Provide a functional JB2 session config, useful to demos and integration testing

Author: bbimber

jbrowse/resources/external/minimalSession.json

@@ -0,0 +1,75 @@
+{
+  "configuration": {},
+  "assemblies": [
+    {
+      "name": "hg38",
+      "aliases": ["GRCh38"],
+      "sequence": {
+        "type": "ReferenceSequenceTrack",
+        "trackId": "P6R5xbRqRr",
+        "adapter": {
+          "type": "BgzipFastaAdapter",
+          "fastaLocation": {
+            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
+          },
+          "faiLocation": {
+            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai"
+          },
+          "gziLocation": {
+            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi"
+          }
+        }
+      },
+      "refNameAliases": {
+        "adapter": {
+          "type": "RefNameAliasAdapter",
+          "location": {
+            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
+          }
+        }
+      }
+    }
+  ],
+  "tracks": [    
+    {
+      "type": "VariantTrack",
+      "trackId": "clinvar_ncbi_hg38",
+      "name": "ClinVar variants (NCBI)",
+      "assemblyNames": ["hg38"],
+      "category": ["Annotation"],
+      "adapter": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz"
+        },
+        "index": {
+          "location": {
+            "uri": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi"
+          }
+        }
+      }
+    },
+    {
+      "type": "FeatureTrack",
+      "trackId": "ncbi_refseq_109_hg38_latest",
+      "name": "NCBI RefSeq (GFF3Tabix)",
+      "assemblyNames": ["hg38"],
+      "category": ["Annotation"],
+      "adapter": {
+        "type": "Gff3TabixAdapter",
+        "gffGzLocation": {
+          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GRCh38_latest_genomic.sort.gff.gz"
+        },
+        "index": {
+          "location": {
+            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GRCh38_latest_genomic.sort.gff.gz.tbi"
+          }
+        }
+      }
+    }
+  ],
+  "connections": [],
+  "defaultSession": {
+    "name": "New Session"
+  }
+}

jbrowse/src/org/labkey/jbrowse/JBrowseController.java

@@ -20,6 +20,7 @@
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFFileReader;
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.NotNull;
 import org.json.JSONArray;
@@ -45,12 +46,15 @@
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.module.Module;
+import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineService;
 import org.labkey.api.pipeline.PipelineValidationException;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.UserSchema;
+import org.labkey.api.resource.FileResource;
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.permissions.AdminOperationsPermission;
 import org.labkey.api.security.permissions.AdminPermission;
@@ -59,6 +63,7 @@
 import org.labkey.api.security.permissions.UpdatePermission;
 import org.labkey.api.util.ExceptionUtil;
 import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.Path;
 import org.labkey.api.view.JspView;
 import org.labkey.api.view.NavTree;
 import org.labkey.api.view.UnauthorizedException;
@@ -67,11 +72,17 @@
 import org.labkey.jbrowse.model.Database;
 import org.labkey.jbrowse.model.JsonFile;
 import org.labkey.jbrowse.pipeline.JBrowseSessionPipelineJob;
+import org.labkey.sequenceanalysis.SequenceAnalysisModule;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -704,4 +715,63 @@ public void setStop(Integer stop)
             _stop = stop;
         }
     }
+
+    @RequiresPermission(ReadPermission.class)
+    public class GetSessionAction extends ReadOnlyApiAction<GetSessionForm>
+    {
+        private static final String DEMO = "demo";
+
+        @Override
+        public void validateForm(GetSessionForm form, Errors errors)
+        {
+            if (StringUtils.isEmpty(form.getSession()))
+            {
+                errors.reject(ERROR_MSG, "Must provide the session Id");
+            }
+        }
+
+        @Override
+        public Object execute(GetSessionForm form, BindException errors) throws Exception
+        {
+            JSONObject resp;
+            if (DEMO.equalsIgnoreCase(form.getSession()))
+            {
+                Module module = ModuleLoader.getInstance().getModule(JBrowseModule.class);
+                FileResource r = (FileResource)module.getModuleResolver().lookup(Path.parse("external/minimalSession.json"));
+                File jsonFile = r.getFile();
+                if (jsonFile == null)
+                {
+                    throw new FileNotFoundException("Unable to find JSON file: external/minimalSession.json");
+                }
+
+
+                try (InputStream is = new FileInputStream(jsonFile))
+                {
+                    resp = new JSONObject(IOUtils.toString(is, StandardCharsets.UTF_8));
+                }
+            }
+            else
+            {
+                resp = new JSONObject();
+                resp.put("session", form.getSession());
+            }
+
+            return new ApiSimpleResponse(resp);
+        }
+    }
+
+    public static class GetSessionForm
+    {
+        private String session;
+
+        public String getSession()
+        {
+            return session;
+        }
+
+        public void setSession(String session)
+        {
+            this.session = session;
+        }
+    }
 }