org.molgenis.pathways.WikiPathwaysController Maven / Gradle / Ivy
package org.molgenis.pathways;
import com.google.common.collect.Multimap;
import org.molgenis.data.DataService;
import org.molgenis.data.Entity;
import org.molgenis.data.Repository;
import org.molgenis.data.meta.model.EntityType;
import org.molgenis.pathways.model.Impact;
import org.molgenis.pathways.model.Pathway;
import org.molgenis.pathways.service.WikiPathwaysService;
import org.molgenis.ui.MolgenisPluginController;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.util.StringUtils;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.ResponseBody;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import javax.validation.Valid;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.io.StringReader;
import java.rmi.RemoteException;
import java.util.*;
import java.util.concurrent.ExecutionException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Stream;
import static java.util.function.BinaryOperator.maxBy;
import static java.util.stream.Collectors.*;
import static java.util.stream.IntStream.range;
import static java.util.stream.StreamSupport.stream;
import static org.molgenis.pathways.WikiPathwaysController.URI;
import static org.molgenis.util.stream.MultimapCollectors.toArrayListMultimap;
import static org.springframework.web.bind.annotation.RequestMethod.GET;
import static org.springframework.web.bind.annotation.RequestMethod.POST;
@Controller
@RequestMapping(URI)
public class WikiPathwaysController extends MolgenisPluginController
{
private static final Logger LOG = LoggerFactory.getLogger(WikiPathwaysController.class);
private static final String ID = "pathways";
public static final String URI = MolgenisPluginController.PLUGIN_URI_PREFIX + ID;
private static final Pattern EFFECT_PATTERN = Pattern
.compile("([A-Z]*\\|)(\\|*[0-9]+\\||\\|+)+([0-9A-Z]+)(\\|*)(.*)");
private static final String HOMO_SAPIENS = "Homo sapiens";
public static final String EFFECT_ATTRIBUTE_NAME = "EFF";
private final WikiPathwaysService wikiPathwaysService;
@Autowired
private DataService dataService;
private static final Pattern GENE_SYMBOL_PATTERN = Pattern.compile("^[0-9A-Za-z\\-]*");
private static final DocumentBuilderFactory DB_FACTORY = DocumentBuilderFactory.newInstance();
@Autowired
public WikiPathwaysController(WikiPathwaysService wikiPathwaysService)
{
super(URI);
this.wikiPathwaysService = wikiPathwaysService;
}
/**
* Shows the start screen.
*
* @param model the {@link Model} to fill
* @return the view name
*/
@RequestMapping(method = GET)
public String init(Model model)
{
model.addAttribute("entitiesMeta", getVCFEntities());
return "view-pathways";
}
/**
* Retrieves the list of VCF entities. They are recognized by the fact that they have an effect attribute.
*
* @return {@link List} of {@link EntityType} for the VCF entities
*/
private List getVCFEntities()
{
return stream(dataService.getEntityTypeIds().spliterator(), false).map(dataService::getEntityType)
.filter(this::hasEffectAttribute).collect(toList());
}
/**
* Determines if an entity has an effect attribute.
*
* @param emd {@link EntityType} of the entity
* @return boolean indicating if the entity has an effect column
*/
private boolean hasEffectAttribute(EntityType emd)
{
return emd.getAttribute(EFFECT_ATTRIBUTE_NAME) != null;
}
/**
* Retrieves all pathways.
*
* @return {@link Collection} of all {@link Pathway}s.
* @throws ExecutionException if load from cache fails
*/
@RequestMapping(value = "/allPathways", method = POST)
@ResponseBody
public Collection getAllPathways() throws ExecutionException
{
return wikiPathwaysService.getAllPathways(HOMO_SAPIENS);
}
/**
* Searches pathways.
*
* @param searchTerm string to search for
* @return {@link Collection} of all {@link Pathway}s found for searchTerm
* @throws RemoteException
* @throws ExecutionException
*/
@RequestMapping(value = "/filteredPathways", method = POST)
@ResponseBody
public Collection getFilteredPathways(@RequestBody String searchTerm)
throws RemoteException, ExecutionException
{
if (StringUtils.isEmpty(searchTerm))
{
return getAllPathways();
}
return wikiPathwaysService.getFilteredPathways(searchTerm, HOMO_SAPIENS);
}
/**
* Retrieves uncolored pathway image.
*
* @param pathwayId the id of the pathway
* @return single-line svg string of the pathway image
* @throws ExecutionException if load from cache fails
*/
@RequestMapping(value = "/pathwayViewer/{pathwayId}", method = GET)
@ResponseBody
public String getPathway(@PathVariable String pathwayId) throws ExecutionException
{
return wikiPathwaysService.getUncoloredPathwayImage(pathwayId);
}
/**
* Retrieves gene symbols plus impact from the EFF attributes of all {@link Entity}s in a VCF repository that have
* an EFF attribute containing a gene symbol.
*
* @param selectedVcf name of the VCF {@link Repository}
* @return Map mapping Gene name to highest {@link Impact} for that gene
*/
private Map getGenesForVcf(String selectedVcf)
{
return stream(dataService.getRepository(selectedVcf).spliterator(), false)
.map(entity -> entity.getString(EFFECT_ATTRIBUTE_NAME))
.filter(eff -> !StringUtils.isEmpty(getGeneFromEffect(eff))).collect(
groupingBy(WikiPathwaysController::getGeneFromEffect,
reducing(Impact.NONE, WikiPathwaysController::getImpactFromEffect,
maxBy((i1, i2) -> i1.compareTo(i2)))));
}
/**
* Parses the impact from an effect attribute. Recognizes the strings HIGH, MODERATE, and LOW.
*
* @param eff String value of the effect attribute
* @return the highest {@link Impact} found in the effect attribute, or {@link Impact#NONE} if none found
*/
private static Impact getImpactFromEffect(String eff)
{
return eff.contains("HIGH") ? Impact.HIGH : eff.contains("MODERATE") ? Impact.MODERATE : eff
.contains("LOW") ? Impact.LOW : Impact.NONE;
}
/**
* Parses the Gene symbol from an effect attribute.
*
* @param eff String value of the effect attribute
* @return the gene symbol or null if none found
*/
private static String getGeneFromEffect(String eff)
{
if (!StringUtils.isEmpty(eff))
{
Matcher effectMatcher = EFFECT_PATTERN.matcher(eff);
if (effectMatcher.find())
{
return effectMatcher.group(3);
}
}
return null;
}
/**
* Retrieves all pathways for the genes in a vcf.
*
* @param selectedVcf the name of the vcf {@link Repository}
* @return {@link Collection} of {@link Pathway}s found for genes in the VCF
* @throws ExecutionException if the loading from cache fails
*/
@RequestMapping(value = "/pathwaysByGenes", method = POST)
@ResponseBody
public Collection getListOfPathwayNamesByGenes(@Valid @RequestBody String selectedVcf)
throws ExecutionException
{
return getGenesForVcf(selectedVcf).keySet().stream().map(this::getPathwaysForGene).flatMap(Collection::stream)
.collect(toCollection(LinkedHashSet::new));
}
/**
* Retrieves all pathways for a gene
*
* @param gene the HGNC name of the gene
* @return Collection of {@link Pathway}s
*/
private Collection getPathwaysForGene(String gene)
{
try
{
return wikiPathwaysService.getPathwaysForGene(gene, HOMO_SAPIENS);
}
catch (ExecutionException e)
{
throw new RuntimeException(e);
}
}
/**
* Retrieves a colored pathway.
*
* @param selectedVcf name of the VCF {@link Repository}
* @param pathwayId ID of the pathway
* @return svg for the pathway, with the genes in the VCF colored according to their {@link Impact}
* @throws ParserConfigurationException if the creation of the {@link DocumentBuilder} fails
* @throws IOException If any IO errors occur when parsing the GPML
* @throws SAXException If any parse errors occur when parsing the GPML
* @throws ExecutionException if the loading of the colored pathway from cache fails
*/
@RequestMapping(value = "/getColoredPathway/{selectedVcf}/{pathwayId}", method = GET)
@ResponseBody
public String getColoredPathway(@PathVariable String selectedVcf, @PathVariable String pathwayId)
throws ParserConfigurationException, SAXException, IOException, ExecutionException
{
return getColoredPathway(selectedVcf, pathwayId, analyzeGPML(wikiPathwaysService.getPathwayGPML(pathwayId)));
}
/**
* Analyses pathway GPML. Determines for each gene in which graphIds it is displayed.
*
* @param gpml String containing the pathway GPML
* @return {@link Multimap} mapping gene symbol to graphIDs
* @throws IllegalArgumentException if the gpml is invalid
*/
Multimap analyzeGPML(String gpml) throws ParserConfigurationException, IOException, SAXException
{
return streamDataNodes(gpml).filter(node -> !node.getAttribute("GraphId").isEmpty()).collect(
toArrayListMultimap(node -> getGeneSymbol(node.getAttribute("TextLabel")),
node -> node.getAttribute("GraphId")));
}
/**
* Finds the DataNode elements in a gpml string.
*
* @param gpml String containing the gpml document
* @return {@link Stream} of DataNode {@link Element}s
* @throws IllegalArgumentException if the gpml is invalid
*/
private Stream streamDataNodes(String gpml)
{
Document document;
try
{
document = DB_FACTORY.newDocumentBuilder().parse(new InputSource(new StringReader(gpml)));
NodeList dataNodes = document.getElementsByTagName("DataNode");
return range(0, dataNodes.getLength()).mapToObj(dataNodes::item).map(Element.class::cast);
}
catch (SAXException | IOException | ParserConfigurationException e)
{
LOG.error("Invalid GPML " + gpml);
throw new IllegalArgumentException("Invalid GPML");
}
}
/**
* Finds the gene symbol in a text label.
*
* @param textLabel the text label to look in
* @return Gene symbol if found, otherwise ""
*/
String getGeneSymbol(String textLabel)
{
String geneSymbol = "";
if (textLabel.contains("""))
{
LOG.warn("Textlabel(" + textLabel
+ ") contains quotes, which is inconsistent with the gene names. Removing the quotes.");
textLabel = textLabel.replace(""", "");
}
Matcher geneSymbolMatcher = GENE_SYMBOL_PATTERN.matcher(textLabel);
if (geneSymbolMatcher.find())
{
geneSymbol = geneSymbolMatcher.group(0);
}
return geneSymbol;
}
/**
* Retrieves a colored pathway. Sometimes WikiPathways returns no graphIds for a pathway, then the pathway is
* returned uncolored.
*
* @param selectedVcf the name of the vcf entity
* @param pathwayId the id of the pathway in WikiPathways
* @param graphIdsPerGene {@link Multimap} mapping gene symbol to graphId
* @return String svg from for the pathway
* @throws ExecutionException if the loading from cache fails
*/
private String getColoredPathway(String selectedVcf, String pathwayId, Multimap graphIdsPerGene)
throws ExecutionException
{
Map impactPerGraphId = new HashMap();
getGenesForVcf(selectedVcf).forEach(
(gene, impact) -> graphIdsPerGene.get(gene).forEach(graphId -> impactPerGraphId.put(graphId, impact)));
if (!impactPerGraphId.isEmpty())
{
return wikiPathwaysService.getColoredPathwayImage(pathwayId, impactPerGraphId);
}
else
{
return wikiPathwaysService.getUncoloredPathwayImage(pathwayId);
}
}
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