Change to mongo 6 and update the executable name

.github/workflows/python-package.yml

@@ -16,6 +16,7 @@ jobs:
     strategy:
       matrix:
         mongodb-version: [4.0.18]
+        mongosh-version: [1.10.6]
         python-version: [3.8, 3.9]
         java-version: [1.11]
         nextflow-version: [21.10.5, 22.10.7]
@@ -33,8 +34,8 @@ jobs:
         wget -qO- https://github.com/nextflow-io/nextflow/releases/download/v${{ matrix.nextflow-version }}/nextflow-${{ matrix.nextflow-version }}-all | bash
         echo "/tmp/nextflow" >> $GITHUB_PATH
         cd -
-    - name: Set up MongoDB sharded environment ${{ matrix.mongodb-version }}
-      run: sudo bash scripts/create_mongo_single_node_sharded_env.sh ${{ matrix.mongodb-version }}
+    - name: Set up MongoDB ${{ matrix.mongodb-version }} and Mongosh ${{ matrix.mongosh-version }} sharded environment
+      run: sudo bash scripts/create_mongo_single_node_sharded_env.sh ${{ matrix.mongodb-version }} ${{ matrix.mongosh-version }}
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:

ebi_eva_internal_pyutils/mongodb/mongo_database.py

@@ -111,9 +111,7 @@ def shard_collections(self, collections_shard_key_map, collections_to_shard):
             shard_collection_command = f'sh.shardCollection(' \
                                        f'"{self.db_name}.{collection_name}", ' \
                                        f'{shard_key_repr}, {str(shard_key_uniqueness_flag).lower()})'
-            sharding_command = f"mongo --host {self.uri}  " \
-                               f"--eval " \
-                               f"'{shard_collection_command}' "
+            sharding_command = f"mongosh --eval '{shard_collection_command}' {self.uri} "
             sharding_command += self._get_optional_secrets_file_stdin()
             run_command_with_output(f"Sharding collection {collection_name} in the database {self.uri_with_db_name} "
                                     f"with key {shard_key_repr}...", sharding_command,

scripts/create_mongo_single_node_sharded_env.sh

@@ -5,11 +5,21 @@ systemctl stop mongod || true
 apt-get remove mongodb-org -y || true
 apt-get autoremove --purge || true
 
-# Proceed with specific MongoDB version installation
+# Proceed with specific MongoDB and Mongosh version installation
 export mongodb_version=$1
+export mongosh_version=$2
+
+BASEDIR=$PWD
 wget http://fastdl.mongodb.org/linux/mongodb-linux-x86_64-${mongodb_version}.tgz
 tar xfz mongodb-linux-x86_64-${mongodb_version}.tgz
-cd $PWD/mongodb-linux-x86_64-${mongodb_version}/bin/
+cd $BASEDIR/mongodb-linux-x86_64-${mongodb_version}/bin/
+for f in *;
+  do ln -s $PWD/$f /usr/bin/; chmod a+x /usr/bin/$f;
+done
+cd $BASEDIR/
+wget https://downloads.mongodb.com/compass/mongosh-${mongosh_version}-linux-x64.tgz
+tar xfz mongosh-${mongosh_version}-linux-x64.tgz
+cd $BASEDIR/mongosh-${mongosh_version}-linux-x64/bin/
 for f in *;
   do ln -s $PWD/$f /usr/bin/; chmod a+x /usr/bin/$f;
 done
@@ -19,7 +29,7 @@ done
 function wait_for_mongo() {
   # Wait until Mongo is ready to accept connections, exit if this does not happen within 2 minutes
   COUNTER=0
-  until mongo --host $1 --eval "printjson(db.serverStatus())"
+  until mongosh --host $1 --eval "printjson(db.serverStatus())"
   do
     sleep 1
     COUNTER=$((COUNTER+1))
@@ -36,11 +46,11 @@ rm -rf /data/mongodb
 mkdir -p /data/mongodb/shard01 /data/mongodb/config
 mongod --shardsvr --port 27018 --replSet rs0 --dbpath /data/mongodb/shard01 &
 wait_for_mongo "localhost:27018"
-mongo --port 27018 --eval 'rs.initiate({_id:"rs0", members: [{_id: 1, host: "localhost:27018"}]})'
+mongosh --port 27018 --eval 'rs.initiate({_id:"rs0", members: [{_id: 1, host: "localhost:27018"}]})'
 
 mongod --configsvr --port 27019 --replSet rs1 --dbpath /data/mongodb/config &
 wait_for_mongo "localhost:27019"
-mongo --port 27019 --eval 'rs.initiate()'
+mongosh --port 27019 --eval 'rs.initiate()'
 mongos --configdb rs1/localhost:27019 --port 27017 &
 wait_for_mongo "localhost:27017"
-mongo --eval 'sh.addShard("rs0/localhost:27018")'
+mongosh --eval 'sh.addShard("rs0/localhost:27018")'

tests/common/test_assembly.py

@@ -135,12 +135,8 @@ def test_get_ncbi_genome_folder_url_and_content_multi(self):
         # GCA_000001405.10, GCA_000001405.11 ...
         assembly = NCBIAssembly('GCA_000001405.1', 'Homo sapiens', self.genome_folder)
         url = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.1_GRCh37'
-        content = ['ALT_REF_LOCI_1', 'ALT_REF_LOCI_2', 'ALT_REF_LOCI_3', 'ALT_REF_LOCI_4', 'ALT_REF_LOCI_5',
-                   'ALT_REF_LOCI_6', 'ALT_REF_LOCI_7', 'ALT_REF_LOCI_8', 'ALT_REF_LOCI_9', 'Primary_Assembly',
-                   'special_requests', 'genomic_regions_definitions.txt', 'ASSEMBLY_INFO', 'RepeatMasker.run',
-                   'windowmasker_nmer.oascii.gz', 'par.txt', 'GCA_000001405.1_GRCh37_assembly_report.txt',
-                   'GCA_000001405.1_GRCh37_assembly_stats.txt', 'GCA_000001405.1_GRCh37_assembly_regions.txt',
-                   'assembly_status.txt', 'md5checksums.txt']
+        content = ['GCA_000001405.1_GRCh37_assembly_regions.txt', 'GCA_000001405.1_GRCh37_assembly_report.txt',
+                   'GCA_000001405.1_GRCh37_assembly_stats.txt', 'md5checksums.txt', 'assembly_status.txt']
 
         self.assertEqual(assembly._ncbi_genome_folder_url_and_content, (url, content))
 

tests/internal/test_mongodb.py

@@ -21,8 +21,8 @@ class TestMongoDatabase(TestCommon):
     def setUp(self) -> None:
         self.test_mongo_db = MongoDatabase(uri=self.uri, db_name=self.dump_db_name)
         self.dump_dir = os.path.join(self.resources_folder, self.dump_db_name)
-        run_command_with_output("Drop target test database if it already exists...", f"mongo {self.dump_db_name} "
-                                                                                     f"--eval 'db.dropDatabase()'")
+        run_command_with_output("Drop target test database if it already exists...",
+                                f"mongosh --eval 'db.dropDatabase()' {self.dump_db_name} ")
         run_command_with_output("Import test database...", f"mongorestore --dir {self.dump_dir}")
 
     def tearDown(self) -> None: