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.bin.Cache;
  12 import jalview.datamodel.DBRefEntry;
  13 import jalview.datamodel.DBRefSource;
  14 import jalview.datamodel.SequenceI;
  15 import jalview.fts.api.FTSData;
  16 import jalview.fts.api.FTSDataColumnI;
  17 import jalview.fts.core.FTSRestRequest;
  18 import jalview.util.DBRefUtils;
  19 import jalview.util.HttpUtils;
  20 import jalview.ws.dbsources.EBIAlfaFold;
  21
  22 public class AlphafoldRestClient
  23 {
  24
  25   /**
  26    * turns a uniprot ID into a fake alphafold entry for the structure chooser -
  27    * fakes PDB fields in response
  28    *
  29    * @param UniprotID
  30    * @return null or an FTS Record (if alphafold thinks it has a structure)
  31    */
  32   public static List<FTSData> getFTSData(// Map<String, Object> pdbJsonDoc,
  33           FTSRestRequest request)
  34   {
  35     List<FTSData> records = new ArrayList<FTSData>();
  36     String primaryKey = null;
  37
  38     Object[] summaryRowData;
  39
  40     SequenceI associatedSequence;
  41
  42     Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
  43     SequenceI associatedSeq = request.getAssociatedSequence();
  44
  45     for (DBRefEntry upref : DBRefUtils
  46             .selectRefs(associatedSeq.getPrimaryDBRefs(), new String[]
  47             { DBRefSource.UNIPROT }))
  48     {
  49       String alphaFoldId = "AF-" + upref.getAccessionId() + "-F1";
  50       try
  51       {
  52         String urls = EBIAlfaFold.getAlphaFoldCifDownloadUrl(alphaFoldId);
  53         URL url = new URL(urls);
  54         if (!HttpUtils.checkUrlAvailable(url, 50))
  55         {
  56           continue;
  57         }
  58       } catch (Exception mfe)
  59       {
  60         Cache.debug("Exception accessing urls", mfe);
  61         continue;
  62       }
  63       int colCounter = 0;
  64       summaryRowData = new Object[(associatedSeq != null)
  65               ? diplayFields.size() + 1
  66               : diplayFields.size()];
  67       if (associatedSeq != null)
  68       {
  69         associatedSequence = associatedSeq;
  70         summaryRowData[0] = associatedSequence;
  71         colCounter = 1;
  72       }
  73
  74       for (FTSDataColumnI field : diplayFields)
  75       {
  76         String fieldData = "alphafold";// (pdbJsonDoc.get(field.getCode()) ==
  77                                        // null) ? ""
  78         // : pdbJsonDoc.get(field.getCode()).toString();
  79         if (field.isPrimaryKeyColumn())
  80         {
  81           primaryKey = alphaFoldId;
  82           summaryRowData[colCounter++] = alphaFoldId;
  83         }
  84         else if (fieldData == null || fieldData.isEmpty())
  85         {
  86           summaryRowData[colCounter++] = null;
  87         }
  88         else
  89         {
  90           try
  91           {
  92             summaryRowData[colCounter++] = (field.getDataType()
  93                     .getDataTypeClass() == Integer.class)
  94                             ? 1
  95                             : (field.getDataType()
  96                                     .getDataTypeClass() == Double.class)
  97                                             ? 1.3131313
  98                                             : "AlphaFold clarity";
  99           } catch (Exception e)
 100           {
 101             e.printStackTrace();
 102             System.out.println("offending value:" + fieldData);
 103           }
 104         }
 105       }
 106
 107       final String primaryKey1 = primaryKey;
 108
 109       final Object[] summaryRowData1 = summaryRowData;
 110       records.add(new FTSData()
 111       {
 112         @Override
 113         public Object[] getSummaryData()
 114         {
 115           return summaryRowData1;
 116         }
 117
 118         @Override
 119         public Object getPrimaryKey()
 120         {
 121           return primaryKey1;
 122         }
 123
 124         /**
 125          * Returns a string representation of this object;
 126          */
 127         @Override
 128         public String toString()
 129         {
 130           StringBuilder summaryFieldValues = new StringBuilder();
 131           for (Object summaryField : summaryRowData1)
 132           {
 133             summaryFieldValues.append(
 134                     summaryField == null ? " " : summaryField.toString())
 135                     .append("\t");
 136           }
 137           return summaryFieldValues.toString();
 138         }
 139
 140         /**
 141          * Returns hash code value for this object
 142          */
 143         @Override
 144         public int hashCode()
 145         {
 146           return Objects.hash(primaryKey1, this.toString());
 147         }
 148
 149         @Override
 150         public boolean equals(Object that)
 151         {
 152           return this.toString().equals(that.toString());
 153         }
 154       });
 155     }
 156     return records;
 157   }
 158 }