j-coll

#!/bin/bash

name=${1:opencga}

if [ "$name" != "opencga" ]; then 
        name=opencga_$name 
fi 
echo "Installation name :" $name

echo "Clean installation dir"

j-coll

// Use migration script https://gist.github.com/j-coll/c2b81a7ff8392ec6b5208b5a8bf0d3d3
// load("utils/migrateCollection.js")

/**
 * #192 -> Collect genotypes
 * #626 -> Populate alts into stage collection
 **/

if ( db.getCollection("variants").exists() == null ) {
    print("================================================================================");

j-coll

// Use migration script https://gist.github.com/j-coll/c2b81a7ff8392ec6b5208b5a8bf0d3d3
var otherKeys = {
    _id : "",
    end : "",
    ref : "",
    alt : ""
};
migrateCollection("stage", {"_i" : {"$exists" : false} }, {}, function(bulk, doc) {
    var _i = [];

j-coll

function migrateCollection(collection, query, projection, migrateFunc) {
    var bulk = db.getCollection(collection).initializeOrderedBulkOp();
    var count = 0;
    var bulkSize = 500;
    db.getCollection(collection).find(query,projection).forEach(function(doc) {
        migrateFunc(bulk, doc);
        if ( bulk.nUpdateOps + bulk.nInsertOps + bulk.nRemoveOps >= bulkSize ) {
            count += bulk.nUpdateOps + bulk.nInsertOps + bulk.nRemoveOps;
            print("Execute bulk! " + count);

j-coll

function migrateCollectionDifferentCollection(inputCollection, outputCollection, query, projection, migrateFunc) {
    var bulk = db.getCollection(outputCollection).initializeOrderedBulkOp();
    var count = 0;
    var bulkSize = 500;
    db.getCollection(inputCollection).find(query,projection).forEach(function(doc) {
        migrateFunc(bulk, doc);
        if ( bulk.nUpdateOps + bulk.nInsertOps + bulk.nRemoveOps >= bulkSize ) {
            count += bulk.nUpdateOps + bulk.nInsertOps + bulk.nRemoveOps;
            print("Execute bulk! " + count);
            bulk.execute();

j-coll

// Use migration script https://gist.github.com/pfurio/f7cd90af08e0073699f0beeeef1958ba
migrateCollection("variants", {"annotation.ct":{$exists:1}, "annotation._gn_so":{$exists:false}}, {"annotation.ct":1}, function (bulk, doc) {
    var id = doc._id;

    var fields = ["gn", "ensg", "enst", "uni_a", "uni_n"];
    var gn_so_obj = {}; /* Use as set */
    for (var i in doc.annotation[0].ct) {
        var ct = doc.annotation[0].ct[i];
        for (var so_idx in ct.so) {

j-coll

// Generic migration utility method
function migrateCollection(collection, query, projection, migrateFunc) {
    var bulk = db.getCollection(collection).initializeOrderedBulkOp();
    var count = 0;
    var bulkSize = 500;
    db.getCollection(collection).find(query,projection).forEach(function(doc) {

        migrateFunc(bulk, doc);

j-coll

Tomcat8 should run with the same user that installs OpenCGA. We will assume that OpenCGA will be installed with user opencga. Run the following to set Tomcat8 to run with user opencga.

cd /var/lib/tomcat8/
# Change owner and group of every folder following links
sudo chown -RL opencga:opencga ./*
sudo service tomcat8 stop

j-coll

// mongo opencga_user_project

/*
var studyId = ??;
var fileIds = [??];
var sampleIds = [??];
*/
function dropFiles(studyId, fileIds, sampleIds) {
  db.variants.update(
    {

j-coll

# Apache phoenix 4.7.0.2.5.0.0-1245 (from HDP-2.5.0) is based on Apache Phoenix 4.7.0-HBase-1.1
# These are ALL the changes on top of Apache Phoenix 4.7.0-HBase-1.1
#
# cd phoenix
# git checkout v4.7.0-HBase-1.1
# git log --pretty=oneline | cut -d " " -f 2 | grep "PHOENIX-" | tr -d ":.[]" | sort | uniq > issues_phoenix-4.7-hbase-1.1.txt 
#
# cd phoenix-release
# git checkout HDP-2.5.3.0-tag
# git log --pretty=oneline | cut -d " " -f 2 | grep "PHOENIX-" | tr -d ":.[]" | sort | uniq > issues_hdp2.5.0.txt