src/jalview/fts/service/alphafold/AlphafoldRestClient.java

   1 package jalview.fts.service.alphafold;
   2
   3 import java.net.MalformedURLException;
   4 import java.net.URL;
   5 import java.util.ArrayList;
   6 import java.util.Collection;
   7 import java.util.List;
   8 import java.util.Map;
   9 import java.util.Objects;
  10
  11 import jalview.datamodel.DBRefEntry;
  12 import jalview.datamodel.DBRefSource;
  13 import jalview.datamodel.SequenceI;
  14 import jalview.fts.api.FTSData;
  15 import jalview.fts.api.FTSDataColumnI;
  16 import jalview.fts.core.FTSRestRequest;
  17 import jalview.util.DBRefUtils;
  18 import jalview.util.HttpUtils;
  19 import jalview.ws.dbsources.EBIAlfaFold;
  20
  21 public class AlphafoldRestClient
  22 {
  23
  24   /**
  25    * turns a uniprot ID into a fake alphafold entry for the structure chooser -
  26    * fakes PDB fields in response
  27    *
  28    * @param UniprotID
  29    * @return null or an FTS Record (if alphafold thinks it has a structure)
  30    */
  31   public static List<FTSData> getFTSData(// Map<String, Object> pdbJsonDoc,
  32           FTSRestRequest request)
  33   {
  34     List<FTSData> records = new ArrayList<FTSData>();
  35     String primaryKey = null;
  36
  37     Object[] summaryRowData;
  38
  39     SequenceI associatedSequence;
  40
  41     Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
  42     SequenceI associatedSeq = request.getAssociatedSequence();
  43
  44     for (DBRefEntry upref : DBRefUtils
  45             .selectRefs(associatedSeq.getPrimaryDBRefs(), new String[]
  46             { DBRefSource.UNIPROT }))
  47     {
  48       String alphaFoldId = "AF-" + upref.getAccessionId() + "-F1";
  49       try
  50       {
  51         String urls = EBIAlfaFold.getAlphaFoldCifDownloadUrl(alphaFoldId);
  52         URL url = new URL(urls);
  53         if (!HttpUtils.checkUrlAvailable(url, 50))
  54         {
  55           continue;
  56         }
  57       } catch (Exception mfe)
  58       {
  59         jalview.bin.Cache.log.debug("Exception accessing urls", mfe);
  60         continue;
  61       }
  62       int colCounter = 0;
  63       summaryRowData = new Object[(associatedSeq != null)
  64               ? diplayFields.size() + 1
  65               : diplayFields.size()];
  66       if (associatedSeq != null)
  67       {
  68         associatedSequence = associatedSeq;
  69         summaryRowData[0] = associatedSequence;
  70         colCounter = 1;
  71       }
  72
  73       for (FTSDataColumnI field : diplayFields)
  74       {
  75         String fieldData = "alphafold";// (pdbJsonDoc.get(field.getCode()) ==
  76                                        // null) ? ""
  77         // : pdbJsonDoc.get(field.getCode()).toString();
  78         if (field.isPrimaryKeyColumn())
  79         {
  80           primaryKey = alphaFoldId;
  81           summaryRowData[colCounter++] = alphaFoldId;
  82         }
  83         else if (fieldData == null || fieldData.isEmpty())
  84         {
  85           summaryRowData[colCounter++] = null;
  86         }
  87         else
  88         {
  89           try
  90           {
  91             summaryRowData[colCounter++] = (field.getDataType()
  92                     .getDataTypeClass() == Integer.class)
  93                             ? 1
  94                             : (field.getDataType()
  95                                     .getDataTypeClass() == Double.class)
  96                                             ? 1.3131313
  97                                             : "AlphaFold clarity";
  98           } catch (Exception e)
  99           {
 100             e.printStackTrace();
 101             System.out.println("offending value:" + fieldData);
 102           }
 103         }
 104       }
 105
 106       final String primaryKey1 = primaryKey;
 107
 108       final Object[] summaryRowData1 = summaryRowData;
 109       records.add(new FTSData()
 110       {
 111         @Override
 112         public Object[] getSummaryData()
 113         {
 114           return summaryRowData1;
 115         }
 116
 117         @Override
 118         public Object getPrimaryKey()
 119         {
 120           return primaryKey1;
 121         }
 122
 123         /**
 124          * Returns a string representation of this object;
 125          */
 126         @Override
 127         public String toString()
 128         {
 129           StringBuilder summaryFieldValues = new StringBuilder();
 130           for (Object summaryField : summaryRowData1)
 131           {
 132             summaryFieldValues.append(
 133                     summaryField == null ? " " : summaryField.toString())
 134                     .append("\t");
 135           }
 136           return summaryFieldValues.toString();
 137         }
 138
 139         /**
 140          * Returns hash code value for this object
 141          */
 142         @Override
 143         public int hashCode()
 144         {
 145           return Objects.hash(primaryKey1, this.toString());
 146         }
 147
 148         @Override
 149         public boolean equals(Object that)
 150         {
 151           return this.toString().equals(that.toString());
 152         }
 153       });
 154     }
 155     return records;
 156   }
 157 }