherPositions, @Nullable Set<ResearcherCategory> researcherCategories, @Nullable Set<String> organUberonIds, @Nullable List<Integer> ontologyTermIds ) {
super( iSearch, researcherPositions, researcherCategories, organUberonIds, ontologyTermIds );
this.nameLike = nameLike;
this.prefix = prefix;
Expand All @@ -101,7 +106,7 @@ public boolean isEmpty() {
}
}

protected static class UserSearchParamsValidator implements Validator {
public static class UserSearchParamsValidator implements Validator {

@Override
public boolean supports( Class<?> clazz ) {
Expand Down Expand Up @@ -129,9 +134,10 @@ protected static class GeneSearchParams extends SearchParams {
@NotNull
private GeneInfo gene;
private Set<TierType> tiers;
@Nullable
private Taxon orthologTaxon;

public GeneSearchParams( GeneInfo gene, Set<TierType> tiers, Taxon orthologTaxon, boolean iSearch, Set<ResearcherPosition> researcherPositions, Set<ResearcherCategory> researcherCategories, Set<String> organUberonIds, List<Integer> ontologyTermIds ) {
public GeneSearchParams( GeneInfo gene, Set<TierType> tiers, @Nullable Taxon orthologTaxon, boolean iSearch, @Nullable Set<ResearcherPosition> researcherPositions, @Nullable Set<ResearcherCategory> researcherCategories, @Nullable Set<String> organUberonIds, @Nullable List<Integer> ontologyTermIds ) {
super( iSearch, researcherPositions, researcherCategories, organUberonIds, ontologyTermIds );
this.gene = gene;
this.tiers = tiers;
Expand Down Expand Up @@ -371,17 +377,13 @@ private static <K, T> Map<K, T> collectAsManyFuturesAsPossible( Map<K, ? extends
return results;
}

protected Collection<OrganInfo> organsFromUberonIds( Set<String> organUberonIds ) {
@Nullable
protected Collection<OrganInfo> organsFromUberonIds( @Nullable Set<String> organUberonIds ) {
return organUberonIds == null ? null : organInfoService.findByUberonIdIn( organUberonIds );
}

/**
* No need to perform the same
*
* @param ontologyTermIds
* @return
*/
protected Map<Ontology, Set<OntologyTermInfo>> ontologyTermsFromIds( List<Integer> ontologyTermIds ) {
@Nullable
protected Map<Ontology, Set<OntologyTermInfo>> ontologyTermsFromIds( @Nullable List<Integer> ontologyTermIds ) {
return ontologyTermIds == null ? null : ontologyService.findAllTermsByIdIn( ontologyTermIds ).stream()
.collect( Collectors.groupingBy( OntologyTermInfo::getOntology, Collectors.toSet() ) );
}
Expand Down
28 changes: 19 additions & 9 deletions src/main/java/ubc/pavlab/rdp/controllers/AdminController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.lang.Nullable;
import org.springframework.security.access.annotation.Secured;
import org.springframework.security.concurrent.DelegatingSecurityContextRunnable;
import org.springframework.stereotype.Controller;
Expand Down Expand Up @@ -713,16 +714,24 @@ public Object importReactomePathways( RedirectAttributes redirectAttributes ) {
}

@PostMapping("/admin/ontologies/{ontology}/update-reactome-pathways")
public Object updateReactomePathways( @PathVariable(required = false) Ontology ontology, RedirectAttributes redirectAttributes, Locale locale ) {
public Object updateReactomePathways( @PathVariable(required = false) @Nullable Ontology ontology, RedirectAttributes redirectAttributes, Locale locale ) {
// null-check is not necessary, but can save a database call
if ( ontology == null || !ontology.equals( reactomeService.findPathwaysOntology() ) ) {
return new ModelAndView( "error/404", HttpStatus.NOT_FOUND )
.addObject( "message", messageSource.getMessage( "AdminController.ontologyNotFoundById", null, locale ) );
}
try {
Ontology reactomeOntology = reactomeService.updatePathwaysOntology();
redirectAttributes.addFlashAttribute( "message", "Successfully updated Reactome pathways ontology." );
return "redirect:/admin/ontologies/" + reactomeOntology.getId();
if ( reactomeOntology != null ) {
redirectAttributes.addFlashAttribute( "message", "Successfully updated Reactome pathways ontology." );
return "redirect:/admin/ontologies/" + reactomeOntology.getId();
} else {
String message = "It seems that Reactome ontology does not setup.";
log.error( message );
redirectAttributes.addFlashAttribute( "message", message );
redirectAttributes.addFlashAttribute( "error", Boolean.TRUE );
return "redirect:/admin/ontologies";
}
} catch ( ReactomeException e ) {
log.error( "Failed to update Reactome pathways. Could this be an issue with the ontology configuration?", e );
redirectAttributes.addFlashAttribute( "message", "Failed to update Reactome pathways: " + e.getMessage() + "." );
Expand All @@ -735,9 +744,9 @@ public Object updateReactomePathways( @PathVariable(required = false) Ontology o
* Update Reactome Pathways summations.
*/
@PostMapping(value = "/admin/ontologies/{ontology}/update-reactome-pathway-summations")
public Object updateReactomePathwaySummations( @PathVariable(required = false) Ontology ontology, Locale locale ) {
public Object updateReactomePathwaySummations( @PathVariable(required = false) @Nullable Ontology ontology, Locale locale ) {
// null-check is not necessary, but can save a database call
if ( ontology == null || !reactomeService.findPathwaysOntology().equals( ontology ) ) {
if ( ontology == null || !Objects.equals( reactomeService.findPathwaysOntology(), ontology ) ) {
return new ModelAndView( "error/404", HttpStatus.NOT_FOUND )
.addObject( "message", messageSource.getMessage( "AdminController.ontologyNotFoundById", null, locale ) );
}
Expand All @@ -756,9 +765,9 @@ public Object updateReactomePathwaySummations( @PathVariable(required = false) O
* @see #updateReactomePathwaySummations(Ontology, Locale)
*/
@GetMapping(value = "/admin/ontologies/{ontology}/update-reactome-pathway-summations", produces = MediaType.TEXT_EVENT_STREAM_VALUE)
public Object updateReactomePathwaySummationsSse( @PathVariable(required = false) Ontology ontology, Locale locale ) {
public Object updateReactomePathwaySummationsSse( @PathVariable(required = false) @Nullable Ontology ontology, Locale locale ) {
// null-check is not necessary, but can save a database call
if ( ontology == null || !reactomeService.findPathwaysOntology().equals( ontology ) ) {
if ( ontology == null || !Objects.equals( reactomeService.findPathwaysOntology(), ontology ) ) {
return ResponseEntity.status( HttpStatus.NOT_FOUND )
.body( messageSource.getMessage( "AdminController.ontologyNotFoundById", null, locale ) );
}
Expand Down Expand Up @@ -1011,6 +1020,7 @@ public static class ImportOntologyForm {
private URL ontologyUrl;
private MultipartFile ontologyFile;

@Nullable
public String getFilename() {
if ( ontologyUrl != null ) {
// path cannot be null, but it can be empty if missing (i.e. http://github.com)
Expand All @@ -1034,13 +1044,13 @@ private Reader getReaderForImportOntologyForm( ImportOntologyForm importOntology
} else if ( !isMultipartFileEmpty( importOntologyForm.ontologyFile ) ) {
is = importOntologyForm.ontologyFile.getInputStream();
} else {
return null;
throw new RuntimeException( "No reader can be created from the import ontology form." );
}
boolean hasGzipExtension = FilenameUtils.isExtension( importOntologyForm.getFilename(), "gz" );
return new InputStreamReader( hasGzipExtension ? new GZIPInputStream( is ) : is );
}

private static boolean isMultipartFileEmpty( MultipartFile mp ) {
private static boolean isMultipartFileEmpty( @Nullable MultipartFile mp ) {
return mp == null || mp.isEmpty();
}

Expand Down
23 changes: 13 additions & 10 deletions src/main/java/ubc/pavlab/rdp/controllers/ApiController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.lang.Nullable;
import org.springframework.security.access.AccessDeniedException;
import org.springframework.security.access.PermissionEvaluator;
import org.springframework.security.core.Authentication;
Expand Down Expand Up @@ -179,7 +180,7 @@ public Page<RemoteOntologyTermInfo> getOntologyTerms( @PathVariable String ontol
}

@GetMapping(value = "/api/ontologies/{ontologyName}/terms", params = { "ontologyTermIds" }, produces = MediaType.APPLICATION_JSON_VALUE)
public List<RemoteOntologyTermInfo> getOntologyTermsByOntologyNameAndTermIds( @PathVariable String ontologyName, @RequestParam List<String> ontologyTermIds, Locale locale ) {
public List<RemoteOntologyTermInfo> getOntologyTermsByOntologyNameAndTermIds( @PathVariable String ontologyName, @Nullable @RequestParam List<String> ontologyTermIds, Locale locale ) {
Ontology ontology = ontologyService.findByName( ontologyName );
if ( ontology == null || !ontology.isActive() ) {
throw new ApiException( HttpStatus.NOT_FOUND, String.format( locale, "No ontology %s.", ontologyName ) );
Expand Down Expand Up @@ -247,13 +248,13 @@ public List<User> searchUsersByNameAndDescription( @RequestParam String nameLike
@GetMapping(value = "/api/genes/search", params = { "symbol", "taxonId" }, produces = MediaType.APPLICATION_JSON_VALUE)
public List<UserGene> searchUsersByGeneSymbol( @RequestParam String symbol,
@RequestParam Integer taxonId,
@RequestParam(required = false) Set<TierType> tiers,
@RequestParam(required = false) Integer orthologTaxonId,
@RequestParam(required = false) Set<ResearcherPosition> researcherPositions,
@RequestParam(required = false) Set<ResearcherCategory> researcherCategories,
@RequestParam(required = false) Set<String> organUberonIds,
@RequestParam(required = false) List<String> ontologyNames,
@RequestParam(required = false) List<String> ontologyTermIds,
@Nullable @RequestParam(required = false) Set<TierType> tiers,
@Nullable @RequestParam(required = false) Integer orthologTaxonId,
@Nullable @RequestParam(required = false) Set<ResearcherPosition> researcherPositions,
@Nullable @RequestParam(required = false) Set<ResearcherCategory> researcherCategories,
@Nullable @RequestParam(required = false) Set<String> organUberonIds,
@Nullable @RequestParam(required = false) List<String> ontologyNames,
@Nullable @RequestParam(required = false) List<String> ontologyTermIds,
Locale locale ) {

Taxon taxon = taxonService.findById( taxonId );
Expand Down Expand Up @@ -448,11 +449,13 @@ private Set<TierType> restrictTiers( Set<TierType> tiers ) {
.collect( Collectors.toSet() );
}

private Collection<OrganInfo> organsFromUberonIds( Set<String> organUberonIds ) {
@Nullable
private Collection<OrganInfo> organsFromUberonIds( @Nullable Set<String> organUberonIds ) {
return organUberonIds == null ? null : organInfoService.findByUberonIdIn( organUberonIds );
}

private Map<Ontology, Set<OntologyTermInfo>> ontologyTermsFromOntologyWithTermIds( List<String> ontologyNames, List<String> termIds ) {
@Nullable
private Map<Ontology, Set<OntologyTermInfo>> ontologyTermsFromOntologyWithTermIds( @Nullable List<String> ontologyNames, @Nullable List<String> termIds ) {
if ( ontologyNames == null || termIds == null ) {
return null;
}
Expand Down
11 changes: 9 additions & 2 deletions src/main/java/ubc/pavlab/rdp/controllers/GeneController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,10 @@
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.ResponseBody;
import ubc.pavlab.rdp.model.GeneInfo;
import ubc.pavlab.rdp.model.Taxon;
import ubc.pavlab.rdp.services.GOService;
Expand Down Expand Up @@ -82,6 +85,10 @@ public Object getGeneByTaxonAndSymbol( @PathVariable Integer taxonId, @PathVaria
if ( taxon == null ) {
return ResponseEntity.notFound().build();
}
return geneService.findBySymbolAndTaxon( symbol, taxon );
GeneInfo gene = geneService.findBySymbolAndTaxon( symbol, taxon );
if ( gene == null ) {
return ResponseEntity.notFound().build();
}
return gene;
}
}
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