diff --git a/.gitignore b/.gitignore
old mode 100644
new mode 100755
diff --git a/.gitmodules b/.gitmodules
old mode 100644
new mode 100755
index e67f8541f8..60a042e5f9
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
[submodule "cellbase-web/lib/jsorolla"]
path = cellbase-web/lib/jsorolla
- url = https://github.com/opencb/jsorolla.git
+ url = https://github.com/Lucioric2000/jsorolla.git
diff --git a/LICENSE b/LICENSE
old mode 100644
new mode 100755
diff --git a/README.md b/README.md
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/bin/obsolete/gene-chunkIds.js b/cellbase-app/app/bin/obsolete/gene-chunkIds.js
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/bin/obsolete/genome-fetcher/CHECKSUMS b/cellbase-app/app/bin/obsolete/genome-fetcher/CHECKSUMS
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/bin/obsolete/genome-fetcher/genome-fetcher.py b/cellbase-app/app/bin/obsolete/genome-fetcher/genome-fetcher.py
index ae2d7c4548..d4e5fa2492 100755
--- a/cellbase-app/app/bin/obsolete/genome-fetcher/genome-fetcher.py
+++ b/cellbase-app/app/bin/obsolete/genome-fetcher/genome-fetcher.py
@@ -101,7 +101,7 @@
logging.debug(sp_obj['assembly'])
outfile = sequence_folder+"/"+sp_short.capitalize() + ".{0}".format(sp_obj['assembly'])+".fa.gz"
logging.debug(outfile)
- command = "wget --tries=10 " + url_seq +" -O '"+outfile+"' -o "+outfile+".log"
+ command = "wget -N --tries=10 " + url_seq +" -O '"+outfile+"' -o "+outfile+".log"
logging.debug(command)
os.system(command)
cmd = "./genome_info.pl --species '{0}' -o {1}/genome_info.json".format(sp, sequence_folder)
@@ -109,7 +109,7 @@
os.system(cmd)
# for i in sp_obj['chromosomes']:
# outfile = seq_folder+"/chrom_"+i+".fa.gz"
- # command = "wget --tries=10 " + url_seq+"/*.dna.chromosome."+i+".fa.gz -O '"+outfile+"' -o "+outfile+".log"
+ # command = "wget -N --tries=10 " + url_seq+"/*.dna.chromosome."+i+".fa.gz -O '"+outfile+"' -o "+outfile+".log"
# logging.debug(command)
# os.system(command)
@@ -121,7 +121,7 @@
url_gtf = sp_obj['sequence_url'].replace("fasta", "gtf")+"{0}".format(sp_short)
logging.debug(url_gtf)
outfile = gene_folder+"/"+sp_short+".gtf.gz"
- command = "wget --tries=10 " + url_gtf+"/*.gtf.gz -O '"+outfile+"' -o "+outfile+".log"
+ command = "wget -N --tries=10 " + url_gtf+"/*.gtf.gz -O '"+outfile+"' -o "+outfile+".log"
logging.debug(command)
os.system(command)
if sp_obj['phylo'] is not 'Bacteria':
@@ -159,7 +159,7 @@
variation_url = sp_obj['variation_url']
for file in variation_files:
outfile = variation_folder+"/"+file
- command = "wget --tries=10 " + variation_url+"/"+file+" -O '"+outfile+"' -o "+outfile+".log"
+ command = "wget -N --tries=10 " + variation_url+"/"+file+" -O '"+outfile+"' -o "+outfile+".log"
logging.debug(command)
os.system(command)
@@ -172,7 +172,7 @@
regulation_url = sp_obj['regulation_url']+sp_short
for file in regulation_files:
outfile = regulation_folder+"/"+file
- command = "wget --tries=10 " + regulation_url+"/"+file+" -O '"+outfile+"' -o "+outfile+".log"
+ command = "wget -N --tries=10 " + regulation_url+"/"+file+" -O '"+outfile+"' -o "+outfile+".log"
logging.debug(command)
os.system(command)
diff --git a/cellbase-app/app/bin/obsolete/genome-fetcher/species.json b/cellbase-app/app/bin/obsolete/genome-fetcher/species.json
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/bin/obsolete/genome-fetcher/species_info.json b/cellbase-app/app/bin/obsolete/genome-fetcher/species_info.json
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/bin/obsolete/genome-fetcher/species_info.txt b/cellbase-app/app/bin/obsolete/genome-fetcher/species_info.txt
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/bin/obsolete/variation-chunkIds.js b/cellbase-app/app/bin/obsolete/variation-chunkIds.js
old mode 100644
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diff --git a/cellbase-app/app/example/5000_variants.vcf.gz b/cellbase-app/app/example/5000_variants.vcf.gz
old mode 100644
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diff --git a/cellbase-app/app/example/BasicTest.Json b/cellbase-app/app/example/BasicTest.Json
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diff --git a/cellbase-app/app/example/BasicTest.gvf b/cellbase-app/app/example/BasicTest.gvf
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diff --git a/cellbase-app/app/example/Escherichia coli.owl b/cellbase-app/app/example/Escherichia coli.owl
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diff --git a/cellbase-app/app/example/Homo_sapiens_incl_consequences_1000.Json b/cellbase-app/app/example/Homo_sapiens_incl_consequences_1000.Json
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/example/Homo_sapiens_incl_consequences_1000.gvf b/cellbase-app/app/example/Homo_sapiens_incl_consequences_1000.gvf
old mode 100644
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diff --git a/cellbase-app/app/mongodb-scripts/add_database_roles_mongo.js b/cellbase-app/app/mongodb-scripts/add_database_roles_mongo.js
old mode 100644
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diff --git a/cellbase-app/app/mongodb-scripts/clinical-indexes.js b/cellbase-app/app/mongodb-scripts/clinical-indexes.js
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diff --git a/cellbase-app/app/mongodb-scripts/clinical-legacy-indexes.js b/cellbase-app/app/mongodb-scripts/clinical-legacy-indexes.js
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diff --git a/cellbase-app/app/mongodb-scripts/conservation-indexes.js b/cellbase-app/app/mongodb-scripts/conservation-indexes.js
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diff --git a/cellbase-app/app/mongodb-scripts/create-biouser.js b/cellbase-app/app/mongodb-scripts/create-biouser.js
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diff --git a/cellbase-app/app/mongodb-scripts/drugbank-indexes.js b/cellbase-app/app/mongodb-scripts/drugbank-indexes.js
old mode 100644
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diff --git a/cellbase-app/app/mongodb-scripts/gene-indexes.js b/cellbase-app/app/mongodb-scripts/gene-indexes.js
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diff --git a/cellbase-app/app/mongodb-scripts/genome_sequence-indexes.js b/cellbase-app/app/mongodb-scripts/genome_sequence-indexes.js
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diff --git a/cellbase-app/app/mongodb-scripts/grant-users.js b/cellbase-app/app/mongodb-scripts/grant-users.js
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diff --git a/cellbase-app/app/mongodb-scripts/mutation-indexes.js b/cellbase-app/app/mongodb-scripts/mutation-indexes.js
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diff --git a/cellbase-app/app/mongodb-scripts/protein-indexes.js b/cellbase-app/app/mongodb-scripts/protein-indexes.js
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diff --git a/cellbase-app/app/mongodb-scripts/protein_functional_prediction-indexes.js b/cellbase-app/app/mongodb-scripts/protein_functional_prediction-indexes.js
old mode 100644
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diff --git a/cellbase-app/app/mongodb-scripts/protein_protein_interaction-indexes.js b/cellbase-app/app/mongodb-scripts/protein_protein_interaction-indexes.js
old mode 100644
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diff --git a/cellbase-app/app/mongodb-scripts/regulatory_region-indexes.js b/cellbase-app/app/mongodb-scripts/regulatory_region-indexes.js
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/mongodb-scripts/repeat-indexes.js b/cellbase-app/app/mongodb-scripts/repeat-indexes.js
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/mongodb-scripts/variation-indexes.js b/cellbase-app/app/mongodb-scripts/variation-indexes.js
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/mongodb-scripts/variation_functional_score-indexes.js b/cellbase-app/app/mongodb-scripts/variation_functional_score-indexes.js
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/mongodb-scripts/variation_phenotype-indexes.js b/cellbase-app/app/mongodb-scripts/variation_phenotype-indexes.js
old mode 100644
new mode 100755
diff --git a/cellbase-app/app/mongodb-scripts/variation_phenotype_annotation-indexes.js b/cellbase-app/app/mongodb-scripts/variation_phenotype_annotation-indexes.js
old mode 100644
new mode 100755
diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
old mode 100644
new mode 100755
index 30708578b8..ca17e70782
--- a/cellbase-app/pom.xml
+++ b/cellbase-app/pom.xml
@@ -47,6 +47,11 @@
commons-io
2.4
+
+ commons-net
+ commons-net
+ ${commons-net.version}
+
org.spockframework
spock-core
diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/CellBaseMain.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/CellBaseMain.java
old mode 100644
new mode 100755
diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/BuildCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/BuildCommandExecutor.java
old mode 100644
new mode 100755
diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/CliOptionsParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/CliOptionsParser.java
old mode 100644
new mode 100755
diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/CommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/CommandExecutor.java
old mode 100644
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java
old mode 100644
new mode 100755
index b0c2948463..94a3ba1e48
--- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java
+++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java
@@ -24,6 +24,8 @@
import org.apache.commons.collections.map.HashedMap;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.IOUtils;
+import org.apache.commons.net.ftp.FTPClient;
+import org.apache.commons.net.ftp.FTPFile;
import org.apache.commons.lang.StringUtils;
import org.opencb.cellbase.core.config.Species;
import org.opencb.commons.utils.FileUtils;
@@ -1165,6 +1167,25 @@ private void downloadFile(String url, String outputFileName) throws IOException,
private void downloadFile(String url, String outputFileName, List wgetAdditionalArgs)
throws IOException, InterruptedException {
+ File file = new File(outputFileName);
+ if (file.exists()) {
+ FTPClient ftpClient = new FTPClient();
+ // code to connect and login....
+
+ FTPFile remotefile = ftpClient.mlistFile(outputFileName);
+ long remotesize = remotefile.getSize();
+ long localsize = file.length();
+ long locallastmodified = file.lastModified();
+ logger.info("File " + outputFileName + " exists, with size " + localsize + " vs "
+ + remotesize + " in remote and will not be downloaded again");
+ if (remotesize == localsize) {
+ logger.info("Download avoided because the files have the same size");
+ return;
+ }
+ //If the filestamps differ, regardless of the timestamps downloads the file
+ Calendar remotets = remotefile.getTimestamp();
+ logger.info("local ts " + locallastmodified + "wheras remote ts is " + remotets.toString());
+ }
List wgetArgs = new ArrayList<>(Arrays.asList("--tries=10", url, "-O", outputFileName, "-o",
outputFileName + ".log"));
if (wgetAdditionalArgs != null && !wgetAdditionalArgs.isEmpty()) {
diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/EtlCommons.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/EtlCommons.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/LoadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/LoadCommandExecutor.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/PostLoadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/PostLoadCommandExecutor.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/QueryCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/QueryCommandExecutor.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/QueryGrpcCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/QueryGrpcCommandExecutor.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/VariantAnnotationCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/VariantAnnotationCommandExecutor.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/BenchmarkDataWriter.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/BenchmarkDataWriter.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/BenchmarkTask.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/BenchmarkTask.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/CellBaseLocalVariantAnnotator.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/CellBaseLocalVariantAnnotator.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/CellBaseWSVariantAnnotator.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/CellBaseWSVariantAnnotator.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/JsonStringAnnotatorTask.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/JsonStringAnnotatorTask.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/PopulationFrequenciesAnnotator.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/PopulationFrequenciesAnnotator.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/SequenceOntologyTermComparisonObject.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/SequenceOntologyTermComparisonObject.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/VariantAnnotationDiff.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/VariantAnnotationDiff.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/VariantAnnotatorTask.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/VariantAnnotatorTask.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/VariationDataReader.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/VariationDataReader.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/VcfStringAnnotatorTask.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/VcfStringAnnotatorTask.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/VcfVariantAnnotator.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/VcfVariantAnnotator.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/indexers/CustomAnnotationVariantIndexer.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/indexers/CustomAnnotationVariantIndexer.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/indexers/PopulationFrequencyVariantIndexer.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/indexers/PopulationFrequencyVariantIndexer.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/indexers/VariantIndexer.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/indexers/VariantIndexer.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/CaddAllAnnotationParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/CaddAllAnnotationParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/CaddScoreParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/CaddScoreParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/CellBaseParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/CellBaseParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/ConservationParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/ConservationParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/DgvParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/DgvParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/DisgenetParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/DisgenetParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/DrugParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/DrugParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GeneExpressionAtlasParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GeneExpressionAtlasParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GeneParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GeneParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GeneParserProto.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GeneParserProto.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GeneParserUtils.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GeneParserUtils.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GenomeSequenceFastaParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GenomeSequenceFastaParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/InteractionParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/InteractionParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/Main.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/Main.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/ProteinParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/ProteinParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/RegulatoryRegionParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/RegulatoryRegionParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/RepeatsParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/RepeatsParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/VariationPhenotypeAnnotationParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/VariationPhenotypeAnnotationParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/ClinVarIndexer.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/ClinVarIndexer.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/ClinVarParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/ClinVarParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/ClinicalIndexer.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/ClinicalIndexer.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/ClinicalVariantParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/ClinicalVariantParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/CosmicIndexer.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/CosmicIndexer.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/CosmicParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/CosmicParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/DOCMIndexer.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/DOCMIndexer.java
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index 9236eb6efd..d2302c750a
--- a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/DOCMIndexer.java
+++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/DOCMIndexer.java
@@ -30,7 +30,7 @@ public class DOCMIndexer extends ClinicalIndexer {
private static final String DISEASE = "disease";
private static final String SOURCE_PUBMED_ID = "source_pubmed_id";
private static final String PMID = "PMID:";
- private static final String URL_PREFIX = "http://docm.genome.wustl.edu/variants/";
+ private static final String URL_PREFIX = "http://docm.info/variants/";
private static final String HGVS = "hgvs";
private static final String GENE = "gene";
private static final String TRANSCRIPT = "transcript";
diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/GwasParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/GwasParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/IARCTP53Indexer.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/IARCTP53Indexer.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/formats/Cadd.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/formats/Cadd.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/formats/ConservedRegionFeature.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/formats/ConservedRegionFeature.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/formats/GeneExpressionAtlas.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/formats/GeneExpressionAtlas.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/utils/GenomeSequenceUtils.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/utils/GenomeSequenceUtils.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/utils/StringUtils.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/utils/StringUtils.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/utils/VariationUtils.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/utils/VariationUtils.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/AbstractVariationFile.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/AbstractVariationFile.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/VariationFeatureFile.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/VariationFeatureFile.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/VariationFile.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/VariationFile.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/VariationParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/VariationParser.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/VariationSynonymFile.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/VariationSynonymFile.java
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diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/VariationTranscriptFile.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/variation/VariationTranscriptFile.java
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diff --git a/cellbase-app/src/test/groovy/org/opencb/cellbase/app/transform/CaddAllAnnotationParserTest.groovy b/cellbase-app/src/test/groovy/org/opencb/cellbase/app/transform/CaddAllAnnotationParserTest.groovy
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diff --git a/cellbase-app/src/test/groovy/org/opencb/cellbase/app/transform/ClinVarParserTest.groovy b/cellbase-app/src/test/groovy/org/opencb/cellbase/app/transform/ClinVarParserTest.groovy
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diff --git a/cellbase-app/src/test/groovy/org/opencb/cellbase/app/transform/CosmicParserTest.groovy b/cellbase-app/src/test/groovy/org/opencb/cellbase/app/transform/CosmicParserTest.groovy
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diff --git a/cellbase-app/src/test/groovy/org/opencb/cellbase/app/transform/GeneParserTest.groovy b/cellbase-app/src/test/groovy/org/opencb/cellbase/app/transform/GeneParserTest.groovy
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diff --git a/cellbase-app/src/test/groovy/org/opencb/cellbase/app/transform/GwasParserTest.groovy b/cellbase-app/src/test/groovy/org/opencb/cellbase/app/transform/GwasParserTest.groovy
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/cli/PostLoadCommandExecutorTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/cli/PostLoadCommandExecutorTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/cli/VariantAnnotationCommandExecutorTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/cli/VariantAnnotationCommandExecutorTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/loaders/mongodb/VariantEffectMongoDBLoaderTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/loaders/mongodb/VariantEffectMongoDBLoaderTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/CaddScoreParserTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/CaddScoreParserTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/DgvParserTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/DgvParserTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/GenericParserTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/GenericParserTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/RegulatoryRegionParserTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/RegulatoryRegionParserTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/RepeatsParserTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/RepeatsParserTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/clinical/variant/ClinicalVariantParserTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/clinical/variant/ClinicalVariantParserTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/utils/GenomeSequenceUtilsTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/utils/GenomeSequenceUtilsTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/variation/VariationParserTest.java b/cellbase-app/src/test/java/org/opencb/cellbase/app/transform/variation/VariationParserTest.java
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diff --git a/cellbase-app/src/test/java/org/opencb/fetcher/testGenerateCellbaseLibProperties.java b/cellbase-app/src/test/java/org/opencb/fetcher/testGenerateCellbaseLibProperties.java
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diff --git a/cellbase-app/src/test/resources/caddTest.tsv.gz b/cellbase-app/src/test/resources/caddTest.tsv.gz
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diff --git a/cellbase-app/src/test/resources/cadd_example.txt.gz b/cellbase-app/src/test/resources/cadd_example.txt.gz
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diff --git a/cellbase-app/src/test/resources/clinvarExample.xml b/cellbase-app/src/test/resources/clinvarExample.xml
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diff --git a/cellbase-app/src/test/resources/clinvarParser/ClinVar_Traits_EFO_Names.csv b/cellbase-app/src/test/resources/clinvarParser/ClinVar_Traits_EFO_Names.csv
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diff --git a/cellbase-app/src/test/resources/clinvarParser/clinvar_v19_test.xml.gz b/cellbase-app/src/test/resources/clinvarParser/clinvar_v19_test.xml.gz
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diff --git a/cellbase-app/src/test/resources/cosmicTest.csv b/cellbase-app/src/test/resources/cosmicTest.csv
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diff --git a/cellbase-app/src/test/resources/disGeNetTest.csv b/cellbase-app/src/test/resources/disGeNetTest.csv
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diff --git a/cellbase-app/src/test/resources/ebolaGenome/Ebola_virus.KM034562v1.fa.gz b/cellbase-app/src/test/resources/ebolaGenome/Ebola_virus.KM034562v1.fa.gz
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diff --git a/cellbase-app/src/test/resources/ebolaGenome/Ebola_virus.gtf.gz b/cellbase-app/src/test/resources/ebolaGenome/Ebola_virus.gtf.gz
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diff --git a/cellbase-app/src/test/resources/entrezIdToEnsemblIdTest.csv b/cellbase-app/src/test/resources/entrezIdToEnsemblIdTest.csv
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diff --git a/cellbase-app/src/test/resources/geneParser/Homo_sapiens.GRCh38.fa b/cellbase-app/src/test/resources/geneParser/Homo_sapiens.GRCh38.fa
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diff --git a/cellbase-app/src/test/resources/geneParser/homo_sapiens.gtf b/cellbase-app/src/test/resources/geneParser/homo_sapiens.gtf
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diff --git a/cellbase-app/src/test/resources/geneParser/tfbs.txt b/cellbase-app/src/test/resources/geneParser/tfbs.txt
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diff --git a/cellbase-app/src/test/resources/gwasTest.csv b/cellbase-app/src/test/resources/gwasTest.csv
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diff --git a/cellbase-app/src/test/resources/regulation/Regulatory_Build.regulatory_features.gff.gz b/cellbase-app/src/test/resources/regulation/Regulatory_Build.regulatory_features.gff.gz
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diff --git a/cellbase-app/src/test/resources/repeats/genomicSuperDups.txt.gz b/cellbase-app/src/test/resources/repeats/genomicSuperDups.txt.gz
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diff --git a/cellbase-app/src/test/resources/repeats/windowMasker.txt.gz b/cellbase-app/src/test/resources/repeats/windowMasker.txt.gz
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diff --git a/cellbase-app/src/test/resources/variant/annotation/Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz b/cellbase-app/src/test/resources/variant/annotation/Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz
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diff --git a/cellbase-app/src/test/resources/variant/annotation/Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz.gzi b/cellbase-app/src/test/resources/variant/annotation/Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz.gzi
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diff --git a/cellbase-app/src/test/resources/variant/annotation/clinicalVariant/ClinVarFullRelease_2020-02.xml.gz b/cellbase-app/src/test/resources/variant/annotation/clinicalVariant/ClinVarFullRelease_2020-02.xml.gz
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diff --git a/cellbase-app/src/test/resources/variant/annotation/clinicalVariant/CosmicMutantExport.tsv.gz b/cellbase-app/src/test/resources/variant/annotation/clinicalVariant/CosmicMutantExport.tsv.gz
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diff --git a/cellbase-app/src/test/resources/variant/annotation/clinicalVariant/datasets/germlineMutationDataIARC TP53 Database, R18.txt b/cellbase-app/src/test/resources/variant/annotation/clinicalVariant/datasets/germlineMutationDataIARC TP53 Database, R18.txt
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diff --git a/cellbase-app/src/test/resources/variant/annotation/clinicalVariant/variant_summary.txt.gz b/cellbase-app/src/test/resources/variant/annotation/clinicalVariant/variant_summary.txt.gz
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/StructuralVariation.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/StructuralVariation.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/TranscriptVariation.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/TranscriptVariation.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Variation.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Variation.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Xref.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Xref.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/CellBaseConfiguration.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/CellBaseConfiguration.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/DatabaseCredentials.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/DatabaseCredentials.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/Databases.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/Databases.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/DownloadProperties.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/DownloadProperties.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/Species.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/Species.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/SpeciesProperties.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/SpeciesProperties.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/loader/CellBaseLoader.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/loader/CellBaseLoader.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/loader/CellBaseTypeConverter.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/loader/CellBaseTypeConverter.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/loader/LoadRunner.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/loader/LoadRunner.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/loader/LoaderException.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/loader/LoaderException.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/monitor/HealthStatus.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/monitor/HealthStatus.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/monitor/Monitor.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/monitor/Monitor.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseFileSerializer.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseFileSerializer.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseJsonFileSerializer.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseJsonFileSerializer.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseSerializer.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseSerializer.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/AnnotationBasedPhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/AnnotationBasedPhasedQueryManager.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/ClinicalPhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/ClinicalPhasedQueryManager.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/CustomAnnotationPhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/CustomAnnotationPhasedQueryManager.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/PhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/PhasedQueryManager.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/PopulationFrequencyPhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/PopulationFrequencyPhasedQueryManager.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/CellBaseNormalizerSequenceAdaptor.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/CellBaseNormalizerSequenceAdaptor.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeBNDCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeBNDCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeCNVGainCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeCNVGainCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeDeletionCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeDeletionCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeGenericRegionCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeGenericRegionCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeInsertionCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeInsertionCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeMNVCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeMNVCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeSNVCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeSNVCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/UnsupportedURLVariantFormat.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/UnsupportedURLVariantFormat.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/CdnaCoord.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/CdnaCoord.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsDeletionCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsDeletionCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsInsertionCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsInsertionCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsSNVCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsSNVCalculator.java
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diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsStringBuilder.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsStringBuilder.java
new file mode 100755
index 0000000000..e6dfc8cb77
--- /dev/null
+++ b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsStringBuilder.java
@@ -0,0 +1,240 @@
+package org.opencb.cellbase.core.variant.annotation.hgvs;
+
+/**
+ * Created by fjlopez on 26/01/17.
+ */
+
+import org.apache.commons.lang.NotImplementedException;
+
+/**
+ * Builder to get the hgvs identifier properly formatted.
+ */
+public class HgvsStringBuilder {
+
+ enum Kind { CODING, NON_CODING }
+
+ // HGVS string parts
+ private String prefix;
+ private String chromosome;
+ private String transcriptId;
+ private String geneId;
+ private Kind kind;
+ private String mutationType;
+ private int start;
+ private int end;
+ private String reference; // reference allele
+ private String alternate; // alternate allele
+
+ // cDNA-specific fields
+ private CdnaCoord cdnaStart;
+ private CdnaCoord cdnaEnd;
+
+ public HgvsStringBuilder() {
+
+ }
+
+ public String getPrefix() {
+ return prefix;
+ }
+
+ public void setPrefix(String prefix) {
+ this.prefix = prefix;
+ }
+
+ public String getChromosome() {
+ return chromosome;
+ }
+
+ public void setChromosome(String chromosome) {
+ this.chromosome = chromosome;
+ }
+
+ public String getTranscriptId() {
+ return transcriptId;
+ }
+
+ public void setTranscriptId(String transcriptId) {
+ this.transcriptId = transcriptId;
+ }
+
+ public String getGeneId() {
+ return geneId;
+ }
+
+ public void setGeneId(String geneId) {
+ this.geneId = geneId;
+ }
+
+ public Kind getKind() {
+ return kind;
+ }
+
+ public void setKind(Kind kind) {
+ this.kind = kind;
+ }
+
+ public String getMutationType() {
+ return mutationType;
+ }
+
+ public void setMutationType(String mutationType) {
+ this.mutationType = mutationType;
+ }
+
+ public int getStart() {
+ return start;
+ }
+
+ public void setStart(int start) {
+ this.start = start;
+ }
+
+ public int getEnd() {
+ return end;
+ }
+
+ public void setEnd(int end) {
+ this.end = end;
+ }
+
+ public String getReference() {
+ return reference;
+ }
+
+ public void setReference(String reference) {
+ this.reference = reference;
+ }
+
+ public String getAlternate() {
+ return alternate;
+ }
+
+ public void setAlternate(String alternate) {
+ this.alternate = alternate;
+ }
+
+ public CdnaCoord getCdnaStart() {
+ return cdnaStart;
+ }
+
+ public void setCdnaStart(CdnaCoord cdnaStart) {
+ this.cdnaStart = cdnaStart;
+ }
+
+ public CdnaCoord getCdnaEnd() {
+ return cdnaEnd;
+ }
+
+ public void setCdnaEnd(CdnaCoord cdnaEnd) {
+ this.cdnaEnd = cdnaEnd;
+ }
+
+ /**
+ * Generate a HGVS string.
+ * @return String containing an HGVS formatted variant representation
+ */
+ public String format() {
+//
+
+ StringBuilder allele = new StringBuilder();
+ allele.append(formatPrefix()); // if use_prefix else ''
+ allele.append(":");
+
+ if (kind.equals(Kind.CODING)) {
+ allele.append("c.").append(formatCdna());
+ } else if (kind.equals(Kind.NON_CODING)) {
+ allele.append("n.").append(formatCdna());
+// elif self.kind == 'p':
+// allele = 'p.' + self.format_protein()
+// elif self.kind == 'g':
+// allele = 'g.' + self.format_genome()
+ } else {
+ throw new NotImplementedException("HGVS calculation not implemented for variant " + chromosome + ":"
+ + start + ":" + reference + ":" + alternate + "; kind: " + kind);
+ }
+// if prefix:
+ return allele.toString();
+// else:
+// return allele
+ }
+
+ /**
+ * Generate HGVS trancript/geneId prefix.
+ * Some examples of full hgvs names with transcriptId include:
+ * NM_007294.3:c.2207A>C
+ * NM_007294.3(BRCA1):c.2207A>C
+ */
+ private String formatPrefix() {
+// if use_gene and self.geneId:
+ StringBuilder stringBuilder = new StringBuilder(transcriptId);
+ stringBuilder.append("(").append(geneId).append(")");
+
+ return stringBuilder.toString();
+// return self.transcriptId
+ }
+
+ /**
+ * Generate HGVS cDNA allele.
+ * Some examples include:
+ * Substitution: 101A>C,
+ * Indel: 3428delCinsTA, 1000_1003delATG, 1000_1001insATG
+ */
+ private String formatCdna() {
+ return formatCdnaCoords() + formatDnaAllele();
+ }
+
+ /**
+ * Generate HGVS DNA allele.
+ * @return
+ */
+ private String formatDnaAllele() {
+
+// We are not considering this case since would mean there's no variant
+// if self.mutation_type == '=':
+// #No change.
+// #example:
+// 101 A =
+// return self.ref_allele + '='
+
+ if (">".equals(mutationType)) {
+ // SNP.
+ // example:
+ // 101 A > C
+ return reference + '>' + alternate;
+ } else if ("delins".equals(mutationType)) {
+ // Indel.
+ // example:
+ // 112_117d elAGGTCAinsTG, 112_117d elinsTG
+ return "del" + reference + "ins" + alternate;
+ } else if ("del".equals(mutationType)) {
+ // Delete, duplication.
+ // example:
+ // 1000_1003d elATG, 1000_1003d upATG
+ return mutationType + reference;
+ } else if ("dup".equals(mutationType)) {
+ // Insertion normalized as duplication
+ // example:
+ // "ENST00000382869.3:c.1735+32dupA"
+ return mutationType + alternate;
+ } else if ("ins".equals(mutationType)) {
+ // Insert.
+ // example:
+ // 1000_1001 insATG
+ return mutationType + alternate;
+ } else {
+ throw new AssertionError("unknown mutation type: '" + mutationType + "'");
+ }
+ }
+
+ /**
+ * Generate HGVS cDNA coordinates string.
+ */
+ private String formatCdnaCoords() {
+ if (cdnaStart.equals(cdnaEnd)) {
+ return cdnaStart.toString();
+ } else {
+ return cdnaStart.toString() + "_" + cdnaEnd.toString();
+ }
+ }
+
+}
diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/gene_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/gene_service.proto
old mode 100644
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diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/generic_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/generic_service.proto
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/genomic_region_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/genomic_region_service.proto
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/regulatory_region_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/regulatory_region_service.proto
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/transcript_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/transcript_service.proto
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/variant_annotation_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/variant_annotation_service.proto
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/variant_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/variant_service.proto
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/main/resources/configuration.json b/cellbase-core/src/main/resources/configuration.json
old mode 100644
new mode 100755
index c562c34789..210d6a7b29
--- a/cellbase-core/src/main/resources/configuration.json
+++ b/cellbase-core/src/main/resources/configuration.json
@@ -1,4 +1,624 @@
{
+<<<<<<< HEAD
+ "version": "v4",
+ "apiVersion": "v3",
+ "wiki": "https://github.com/opencb/cellbase/wiki",
+ "maintenanceFlagFile": "/tmp/maintenance",
+ "maintainerContact": "javier.lopez@genomicsengland.co.uk",
+ "databases": {
+ "mongodb": {
+ "host": "localhost:27017",
+ "user": "",
+ "password": "",
+ "options": {
+ "authenticationDatabase": "admin",
+ "readPreference": "nearest",
+ "replicaSet": "",
+ "connectionsPerHost": 20
+ }
+ },
+ "neo4j": {
+ "hsapiens": {
+ "host": "localhost:27017",
+ "user": "",
+ "password": ""
+ },
+ "mmusculus": {
+ "host": "localhost:27017",
+ "user": "",
+ "password": ""
+ }
+ }
+ },
+ "defaultOutdir": "/tmp",
+ "download": {
+ "ensembl": {
+ "database": {
+ "host": "ensembldb.ensembl.org:3306",
+ "user": "anonymous",
+ "password": ""
+ },
+ "libs": "/srv/qgen/ensembl/ensembl-io",
+ "url": {
+ "host": "ftp://ftp.ensembl.org/pub"
+ }
+ },
+ "ensemblGenomes":{
+ "database":{
+ "host": "mysql-eg-publicsql.ebi.ac.uk:4157",
+ "user": "anonymous",
+ "password": ""
+ },
+ "libs": "/srv/qgen/ensembl/ensembl-io",
+ "url":{
+ "host":"ftp://ftp.ensemblgenomes.org/pub"
+ }
+ },
+ "geneUniprotXref": {
+ "host": "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/"
+ },
+ "geneExpressionAtlas": {
+ "host": "ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/gxa/allgenes_updown_in_organism_part_2.0.14.tab.gz"
+ },
+ "mirbase": {
+ "host": "ftp://mirbase.org/pub/mirbase/CURRENT/"
+ },
+ "mirbaseReadme": {
+ "host": "ftp://mirbase.org/pub/mirbase/CURRENT/README"
+ },
+ "targetScan": {
+ "host": "http://hgdownload.cse.ucsc.edu/goldenPath/"
+ },
+ "miRTarBase": {
+ "host": "http://mirtarbase.mbc.nctu.edu.tw/cache/download/4.5/"
+ },
+ "uniprot": {
+ "host": "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz"
+ },
+ "uniprotRelNotes": {
+ "host": "ftp://ftp.uniprot.org/pub/databases/uniprot/relnotes.txt"
+ },
+ "intact": {
+ "host": "ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.txt"
+ },
+ "interpro": {
+ "host": "ftp://ftp.ebi.ac.uk/pub/databases/interpro/current/protein2ipr.dat.gz"
+ },
+ "interproRelNotes": {
+ "host": "ftp://ftp.ebi.ac.uk/pub/databases/interpro/current/release_notes.txt"
+ },
+ "conservation": {
+ "host": "ftp://hgdownload.cse.ucsc.edu/goldenPath/"
+ },
+ "gerp": {
+ "host": "http://mendel.stanford.edu/SidowLab/downloads/gerp/hg19.GERP_scores.tar.gz"
+ },
+ "clinvar": {
+ "host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2018-10.xml.gz"
+ },
+ "clinvarSummary": {
+ "host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz"
+ },
+ "clinvarVariationAllele": {
+ "host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variation_allele.txt.gz"
+ },
+ "clinvarEfoTerms": {
+ "host": "ftp://ftp.ebi.ac.uk/pub/databases/eva/ClinVar/2015/ClinVar_Traits_EFO_Names_260615.csv"
+ },
+ "iarctp53": {
+ "host": "http://p53.iarc.fr/ajax/Zipper.ashx"
+ },
+ "docm": {
+ "host": "http://docm.info/api/"
+ },
+ "docmVersion": {
+ "host": "http://docm.info"
+ },
+ "dgv": {
+ "host": "http://dgv.tcag.ca/v106/docs"
+ },
+ "simpleRepeats": {
+ "host": "http://hgdownload.cse.ucsc.edu/goldenPath"
+ },
+ "windowMasker": {
+ "host": "http://hgdownload.cse.ucsc.edu/goldenPath"
+ },
+ "genomicSuperDups": {
+ "host": "http://hgdownload.cse.ucsc.edu/goldenPath"
+ },
+ "gwasCatalog": {
+ "host": "ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/2016/09/28/gwas-catalog-associations.tsv"
+ },
+ "hpo": {
+ "host": "http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt"
+ },
+ "disgenet": {
+ "host": "http://www.disgenet.org/static/disgenet_ap1/files/downloads/all_gene_disease_associations.tsv.gz"
+ },
+ "disgenetReadme": {
+ "host": "http://www.disgenet.org/static/disgenet_ap1/files/downloads/readme.txt"
+ },
+ "dgidb": {
+ "host": "http://dgidb.org/data/interactions.tsv"
+ },
+ "cadd": {
+ "host": "http://krishna.gs.washington.edu/download/CADD/v1.3/whole_genome_SNVs.tsv.gz"
+ },
+ "reactome": {
+ "host": "http://www.reactome.org/download/current/biopax.zip"
+ }
+ },
+ "species": {
+ "vertebrates": [
+ {
+ "id": "hsapiens",
+ "scientificName": "Homo sapiens",
+ "assemblies": [
+ {
+ "ensemblVersion":"82_37",
+ "name":"GRCh37"
+ },
+ {
+ "ensemblVersion":"89_38",
+ "name":"GRCh38_89"
+ },
+ {
+ "ensemblVersion":"89",
+ "name":"GRCh38"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "gene_disease_association",
+ "variation",
+ "variation_functional_score",
+ "regulation",
+ "protein",
+ "conservation",
+ "clinical_variants",
+ "clinical",
+ "svs",
+ "repeats"
+ ]
+ },
+ {
+ "id":"mmusculus",
+ "scientificName":"Mus musculus",
+ "assemblies":[
+ {
+ "ensemblVersion":"82_38",
+ "name":"GRCm38"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation",
+ "regulation",
+ "protein",
+ "conservation"
+ ]
+ },
+ {
+ "id":"drerio",
+ "scientificName":"Danio rerio",
+ "assemblies":[
+ {
+ "ensemblVersion":"82_10",
+ "name":"GRCz10"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation",
+ "protein"
+ ]
+ },
+ {
+ "id":"rnorvegicus",
+ "scientificName":"Rattus norvegicus",
+ "assemblies":[
+ {
+ "ensemblVersion":"82_6",
+ "name":"Rnor_6.0"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation",
+ "protein"
+ ]
+ },
+ {
+ "id":"ptroglodytes",
+ "scientificName":"Pan troglodytes",
+ "assemblies":[
+ {
+ "ensemblVersion":"82_214",
+ "name":"CHIMP2.1.4"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation"
+ ]
+ },
+ {
+ "id":"ggorilla",
+ "scientificName":"Gorilla gorilla",
+ "assemblies":[
+ {
+ "ensemblVersion":"82_31",
+ "name":"gorGor3.1"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene"
+ ]
+ },
+ {
+ "id":"csabaeus",
+ "scientificName":"Chlorocebus sabaeus",
+ "assemblies":[
+ {
+ "ensemblVersion":"82_1",
+ "name":"ChlSab1.1"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene"
+ ]
+ },
+ {
+ "id":"sscrofa",
+ "scientificName":"Sus scrofa",
+ "assemblies":[
+ {
+ "ensemblVersion":"82_102",
+ "name":"Sscrofa10.2"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation",
+ "protein"
+ ]
+ },
+ {
+ "id":"cfamiliaris",
+ "scientificName":"Canis familiaris",
+ "assemblies":[
+ {
+ "ensemblVersion":"82_31",
+ "name":"CanFam3.1"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation"
+ ]
+ }
+ ],
+ "metazoa":[
+ {
+ "id":"celegans",
+ "scientificName":"Caenorhabditis elegans",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_245",
+ "name":"WBcel235"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation",
+ "protein"
+ ]
+ },
+ {
+ "id":"dmelanogaster",
+ "scientificName":"Drosophila melanogaster",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_6",
+ "name":"BDGP6"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation",
+ "protein"
+ ]
+ },
+ {
+ "id":"agambiae",
+ "scientificName":"Anopheles gambiae",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_4",
+ "name":"AgamP4"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation",
+ "protein"
+ ]
+ }
+ ],
+ "fungi":[
+ {
+ "id":"scerevisiae",
+ "scientificName":"Saccharomyces cerevisiae",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_4",
+ "name":"R64-1-1"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation",
+ "protein"
+ ]
+ },
+ {
+ "id":"afumigatus",
+ "scientificName":"Aspergillus fumigatus",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_2",
+ "name":"CADRE"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene"
+ ]
+ },
+ {
+ "id":"anidulans",
+ "scientificName":"Aspergillus nidulans",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_6",
+ "name":"ASM1142v1"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene"
+ ]
+ }
+ ],
+ "protist":[
+ {
+ "id":"pfalciparum",
+ "scientificName":"Plasmodium falciparum",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_3",
+ "name":"ASM276v1"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation",
+ "protein"
+ ]
+ },
+ {
+ "id":"lmajor",
+ "scientificName":"Leishmania major",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_2",
+ "name":"ASM272v2"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene"
+ ]
+ }
+ ],
+ "plants":[
+ {
+ "id":"athaliana",
+ "scientificName":"Arabidopsis thaliana",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_10",
+ "name":"TAIR10"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation",
+ "protein"
+ ]
+ },
+ {
+ "id":"osativa",
+ "scientificName":"Oryza sativa",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_7",
+ "name":"IRGSP-1.0"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation"
+ ]
+ },
+ {
+ "id":"gmax",
+ "scientificName":"Glycine max",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_1",
+ "name":"V1.0"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene"
+ ]
+ },
+ {
+ "id":"vvinifera",
+ "scientificName":"Vitis vinifera",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_3",
+ "name":"IGGP_12x"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation"
+ ]
+ },
+ {
+ "id":"zmays",
+ "scientificName":"Zea mays",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_6",
+ "name":"AGPv3"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation"
+ ]
+ },
+ {
+ "id":"sbicolor",
+ "scientificName":"Sorghum bicolor",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_14",
+ "name":"Sorbi1"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation"
+ ]
+ },
+ {
+ "id":"slycopersicum",
+ "scientificName":"Solanum lycopersicum",
+ "assemblies":[
+ {
+ "ensemblVersion":"29_82_250",
+ "name":"GCA_000188115.2"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "variation"
+ ]
+ }
+ ],
+ "virus" : [
+ {
+ "id":"evirus",
+ "scientificName":"Ebola virus",
+ "assemblies":[
+ {
+ "name":"KM034562v1"
+ }
+ ],
+ "data":[
+ "genome",
+ "gene"
+ ]
+ }
+ ],
+ "bacteria": [
+ {
+ "id": "mpneumoniae",
+ "scientificName": "Mycoplasma pneumoniae M129",
+ "assemblies": [
+ {
+ "ensemblVersion":"29_82_1",
+ "ensemblCollection":"bacteria_0_collection",
+ "name":"ASM2734v1"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "protein"
+ ]
+ },
+ {
+ "id": "ecoli",
+ "scientificName": "Escherichia coli",
+ "assemblies": [
+ {
+ "ensemblVersion":"29_82_1",
+ "ensemblCollection":"bacteria_91_collection",
+ "name":"HUSEC2011CHR1"
+ }
+ ],
+ "data":[
+ "genome",
+ "genome_info",
+ "gene",
+ "protein"
+ ]
+ }
+ ]
+ }
+=======
"version": "v4",
"apiVersion": "${cellbase.version}",
"wiki": "https://github.com/opencb/cellbase/wiki",
@@ -614,4 +1234,5 @@
}
]
}
+>>>>>>> a06ad91c3ea228e658c3495fc957d56b2572a9be
}
diff --git a/cellbase-core/src/main/resources/log4j.properties b/cellbase-core/src/main/resources/log4j.properties
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/main/resources/org/opencb/cellbase/core/variation/variation_consequences.properties b/cellbase-core/src/main/resources/org/opencb/cellbase/core/variation/variation_consequences.properties
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/test/java/org/opencb/cellbase/core/CellBaseConfigurationTest.java b/cellbase-core/src/test/java/org/opencb/cellbase/core/CellBaseConfigurationTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/test/java/org/opencb/cellbase/core/variant/VariantAnnotatorRunnerTest.java b/cellbase-core/src/test/java/org/opencb/cellbase/core/variant/VariantAnnotatorRunnerTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/test/resources/cellBaseProperties_test.json b/cellbase-core/src/test/resources/cellBaseProperties_test.json
old mode 100644
new mode 100755
diff --git a/cellbase-core/src/test/resources/gene.json b/cellbase-core/src/test/resources/gene.json
old mode 100644
new mode 100755
diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/MongoDBCollectionConfiguration.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/MongoDBCollectionConfiguration.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/VariantMongoIterator.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/VariantMongoIterator.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ClinicalLegacyMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ClinicalLegacyMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ClinicalMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ClinicalMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ConservationMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ConservationMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/GeneMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/GeneMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/GenomeMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/GenomeMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/MetaMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/MetaMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/MongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/MongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/MongoDBAdaptorFactory.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/MongoDBAdaptorFactory.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ProteinMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ProteinMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ProteinProteinInteractionMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ProteinProteinInteractionMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/RegulationMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/RegulationMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/RepeatsMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/RepeatsMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/TranscriptMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/TranscriptMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/VariantMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/VariantMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/XRefMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/XRefMongoDBAdaptor.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/loader/MongoDBCellBaseLoader.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/loader/MongoDBCellBaseLoader.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/loader/converters/GeneConverter.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/loader/converters/GeneConverter.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/loader/converters/MongoDBTypeConverter.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/loader/converters/MongoDBTypeConverter.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/loader/converters/VariationConverter.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/loader/converters/VariationConverter.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/model/ClinicalVariation.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/model/ClinicalVariation.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/GenericMongoDBAdaptorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/GenericMongoDBAdaptorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/CellBaseNormalizerSequenceAdaptorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/CellBaseNormalizerSequenceAdaptorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/ClinicalLegacyMongoDBAdaptorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/ClinicalLegacyMongoDBAdaptorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/ClinicalMongoDBAdaptorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/ClinicalMongoDBAdaptorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/GeneMongoDBAdaptorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/GeneMongoDBAdaptorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/GenomeMongoDBAdaptorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/GenomeMongoDBAdaptorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/ProteinMongoDBAdaptorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/ProteinMongoDBAdaptorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/TranscriptMongoDBAdaptorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/TranscriptMongoDBAdaptorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantAnnotationCalculatorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantAnnotationCalculatorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantMongoDBAdaptorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantMongoDBAdaptorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/XRefMongoDBAdaptorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/XRefMongoDBAdaptorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/loader/LoadRunnerTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/loader/LoadRunnerTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/loader/MongoDBCellBaseLoaderTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/loader/MongoDBCellBaseLoaderTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/monitor/MonitorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/monitor/MonitorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/variant/hgvs/HgvsCalculatorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/variant/hgvs/HgvsCalculatorTest.java
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/resources/clinicalMongoDBAdaptor/nativeGet/clinical_variants.full.test.json.gz b/cellbase-lib/src/test/resources/clinicalMongoDBAdaptor/nativeGet/clinical_variants.full.test.json.gz
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/resources/clinicalMongoDBAdaptor/phasedQueries/clinical_variants.full.test.json.gz b/cellbase-lib/src/test/resources/clinicalMongoDBAdaptor/phasedQueries/clinical_variants.full.test.json.gz
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/resources/clinvar.json.gz b/cellbase-lib/src/test/resources/clinvar.json.gz
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/resources/configuration.test.json b/cellbase-lib/src/test/resources/configuration.test.json
old mode 100644
new mode 100755
index 95264e5eb5..3deb3417cc
--- a/cellbase-lib/src/test/resources/configuration.test.json
+++ b/cellbase-lib/src/test/resources/configuration.test.json
@@ -108,10 +108,10 @@
"host": "http://p53.iarc.fr/ajax/Zipper.ashx"
},
"docm": {
- "host": "http://docm.genome.wustl.edu/api/"
+ "host": "http://docm.info/api/"
},
"docmVersion": {
- "host": "http://docm.genome.wustl.edu"
+ "host": "http://docm.info"
},
"dgv": {
"host": "http://dgv.tcag.ca/v106/docs"
diff --git a/cellbase-lib/src/test/resources/cosmic.json.gz b/cellbase-lib/src/test/resources/cosmic.json.gz
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/resources/gene.test.json.gz b/cellbase-lib/src/test/resources/gene.test.json.gz
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/resources/genome/genome_info.json b/cellbase-lib/src/test/resources/genome/genome_info.json
old mode 100644
new mode 100755
diff --git a/cellbase-lib/src/test/resources/genome/genome_sequence.test.json.gz b/cellbase-lib/src/test/resources/genome/genome_sequence.test.json.gz
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diff --git a/cellbase-test/fitnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/HSapiensTests/VariationTests.wiki b/cellbase-test/fitnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/HSapiensTests/VariationTests.wiki
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diff --git a/cellbase-test/fitnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/HSapiensTests/XrefTests.wiki b/cellbase-test/fitnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/HSapiensTests/XrefTests.wiki
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diff --git a/cellbase-test/fitnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/SuiteSetUp.wiki b/cellbase-test/fitnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/SuiteSetUp.wiki
old mode 100644
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index 05ad09705e..2ac7b7a7c2
--- a/cellbase-test/fitnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/SuiteSetUp.wiki
+++ b/cellbase-test/fitnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/SuiteSetUp.wiki
@@ -14,13 +14,8 @@ Test
|smartrics.rest.fitnesse.fixture|
!|Table: Rest Fixture | http://bioinfoint.hpc.cam.ac.uk/|
-<<<<<<< HEAD
-|let|baseURL|const|http://${TEST_HOST}/${CELLBASE_WAR}/webservices/rest/${CELLBASE_VERSION}|http://bioinfodev.hpc.cam.ac.uk/cellbase-4.6.0-SNAPSHOT/webservices/rest/v4|
-|let|baseURL_hsapiens|const|http://${TEST_HOST}/${CELLBASE_WAR}/webservices/rest/${CELLBASE_VERSION}/hsapiens|http://bioinfodev.hpc.cam.ac.uk/cellbase-4.6.0-SNAPSHOT/webservices/rest/v4/hsapiens|
-=======
|let|baseURL|const|http://${TEST_HOST}/${CELLBASE_WAR}/webservices/rest/${CELLBASE_VERSION}|http://bioinfodev.hpc.cam.ac.uk/cellbase-4.5.5/webservices/rest/v4|
|let|baseURL_hsapiens|const|http://${TEST_HOST}/${CELLBASE_WAR}/webservices/rest/${CELLBASE_VERSION}/hsapiens|http://bioinfodev.hpc.cam.ac.uk/cellbase-4.5.5/webservices/rest/v4/hsapiens|
->>>>>>> hotfix-4.5.x
|let|useCache|const|false|false|
| Table: Rest Fixture Config | with-compareJSON.js |
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diff --git a/cellbase-web/Gruntfile.js b/cellbase-web/Gruntfile.js
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diff --git a/cellbase-web/LICENSE b/cellbase-web/LICENSE
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diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla
index bb4156e230..c9ba7f9ece 160000
--- a/cellbase-web/lib/jsorolla
+++ b/cellbase-web/lib/jsorolla
@@ -1 +1 @@
-Subproject commit bb4156e2301ba4e0b3fb49aba9d945faf4fa604a
+Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0
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diff --git a/pom.xml b/pom.xml
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index cd579a4370..320a2e3008
--- a/pom.xml
+++ b/pom.xml
@@ -25,7 +25,12 @@
4.8.1
1.8
3.7.0
+<<<<<<< HEAD
+ 3.6
+ 1.4.3
+=======
1.5.3
+>>>>>>> a06ad91c3ea228e658c3495fc957d56b2572a9be
0.1.0
2.9.8
3.1.0
diff --git a/regulatory_region.test.json b/regulatory_region.test.json
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