diff --git a/.gitignore b/.gitignore index 5185cc1a..c15bda1c 100644 --- a/.gitignore +++ b/.gitignore @@ -6,6 +6,7 @@ terraform/terraform.tfstate.d/test/*.backup terraform/sequence_search_rsa terraform/sequence_search_rsa.pub terraform/.terraform +terraform/current_state terraform_load_balancer/providers.tf terraform_load_balancer/terraform.tfstate.backup @@ -14,14 +15,17 @@ terraform_load_balancer/load_balancer_rsa.pub terraform_load_balancer/.terraform __pycache__/ +.idea/ *.pyc *.pyo *.retry ansible/hosts +ansible/producer_latest.dump node_modules/ ENV/ sequence_search/consumer/hmmer-3.2.1/ sequence_search/consumer/results sequence_search/consumer/queries sequence_search/consumer/databases +sequence_search/monitor/.conf-file diff --git a/README.md b/README.md index a4383081..1e7821e0 100644 --- a/README.md +++ b/README.md @@ -30,13 +30,15 @@ running unit-tests on local machine only, it is not using any database or networ - [Terraform inventory](https://github.com/adammck/terraform-inventory) - [Virtual environment](https://virtualenv.pypa.io/en/latest/) with installed dependencies -1. Generate `sequence_search_rsa` key: +1. Create `terraform/providers.tf` using the `providers.tf.template` file. + +2. Generate `sequence_search_rsa` key: `cd terraform && ssh-keygen -t rsa -b 4096` See: https://help.github.com/en/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent -2. Follow steps in `redeploy.jenkinsfile`. +3. Follow steps in `redeploy.jenkinsfile`. - Install SSH keys - Run `terraform init && terraform apply` to create the infrastructure @@ -158,18 +160,16 @@ https://github.com/webpack/webpack.js.org/issues/1854. 1. `pushd terraform_load_balancer; terraform apply; popd` -2. Update IP address in `load_balancer.yml`, then run: +2. Run the command bellow passing the IPs as variables on the command line: ``` cd ansible_load_balancer - ansible-playbook -i hosts --private-key=../terraform_load_balancer/load_balancer_rsa load_balancer.yml + ansible-playbook -i hosts --private-key=../terraform_load_balancer/load_balancer_rsa --extra-vars "main_ip=main.ip.address fallback_ip=fallback.ip.address" load_balancer.yml ``` -The load balancer is an nginx server that proxies http requests to the -currently selected producer machine's `8002` port. If you want to -configure the ip and port of producer machine, go to `load_balancer.yml` -playbook and change the `nginx_backend_ip` and `nginx_backend_port` -variables. +The load balancer is an nginx server that proxies http requests to the currently selected producer machine's `8002` +port. If you want to change the port of producer machine, go to `load_balancer.yml` playbook and change the +`nginx_backend_port` variable. If you want to update nginx configuration, make changes in `ansible_load_balancer/roles/ansible_load_balancer/templates/upstream.conf.js`. diff --git a/ansible/consumers.yml b/ansible/consumers.yml index c58d3acf..cbaabc2c 100644 --- a/ansible/consumers.yml +++ b/ansible/consumers.yml @@ -8,3 +8,5 @@ ansible_ssh_private_key_file: "../terraform/sequence_search_rsa" roles: - {role: consumer, tags: 'consumer'} + - ssh + - iptables diff --git a/ansible/download-sequences.yml b/ansible/download-sequences.yml new file mode 100644 index 00000000..75bec1a5 --- /dev/null +++ b/ansible/download-sequences.yml @@ -0,0 +1,17 @@ +- name: Download sequence database + hosts: producer + become: true + gather_facts: no + user: centos + + tasks: + - name: Download compressed archive from RNAcentral FTP + get_url: + url: ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/sequences/.internal/sequence-database.fa.tar.gz + dest: /nfs/sequence-database.fa.tar.gz + + - name: Uncompress the archive + shell: tar -xf sequence-database.fa.tar.gz + args: + chdir: /nfs + creates: /nfs/zwd.fasta diff --git a/ansible/hosts b/ansible/hosts deleted file mode 100644 index b04e9195..00000000 --- a/ansible/hosts +++ /dev/null @@ -1,74 +0,0 @@ -[all] -192.168.0.10 -192.168.0.11 -192.168.0.6 -192.168.0.7 -192.168.0.8 -192.168.0.9 -193.62.55.122 -193.62.55.123 -192.168.0.5 - -[all:vars] -floating_ip=["193.62.55.123"] -tfstate_file=["terraform.tfstate.d/test/terraform.tfstate"] - -[associate_postgres_floating_ip] -193.62.55.122 - -[associate_postgres_floating_ip.0] -193.62.55.122 - -[consumers] -192.168.0.7 -192.168.0.8 -192.168.0.9 -192.168.0.10 -192.168.0.11 - -[consumers.0] -192.168.0.7 - -[consumers.1] -192.168.0.8 - -[consumers.2] -192.168.0.9 - -[consumers.3] -192.168.0.10 - -[consumers.4] -192.168.0.11 - -[postgres] -192.168.0.6 - -[postgres.0] -192.168.0.6 - -[producer] -192.168.0.5 - -[producer.0] -192.168.0.5 - -[sequence_search] -193.62.55.123 - -[sequence_search.0] -193.62.55.123 - -[type_openstack_compute_floatingip_associate_v2] -193.62.55.122 -193.62.55.123 - -[type_openstack_compute_instance_v2] -192.168.0.10 -192.168.0.11 -192.168.0.6 -192.168.0.7 -192.168.0.8 -192.168.0.9 -192.168.0.5 - diff --git a/ansible/main.yml b/ansible/main.yml new file mode 100644 index 00000000..3444ba7e --- /dev/null +++ b/ansible/main.yml @@ -0,0 +1,24 @@ +--- +- import_playbook: nfs-server.yml +- import_playbook: nfs-client.yml +- import_playbook: download-sequences.yml +- import_playbook: postgres.yml +- import_playbook: producer.yml + + +- hosts: producer + gather_facts: Yes + remote_user: centos + become: true + become_method: sudo + vars: + ansible_ssh_private_key_file: "../terraform/sequence_search_rsa" + tasks: + - name: Drop the database and re-create it + shell: + chdir: /srv + cmd: ENVIRONMENT=PRODUCTION python3 -m sequence_search.db + + +- import_playbook: consumers.yml +- import_playbook: monitor.yml diff --git a/ansible/monitor.yml b/ansible/monitor.yml new file mode 100644 index 00000000..4471874a --- /dev/null +++ b/ansible/monitor.yml @@ -0,0 +1,12 @@ +--- +- hosts: monitor + remote_user: centos + become: true + become_method: sudo + vars: + ansible_ssh_private_key_file: "../terraform/sequence_search_rsa" + floating_ip: "{{ lookup('pipe', 'cd ../terraform && terraform output floating_ip') }}" + roles: + - monitor + - ssh + - iptables diff --git a/ansible/nfs-client.yml b/ansible/nfs-client.yml new file mode 100644 index 00000000..a0db4aab --- /dev/null +++ b/ansible/nfs-client.yml @@ -0,0 +1,32 @@ +- name: NFS client installation and nfs server mount + vars: + ansible_ssh_private_key_file: "../terraform/sequence_search_rsa" + nfs_server_ip: 192.168.0.7 + nfs_mount_path: "/nfs" + hosts: producer:consumers + become: true + gather_facts: no + user: centos + + tasks: + - name: Upgrade all packages + yum: name=* state=latest + + - name: Install yum dependencies + yum: + name: + - nfs-utils + + - name: Create an nfs directory where to mount nfs server dir + file: + path: "{{ nfs_mount_path }}" + state: directory + mode: "u=r,g=r,o=rwx" # might need to change these privileges + recurse: yes + + - name: Mount nfs server directory on clients + mount: + path: "{{ nfs_mount_path }}" + src: "{{ nfs_server_ip }}:/" + fstype: nfs + state: mounted diff --git a/ansible/nfs-server.yml b/ansible/nfs-server.yml new file mode 100644 index 00000000..6b40434b --- /dev/null +++ b/ansible/nfs-server.yml @@ -0,0 +1,85 @@ +- name: NFS server installation and setup + hosts: nfs_server + vars: + ansible_python_interpreter: "/usr/bin/python3" # set ansible interpreter to python3 + ansible_ssh_private_key_file: "../terraform/sequence_search_rsa" + network_ip: 192.168.0.0/24 + become: true + gather_facts: no + user: ubuntu + + tasks: + - name: Update and upgrade apt packages + apt: + upgrade: yes + update_cache: yes + cache_valid_time: 86400 + + - name: Update apt + apt: + update_cache: yes + state: present + + - name: Install nfs on the compute instance + apt: + name: "{{ packages }}" + state: present + vars: + packages: + - python3-pip + - nfs-kernel-server + + - name: Create the export nfs directory + file: + path: /nfs + state: directory + mode: "u=r,g=r,o=rwx" + recurse: yes + + - name: Format the volume + filesystem: + fstype: xfs + dev: /dev/vdb + + - name: Mount volume to nfs directory + mount: + path: /nfs + src: /dev/vdb + fstype: xfs + state: mounted + + - name: Make nfs directory accessible to all + file: + path: /nfs + owner: nobody + group: nogroup + + - name: chmod 777 equivalent + file: + path: /nfs + mode: u=rwX,g=rwX,o=rwX + recurse: yes + + - name: Create exports file + lineinfile: + dest: /etc/exports + regexp: '^#*' + insertafter: '^#*' + line: "/nfs {{ network_ip }}(rw,sync,fsid=0,crossmnt,no_subtree_check,no_root_squash)" + owner: root + group: root + mode: 0644 + state: present + + - name: restart nfs server + service: + name: nfs-kernel-server + state: restarted + + - name: Import ssh role + import_role: + name: ssh + + - name: Import iptables role + import_role: + name: iptables diff --git a/ansible/postgres.yml b/ansible/postgres.yml index 876e8849..c4c0ee26 100644 --- a/ansible/postgres.yml +++ b/ansible/postgres.yml @@ -68,4 +68,6 @@ - '*' roles: - - postgresql \ No newline at end of file + - postgresql + - ssh + - iptables \ No newline at end of file diff --git a/ansible/postgres_restore.yml b/ansible/postgres_restore.yml new file mode 100644 index 00000000..2d252898 --- /dev/null +++ b/ansible/postgres_restore.yml @@ -0,0 +1,13 @@ +--- +# Playbook to restore a PostgreSQL database from an archive file created by pg_dump +- hosts: postgres + remote_user: centos + become: true + become_method: sudo + vars: + ansible_ssh_private_key_file: "../terraform/sequence_search_rsa" + tasks: + - copy: src=producer_latest.dump dest=/tmp/producer_latest.dump mode=0777 + - shell: pg_restore -U docker -c -n public -n pg_catalog -d producer /tmp/producer_latest.dump + +- import_playbook: consumers.yml \ No newline at end of file diff --git a/ansible/producer.yml b/ansible/producer.yml index b3ec7fdc..c71869f0 100644 --- a/ansible/producer.yml +++ b/ansible/producer.yml @@ -9,4 +9,6 @@ roles: - {role: 'bastion-private-key', tags: 'bastion'} # - {role: 'docker', tags: 'docker'} - - {role: 'producer', tags: 'producer'} \ No newline at end of file + - {role: 'producer', tags: 'producer'} + - ssh + - iptables \ No newline at end of file diff --git a/ansible/roles/consumer/tasks/main.yml b/ansible/roles/consumer/tasks/main.yml index b1696e77..52025af0 100644 --- a/ansible/roles/consumer/tasks/main.yml +++ b/ansible/roles/consumer/tasks/main.yml @@ -59,13 +59,11 @@ src: ../../../../sequence_search dest: /srv rsync_opts: - - "--exclude=/sequence_search/consumer/databases.iso" - "--exclude=/sequence_search/consumer/databases" - - "--exclude=/sequence_search/consumer/databases_back" - "--exclude=/sequence_search/consumer/queries/*.fasta" - "--exclude=/sequence_search/consumer/results/*.fasta" - "--exclude=/sequence_search/producer/static/node_modules" - tags: [ quick ] + tags: [ rsync, quick ] @@ -120,16 +118,6 @@ tags: [ results, quick ] - - - name: Umount volume for databases (so that chown doesn't complain) - mount: - path: /srv/sequence_search/consumer/databases - src: /dev/vdb - fstype: iso9660 - state: unmounted - ignore_errors: yes - tags: [ quick ] - # Ansible chown is slow, cause it checks ownership before assigning it - so just run chown imperatively # https://groups.google.com/forum/#!topic/ansible-project/2O5u8GIZ5Rw @@ -156,14 +144,12 @@ args: chdir: /srv/sequence_search - - name: Mount volume for databases - mount: - path: /srv/sequence_search/consumer/databases - src: /dev/vdb - fstype: iso9660 - state: mounted - tags: [ quick ] + - name: Create a symbolic link to sequence databases + file: + src: /nfs + dest: /srv/sequence_search/consumer/databases + state: link - name: Get running processes @@ -203,5 +189,5 @@ shell: chdir: /srv # cmd: /usr/local/bin/gunicorn consumer.main:app --daemon --bind 0.0.0.0:8000 --worker-class aiohttp.worker.GunicornWebWorker --access-logfile /var/log/gunicorn/access_log --error-logfile /var/log/gunicorn/error_log --env ENVIRONMENT=PRODUCTION --log-level=DEBUG - cmd: ENVIRONMENT=PRODUCTION nohup python36 -m sequence_search.consumer &> /var/log/gunicorn/access_log & + cmd: ENVIRONMENT=PRODUCTION nohup python3 -m sequence_search.consumer &> /var/log/gunicorn/access_log & tags: [ restart, quick ] diff --git a/ansible/roles/iptables/tasks/main.yml b/ansible/roles/iptables/tasks/main.yml new file mode 100644 index 00000000..fce4efa6 --- /dev/null +++ b/ansible/roles/iptables/tasks/main.yml @@ -0,0 +1,93 @@ +# file: iptables/tasks/main.yml + +--- + - name: Flush existing firewall rules + iptables: + flush: true + + - name: Allow related and established connections + iptables: + chain: INPUT + ctstate: ESTABLISHED,RELATED + jump: ACCEPT + + - name: Allow port ping traffic + iptables: + chain: INPUT + protocol: icmp + jump: ACCEPT + + - name: Allow port 22 / SSH traffic + iptables: + chain: INPUT + destination_port: 22 + protocol: tcp + jump: ACCEPT + + - name: Allow port 80 / HTTP traffic + iptables: + chain: INPUT + destination_port: 80 + jump: ACCEPT + protocol: tcp + + - name: Allow port 8000 / HTTP traffic + iptables: + chain: INPUT + destination_port: 8000 + jump: ACCEPT + protocol: tcp + + - name: Allow port 8002 / HTTP traffic + iptables: + chain: INPUT + destination_port: 8002 + jump: ACCEPT + protocol: tcp + + - name: Allow port 5432 / PostgreSQL + iptables: + chain: INPUT + destination_port: 5432 + jump: ACCEPT + protocol: tcp + + - name: Allow port 2049 (tcp) / NFS + iptables: + chain: INPUT + destination_port: 2049 + jump: ACCEPT + protocol: tcp + + - name: Allow port 2049 (udp) / NFS + iptables: + chain: INPUT + destination_port: 2049 + jump: ACCEPT + protocol: udp + + - name: Allow port 111 (tcp) / Portmapper + iptables: + chain: INPUT + destination_port: 111 + jump: ACCEPT + protocol: tcp + + - name: Allow port 111 (udp) / Portmapper + iptables: + chain: INPUT + destination_port: 111 + jump: ACCEPT + protocol: udp + + - name: Allow port 11211 (tcp) / Memcache + iptables: + chain: INPUT + destination_port: 11211 + jump: ACCEPT + protocol: tcp + + - name: Drop any traffic without rule + iptables: + chain: INPUT + jump: DROP diff --git a/ansible/roles/monitor/tasks/main.yml b/ansible/roles/monitor/tasks/main.yml new file mode 100644 index 00000000..db663d41 --- /dev/null +++ b/ansible/roles/monitor/tasks/main.yml @@ -0,0 +1,69 @@ +# file: monitor/tasks/main.yml + +--- + # This role is related to monitor installation + - name: Enable epel repository + yum_repository: + name: epel + baseurl: https://download.fedoraproject.org/pub/epel/$releasever/$basearch/ + enabled: yes + state: present + description: epel repostiory + gpgcheck: no + tags: [ install-deps ] + + - name: Upgrade all packages + yum: name=* state=latest + + - name: Install yum dependencies + yum: + name: + - epel-release + - jq + - memcached + tags: [ install-deps ] + + - name: Copy script + copy: src=../../../../sequence_search/monitor/monitor.sh dest=/home/centos owner=centos mode=0744 + tags: [ copy-script ] + + - name: Copy config + copy: src=../../../../sequence_search/monitor/.conf-file dest=/home/centos owner=centos mode=0744 + tags: [ copy-config ] + + - name: Insert the floating_ip + lineinfile: + path: /home/centos/.conf-file + line: "FLOATING_IP={{ floating_ip }}" + tags: [ copy-floating-ip ] + + - name: Add cronjob + cron: + name: "Check the Sequence Search service" + user: "centos" + minute: 0 + job: "sh /home/centos/monitor.sh" + tags: [ cronjob ] + + - name: Set Time Zone + timezone: + name: Europe/London + tags: [ timezone ] + + - name: Update memcached configuration + lineinfile: + dest: /etc/sysconfig/memcached + regexp: "{{item.regexp}}" + line: "{{item.line}}" + state: present + with_items: + - regexp: '^#?MAXCONN="1024"' + line: 'MAXCONN="2048"' + - regexp: '^#?CACHESIZE="64"' + line: 'CACHESIZE="1024"' + - regexp: '^#?OPTIONS=""' + line: 'OPTIONS="-l 192.168.0.8 -U 0 -vv >> /var/log/memcached 2>&1"' + + - name: Ensure Memcached is started and set to run on startup + service: name=memcached state=started enabled=yes + tags: [ memcached ] \ No newline at end of file diff --git a/ansible/roles/postgresql/tasks/backup.yml b/ansible/roles/postgresql/tasks/backup.yml new file mode 100644 index 00000000..e61e9bcb --- /dev/null +++ b/ansible/roles/postgresql/tasks/backup.yml @@ -0,0 +1,15 @@ +--- + # Added by cribas + - name: Copy the script to do backups + copy: src=../postgres/backup.sh dest=/etc/cron.hourly/backup.sh owner=postgres group=postgres mode=0755 + + - name: Create backup directory + file: + path: /backup + state: directory + owner: postgres + mode: '0777' + + - name: Set Time Zone + timezone: + name: Europe/London \ No newline at end of file diff --git a/ansible/roles/postgresql/tasks/install_yum.yml b/ansible/roles/postgresql/tasks/install_yum.yml index faacfa3a..c2a3fc03 100644 --- a/ansible/roles/postgresql/tasks/install_yum.yml +++ b/ansible/roles/postgresql/tasks/install_yum.yml @@ -4,6 +4,9 @@ # validate www.postgresql.org (or probably any other source). - block: + - name: Upgrade all packages + yum: name=* state=latest + - name: PostgreSQL | Install all the required dependencies | yum yum: name: ["ca-certificates","python-psycopg2", "python-pycurl", "glibc-common","epel-release","libselinux-python"] diff --git a/ansible/roles/postgresql/tasks/main.yml b/ansible/roles/postgresql/tasks/main.yml index 61efd684..fe5ad81c 100644 --- a/ansible/roles/postgresql/tasks/main.yml +++ b/ansible/roles/postgresql/tasks/main.yml @@ -39,3 +39,7 @@ - import_tasks: monit.yml when: monit_protection is defined and monit_protection == true tags: [postgresql, postgresql-monit] + +# Added by cribas +- import_tasks: backup.yml + tags: backup diff --git a/ansible/roles/producer/tasks/main.yml b/ansible/roles/producer/tasks/main.yml index d71bd172..74879234 100644 --- a/ansible/roles/producer/tasks/main.yml +++ b/ansible/roles/producer/tasks/main.yml @@ -45,23 +45,13 @@ src: ../../../../sequence_search dest: /srv rsync_opts: - - "--exclude=/sequence_search/consumer/databases.iso" - "--exclude=/sequence_search/consumer/databases" - - "--exclude=/sequence_search/consumer/databases_back" - "--exclude=/sequence_search/consumer/queries/*.fasta" - "--exclude=/sequence_search/consumer/results/*.fasta" - "--exclude=/sequence_search/producer/static/node_modules" - "--exclude=/sequence_search/producer/static/package-lock.json" tags: [ rsync, quick ] - - name: Umount volume for databases (so that chown doesn't complain) - mount: - path: /srv/sequence_search/consumer/databases - src: /dev/vdb - fstype: iso9660 - state: unmounted - ignore_errors: yes - tags: [ rsync, quick ] - name: Chown aiohttp code command: "chown -R centos:centos /srv/sequence_search" @@ -108,14 +98,11 @@ tags: [ logs ] - - name: Mount volume for databases - mount: - path: /srv/sequence_search/consumer/databases - src: /dev/vdb - fstype: iso9660 - state: mounted - tags: [ volume, volume-mount, quick ] - + - name: Create a symbolic link to sequence databases + file: + src: /nfs + dest: /srv/sequence_search/consumer/databases + state: link - name: Install node_modules @@ -142,7 +129,7 @@ - name: Drop the database and re-create it shell: chdir: /srv - cmd: ENVIRONMENT=PRODUCTION python36 -m sequence_search.db + cmd: ENVIRONMENT=PRODUCTION python3 -m sequence_search.db tags: [ never, migrate ] @@ -182,12 +169,12 @@ - name: Clean database shell: chdir: /srv - cmd: ENVIRONMENT=PRODUCTION python36 -m sequence_search.db + cmd: ENVIRONMENT=PRODUCTION python3 -m sequence_search.db tags: [ never, clean-db ] - name: Run producer service shell: chdir: /srv # cmd: /usr/local/bin/gunicorn producer.main:app --daemon --bind 0.0.0.0:8002 --worker-class aiohttp.worker.GunicornWebWorker --access-logfile /var/log/gunicorn/access_log --error-logfile /var/log/gunicorn/error_log --env ENVIRONMENT=PRODUCTION --log-level=DEBUG --timeout 120 - cmd: ENVIRONMENT=PRODUCTION nohup python36 -m sequence_search.producer &> /var/log/gunicorn/access_log & + cmd: ENVIRONMENT=PRODUCTION nohup python3 -m sequence_search.producer &> /var/log/gunicorn/access_log & tags: [ restart, quick ] diff --git a/ansible/roles/ssh/tasks/main.yml b/ansible/roles/ssh/tasks/main.yml new file mode 100644 index 00000000..c3c18dff --- /dev/null +++ b/ansible/roles/ssh/tasks/main.yml @@ -0,0 +1,20 @@ +# file: ssh/tasks/main.yml + +--- + - name: Harden sshd configuration + lineinfile: + dest: /etc/ssh/sshd_config + regexp: "{{item.regexp}}" + line: "{{item.line}}" + state: present + with_items: + - regexp: "^#?PermitRootLogin" + line: "PermitRootLogin no" + - regexp: "^#?PasswordAuthentication" + line: "PasswordAuthentication no" + + - name: Restart sshd + systemd: + state: restarted + daemon_reload: yes + name: sshd \ No newline at end of file diff --git a/ansible_load_balancer/load_balancer.yml b/ansible_load_balancer/load_balancer.yml index 6d1b29fa..502160ac 100644 --- a/ansible_load_balancer/load_balancer.yml +++ b/ansible_load_balancer/load_balancer.yml @@ -4,11 +4,14 @@ become: yes become_user: root gather_facts: True + vars: + main_ip: "{{ main_ip }}" + fallback_ip: "{{ fallback_ip }}" roles: - role: ansible-role-nginx nginx_sites: upstream: template: upstream.conf.j2 - nginx_backend_ip: "193.62.55.44" - nginx_fallback_backend_ip: "193.62.55.123" + nginx_backend_ip: "{{ main_ip }}" + nginx_fallback_backend_ip: "{{ fallback_ip }}" nginx_backend_port: "8002" diff --git a/ansible_load_balancer/roles/ansible-role-nginx/defaults/main.yml b/ansible_load_balancer/roles/ansible-role-nginx/defaults/main.yml index 3e0003f4..51447234 100644 --- a/ansible_load_balancer/roles/ansible-role-nginx/defaults/main.yml +++ b/ansible_load_balancer/roles/ansible-role-nginx/defaults/main.yml @@ -85,5 +85,5 @@ nginx_amplify_script_url: "https://github.com/nginxinc/nginx-amplify-agent/raw/m nginx_amplify_script_path: "/tmp/install-amplify-agent.sh" # added by burkov -nginx_backend_ip: "193.62.55.44" +nginx_backend_ip: "{{ main_ip }}" nginx_backend_port: "8002" diff --git a/postgres/backup.sh b/postgres/backup.sh new file mode 100755 index 00000000..7f894234 --- /dev/null +++ b/postgres/backup.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +TODAY=$(date +"%Y%m%d") +TIME=$(date +"%T") +REMOVE=$(date +"%Y%m%d_%H" -d "5 days ago") + +echo "Removing old files" +find /backup -name "producer_${REMOVE}*" -type f -exec rm -f {} \; + +echo "Starting a temporary backup" +pg_dump producer -U docker > /backup/producer_tmp.dump + +echo "Create a temporary database" +createdb -U docker -T template0 producer_tmp +psql -U docker producer_tmp -f /backup/producer_tmp.dump + +echo "Update the consumer column of the job_chunks table with null values" +psql -U docker producer_tmp -c 'update job_chunks set consumer = NULL;' + +echo "Backup the temporary database" +pg_dump -Fc producer_tmp -U docker -T 'consumer' > /backup/producer_${TODAY}_${TIME}.dump + +echo "Remove the temporary database" +dropdb -U docker producer_tmp +rm /backup/producer_tmp.dump \ No newline at end of file diff --git a/sequence_search/consumer/__main__.py b/sequence_search/consumer/__main__.py index 94bb3d77..4a4e12e7 100644 --- a/sequence_search/consumer/__main__.py +++ b/sequence_search/consumer/__main__.py @@ -20,7 +20,7 @@ from aiohttp import web, web_middlewares from . import settings -from ..db.models import init_pg +from ..db.models import close_pg, init_pg from ..db.consumers import register_consumer_in_the_database from ..db.settings import get_postgres_credentials from .urls import setup_routes @@ -59,13 +59,15 @@ def create_app(): app.update(name='consumer', settings=settings) # setup Jinja2 template renderer - aiohttp_jinja2.setup(app, loader=jinja2.PackageLoader('sequence_search', 'consumer', 'templates')) + aiohttp_jinja2.setup(app, loader=jinja2.FileSystemLoader(str(settings.PROJECT_ROOT / 'templates'))) - # create db connection on startup, shutdown on exit + # get credentials of the correct environment for key, value in get_postgres_credentials(settings.ENVIRONMENT)._asdict().items(): setattr(app['settings'], key, value) + # create db connection on startup, shutdown on exit app.on_startup.append(on_startup) + app.on_cleanup.append(close_pg) # setup views and routes setup_routes(app) diff --git a/sequence_search/consumer/results/.gitignore b/sequence_search/consumer/results/.gitignore index 5e7d2734..86d0cb27 100644 --- a/sequence_search/consumer/results/.gitignore +++ b/sequence_search/consumer/results/.gitignore @@ -1,4 +1,4 @@ # Ignore everything in this directory * # Except this file -!.gitignore +!.gitignore \ No newline at end of file diff --git a/sequence_search/consumer/rnacentral_databases.py b/sequence_search/consumer/rnacentral_databases.py index bd3f4ca8..84e63e9c 100644 --- a/sequence_search/consumer/rnacentral_databases.py +++ b/sequence_search/consumer/rnacentral_databases.py @@ -20,11 +20,28 @@ RnacentralDatabases = namedtuple("rnacentral_databases", ["id", "label"]) +# TODO: get the bds from elsewhere and not leave them hard coded rnacentral_databases = [ + RnacentralDatabases("dictybase", "dictyBase"), RnacentralDatabases("ena", "ENA"), + RnacentralDatabases("ensembl", "Ensembl"), + RnacentralDatabases("ensembl_fungi", "Ensembl Fungi"), + RnacentralDatabases("ensembl_metazoa", "Ensembl Metazoa"), + RnacentralDatabases("ensembl_plants", "Ensembl Plants"), + RnacentralDatabases("ensembl_protists", "Ensembl Protists"), + RnacentralDatabases("flybase", "FlyBase"), + RnacentralDatabases("gencode", "GENCODE"), RnacentralDatabases("greengenes", "GreenGenes"), + RnacentralDatabases("gtrnadb", "GtRNAdb"), + RnacentralDatabases("hgnc", "HGNC"), + RnacentralDatabases("lncbase", "LncBase"), + RnacentralDatabases("lncbook", "LncBook"), + RnacentralDatabases("lncipedia", "LNCipedia"), RnacentralDatabases("lncrnadb", "lncRNAdb"), + RnacentralDatabases("mgi", "MGI"), RnacentralDatabases("mirbase", "miRBase"), + RnacentralDatabases("modomics", "Modomics"), + RnacentralDatabases("noncode", "NONCODE"), RnacentralDatabases("pdbe", "PDBe"), RnacentralDatabases("pombase", "PomBase"), RnacentralDatabases("rdp", "RDP"), @@ -32,11 +49,14 @@ RnacentralDatabases("rfam", "Rfam"), RnacentralDatabases("rgd", "RGD"), RnacentralDatabases("sgd", "SGD"), + RnacentralDatabases("silva", "SILVA"), RnacentralDatabases("snopy", "snOPY"), RnacentralDatabases("srpdb", "SRPDB"), RnacentralDatabases("tair", "TAIR"), + RnacentralDatabases("tarbase", "TarBase"), RnacentralDatabases("tmrna_web", "tmRNA Website"), - RnacentralDatabases("wormbase", "WormBase") + RnacentralDatabases("wormbase", "WormBase"), + RnacentralDatabases("zwd", "ZWD") ] @@ -69,19 +89,18 @@ def producer_to_consumers_databases(databases): """ output = [] - # in case of empty databases list, return output - if databases == []: + if databases: + # new fasta files have been split into files up to 150 MB; + # therefore, we can now have more than one file for each database.  + for database in databases: + for file in get_database_files(): + if file.name.startswith(database): + output.append(file.name) + else: + # in case of empty databases list, use all-except-rrna and whitelist-rrna fasta files for file in get_database_files(): if file.name.startswith('all-except-rrna') or file.name.startswith('whitelist-rrna'): output.append(file.name) - else: - for database in databases: - if database == 'ena': # ena needs to be split into multiple files - for file in get_database_files(): - if file.name.startswith('ena'): # WARNING: this might be overzealous! - output.append(file.name) - else: - output.append(database + '.fasta') return output diff --git a/sequence_search/consumer/views/submit_job.py b/sequence_search/consumer/views/submit_job.py index d2947b2d..5b32bd35 100644 --- a/sequence_search/consumer/views/submit_job.py +++ b/sequence_search/consumer/views/submit_job.py @@ -14,6 +14,7 @@ import os import logging import asyncio +import datetime from aiohttp import web from aiojobs.aiohttp import spawn @@ -60,8 +61,12 @@ async def nhmmer(engine, job_id, sequence, database): process, filename = await nhmmer_search(sequence=sequence, job_id=job_id, database=database) try: + t0 = datetime.datetime.now() task = asyncio.ensure_future(process.communicate()) await asyncio.wait_for(task, MAX_RUN_TIME) + logging.debug("Time - Nhmmer searched for sequences in {} for {} seconds".format( + database, (datetime.datetime.now() - t0).total_seconds()) + ) return_code = process.returncode if return_code != 0: @@ -82,8 +87,12 @@ async def nhmmer(engine, job_id, sequence, database): try: # save results of the job_chunk to the database results = [record for record in nhmmer_parse(filename=filename)] # parse nhmmer results to python - await set_job_chunk_results(engine, job_id, database, results) - + if results: + t0 = datetime.datetime.now() + await set_job_chunk_results(engine, job_id, database, results) + logging.debug("Time - saving {} results in {} seconds".format( + len(results), (datetime.datetime.now() - t0).total_seconds()) + ) # set status of the job_chunk to the database await set_job_chunk_status(engine, job_id, database, status=JOB_CHUNK_STATUS_CHOICES.success) except (DatabaseConnectionError, SQLError) as e: diff --git a/sequence_search/db/job_chunk_results.py b/sequence_search/db/job_chunk_results.py index 82826a9f..667441d9 100644 --- a/sequence_search/db/job_chunk_results.py +++ b/sequence_search/db/job_chunk_results.py @@ -33,10 +33,12 @@ async def set_job_chunk_results(engine, job_id, database, results): break for result in results: - await connection.scalar(JobChunkResult.insert().values(job_chunk_id=job_chunk_id, **result)) + result['job_chunk_id'] = job_chunk_id + + await connection.execute(JobChunkResult.insert().values(results)) except Exception as e: raise SQLError("Failed to set_job_chunk_results in the database, " - "job_id = %s, database = %s" % (job_id, database)) from e + "job_id = %s, database = %s" % (job_id, database)) from e except psycopg2.Error as e: - raise DatabaseConnectionError("Failed to open connection to the database in " - "set_job_chunk_results, job_id = %s, database = %s" % (job_id, database)) from e + raise DatabaseConnectionError("Failed to open connection to the database in set_job_chunk_results, " + "job_id = %s, database = %s" % (job_id, database)) from e diff --git a/sequence_search/db/job_chunks.py b/sequence_search/db/job_chunks.py index 8b9ec41d..30021440 100644 --- a/sequence_search/db/job_chunks.py +++ b/sequence_search/db/job_chunks.py @@ -67,13 +67,12 @@ async def save_job_chunk(engine, job_id, database): JobChunk.insert().values( job_id=job_id, database=database, - status=JOB_CHUNK_STATUS_CHOICES.pending + status=JOB_CHUNK_STATUS_CHOICES.created ) ) return job_chunk_id except Exception as e: - raise SQLError("Failed to save job_chunk for " - "job_id = %s, database = %s" % (job_id, database)) from e + raise SQLError("Failed to save job_chunk for job_id = %s, database = %s" % (job_id, database)) from e except psycopg2.Error as e: raise DatabaseConnectionError("Failed to open database connection in save_job_chunk " "for job_id = %s, database = %s" % (job_id, database)) from e @@ -195,7 +194,7 @@ async def set_job_chunk_status(engine, job_id, database, status): return id except Exception as e: raise SQLError("Failed to set_job_chunk_status in the database," - " job_id = %s, database = %s" % (job_id, database)) from e + " job_id = %s, database = %s, status = %s" % (job_id, database, status)) from e except psycopg2.Error as e: raise DatabaseConnectionError("Failed to open connection to the database in " "set_job_chunk_status, job_id = %s, database = %s" % (job_id, database)) from e diff --git a/sequence_search/db/models.py b/sequence_search/db/models.py index 20a6e4c1..b43ece0a 100644 --- a/sequence_search/db/models.py +++ b/sequence_search/db/models.py @@ -36,6 +36,14 @@ async def init_pg(app): ) +# Graceful shutdown +# ----------------- + +async def close_pg(app): + app['engine'].close() + await app['engine'].wait_closed() + + # Models schema # ------------- @@ -48,6 +56,7 @@ class JOB_STATUS_CHOICES(object): class JOB_CHUNK_STATUS_CHOICES(object): + created = 'created' pending = 'pending' started = 'started' error = 'error' diff --git a/sequence_search/monitor/.conf-file-template b/sequence_search/monitor/.conf-file-template new file mode 100644 index 00000000..250f6928 --- /dev/null +++ b/sequence_search/monitor/.conf-file-template @@ -0,0 +1 @@ +WEBHOOK_URL="YOUR_WEBHOOK_URL" \ No newline at end of file diff --git a/sequence_search/monitor/monitor.sh b/sequence_search/monitor/monitor.sh new file mode 100755 index 00000000..d2c97948 --- /dev/null +++ b/sequence_search/monitor/monitor.sh @@ -0,0 +1,64 @@ +# Script to regularly run a specific search and check the results + +# -o allexport enables all following variable definitions to be exported. +# +o allexport disables this feature. +set -o allexport +source $PWD/.conf-file +set +o allexport + +CONTENT_TYPE="Content-Type: application/json" +DATABASE_AND_QUERY="{\"databases\": [\"mirbase\"], \"query\": \">sequence-search-test\nCUGUACUAUCUACUGUCUCUC\"}" + +# Run search on the correct target (test or default). +# Ansible adds the correct floating_ip to the .conf-file +HOST="http://$(echo $FLOATING_IP | sed 's/[][]//g'):8002" + +# First check if the $HOST is up +if curl -s --head --request GET $HOST | grep "200 OK" > /dev/null; then + # Submit a job + JOB_ID=$(curl -s -H "${CONTENT_TYPE}" -d "${DATABASE_AND_QUERY}" ${HOST}/api/submit-job | jq -r '.job_id') + + # Job status + STATUS=$(curl -s ${HOST}/api/job-status/$JOB_ID | jq -r '.chunks | .[] | .status') + + # Wait up to 30 minutes to finish + PAUSE="0" + if [ "$STATUS" == "started" ] || [ "$STATUS" == "pending" ] + then + while [ $PAUSE -lt 30 ] + do + sleep 60 + STATUS=$(curl -s ${HOST}/api/job-status/$JOB_ID | jq -r '.chunks | .[] | .status') + if [ "$STATUS" == "success" ] || [ "$STATUS" == "error" ] || [ "$STATUS" == "timeout" ] + then + break + fi + PAUSE=$[$PAUSE+1] + done + fi + + # Facets search + # Expected response: "hitCount = 23 and textSearchError = false" + FACETS_SEARCH=$(curl -s ${HOST}/api/facets-search/$JOB_ID | jq '[.hitCount,.textSearchError]') + HIT_COUNT=$(echo ${FACETS_SEARCH} | jq '.[0]') + SEARCH_ERROR=$(echo ${FACETS_SEARCH} | jq '.[1]') + + # Send message in case of unexpected result + if [ "$STATUS" != "success" ] || [ "$HIT_COUNT" != "23" ] || [ "$SEARCH_ERROR" != "false" ] + then + text="Ops! There is something wrong with the RNAcentral sequence search. Please check the links below: \n + \n + To check the status see: ${HOST}/api/job-status/$JOB_ID \n + The job status is ${STATUS} (the expected status is success). \n + \n + To check the results see: ${HOST}/api/facets-search/$JOB_ID \n + The job results are ${HIT_COUNT} and ${SEARCH_ERROR} (the expected results are 23 and false)." + escapedText=$(echo ${text} | sed 's/"/\"/g' | sed "s/'/\'/g" ) + json="{\"text\": \"$escapedText\"}" + curl -s -d "payload=$json" $WEBHOOK_URL + exit + fi +# No worries if it's not up, UptimeRobot will notify the team. +else + echo "${HOST} is DOWN!" +fi diff --git a/sequence_search/monitor/test_service.sh b/sequence_search/monitor/test_service.sh new file mode 100755 index 00000000..cb7a648f --- /dev/null +++ b/sequence_search/monitor/test_service.sh @@ -0,0 +1,71 @@ +# Script to do a lot of queries and check the service. This script will submit a job and check its status. +# To do 5 searches, run: ./test_service.sh 5 +# +# The output will look something like: +# 0: 9b1c63b6-fe6e-468f-90ac-0075a9933599 - successfully completed +# 1: 07f3e6f6-3be0-4b70-bd84-6f032353e346 - successfully completed +# 2: d9b18a2f-65fb-45be-90f8-d76af04525ad - successfully completed +# 3: 419e2783-43c3-4ccb-b282-40f4348329ce - successfully completed +# 4: ea23a5ef-17ca-44f3-80b6-76509af0c803 - successfully completed +# +# import HOST_TO_TEST +# -o allexport enables all following variable definitions to be exported. +# +o allexport disables this feature. +set -o allexport +source $PWD/.conf-file +set +o allexport + +CONTENT_TYPE="Content-Type: application/json" +TOTAL=$1 + +# First check if the $HOST_TO_TEST is up +if curl -s --head --request GET $HOST_TO_TEST | grep "200 OK" > /dev/null; then + # Create an array to store job ids + declare -a arr + + # Submit jobs + # Each job searches a different sequence with a different size + for ((i=1;i<=$TOTAL;i++)); do + SIZE=$(( $RANDOM % 80 + 20 )) + NEW_SEQUENCE=$(cat /dev/urandom | env LC_CTYPE=C tr -dc ACGTU | head -c $SIZE) + DATABASE_AND_QUERY_TEST="{\"databases\": [], \"query\": \"$NEW_SEQUENCE\"}" + JOB_ID=$(curl -s -H "${CONTENT_TYPE}" -d "${DATABASE_AND_QUERY_TEST}" ${HOST_TO_TEST}/api/submit-job | jq -r '.job_id') + arr=("${arr[@]}" $JOB_ID) + sleep 0.1 + done + + # Now loop through the above array and check the status of the job + for job in ${!arr[*]} + do + # Verify job status + STATUS=$(curl -s ${HOST_TO_TEST}/api/job-status/${arr[$job]} | jq -r '.status') + + if [ "$STATUS" == "success" ] + then + printf "%4d: %s - successfully completed\n" $job ${arr[$job]} + elif [ "$STATUS" == "started" ] || [ "$STATUS" == "pending" ] + then + # Wait some seconds + PAUSE="0" + while [ $PAUSE -lt 300 ] + do + sleep 10 + STATUS=$(curl -s ${HOST_TO_TEST}/api/job-status/${arr[$job]} | jq -r '.status') + if [ "$STATUS" == "success" ] + then + printf "%4d: %s - successfully completed\n" $job ${arr[$job]} + break + elif [ "$STATUS" == "error" ] || [ "$STATUS" == "timeout" ] + then + printf "%4d: %s - with error or timeout status\n" $job ${arr[$job]} + break + fi + PAUSE=$[$PAUSE+1] + done + else + printf "%4d: %s - with unexpected result\n" $job ${arr[$job]} + fi + done +else + echo "${HOST_TO_TEST} is DOWN!" +fi diff --git a/sequence_search/producer/__main__.py b/sequence_search/producer/__main__.py index ab32506f..6a5e68a9 100644 --- a/sequence_search/producer/__main__.py +++ b/sequence_search/producer/__main__.py @@ -22,7 +22,7 @@ from aiohttp import web, web_middlewares from . import settings -from ..db.models import init_pg, migrate +from ..db.models import close_pg, init_pg, migrate from ..db.job_chunks import find_highest_priority_job_chunks, get_job_chunk from ..db.jobs import get_job_query from ..db.consumers import delegate_job_chunk_to_consumer, find_available_consumers, find_busy_consumers, \ @@ -110,13 +110,13 @@ def create_app(): # setup Jinja2 template renderer; jinja2 contains various loaders, can also try PackageLoader etc. aiohttp_jinja2.setup(app, loader=jinja2.FileSystemLoader(str(settings.PROJECT_ROOT / 'static'))) - # create db connection on startup, shutdown on exit + # get credentials of the correct environment for key, value in get_postgres_credentials(settings.ENVIRONMENT)._asdict().items(): setattr(app['settings'], key, value) # create db connection on startup, shutdown on exit app.on_startup.append(on_startup) - # app.on_cleanup.append(close_pg) + app.on_cleanup.append(close_pg) # setup views and routes setup_routes(app) diff --git a/sequence_search/producer/cache/.gitignore b/sequence_search/producer/cache/.gitignore new file mode 100644 index 00000000..d6b7ef32 --- /dev/null +++ b/sequence_search/producer/cache/.gitignore @@ -0,0 +1,2 @@ +* +!.gitignore diff --git a/sequence_search/producer/tests/test_show_searches.py b/sequence_search/producer/tests/test_show_searches.py new file mode 100644 index 00000000..9093f64d --- /dev/null +++ b/sequence_search/producer/tests/test_show_searches.py @@ -0,0 +1,92 @@ +""" +Copyright [2009-2019] EMBL-European Bioinformatics Institute +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + http://www.apache.org/licenses/LICENSE-2.0 +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. +""" + +import datetime +import logging +import uuid + +from aiohttp.test_utils import unittest_run_loop + +from ..__main__ import create_app +from ...db.models import Job, JOB_STATUS_CHOICES +from aiohttp.test_utils import AioHTTPTestCase + + +""" +Run these tests with: + +ENVIRONMENT=TEST python3 -m unittest sequence_search.producer.tests.test_show_searches +""" + + +class ShowSearchesTestCase(AioHTTPTestCase): + async def get_application(self): + logging.basicConfig(level=logging.ERROR) # subdue messages like 'DEBUG:asyncio:Using selector: KqueueSelector' + app = create_app() + return app + + async def setUpAsync(self): + await super().setUpAsync() + + logging.info("settings = %s" % self.app['settings'].__dict__) + + self.job_id_01 = str(uuid.uuid4()) + self.job_id_02 = str(uuid.uuid4()) + self.job_id_03 = str(uuid.uuid4()) + + async with self.app['engine'].acquire() as connection: + await connection.execute( + Job.insert().values( + id=self.job_id_01, + query='', + submitted=datetime.datetime.now(), + status=JOB_STATUS_CHOICES.started + ) + ) + + await connection.execute( + Job.insert().values( + id=self.job_id_02, + query='', + submitted=datetime.datetime.now() - datetime.timedelta(days=2), + status=JOB_STATUS_CHOICES.started + ) + ) + + await connection.execute( + Job.insert().values( + id=self.job_id_03, + query='', + submitted=datetime.datetime.now() - datetime.timedelta(days=8), + status=JOB_STATUS_CHOICES.started + ) + ) + + async def tearDownAsync(self): + async with self.app['engine'].acquire() as connection: + await connection.execute('DELETE FROM jobs') + + await super().tearDownAsync() + + @unittest_run_loop + async def test_show_searches_success(self): + url = self.app.router["show-searches"].url_for() + async with self.client.get(path=url) as response: + assert response.status == 200 + data = await response.json() + + assert data == [ + {"count": 3, "avg_time": 0, "search": "all"}, + {"count": 1, "avg_time": 0, "search": "last-24-hours"}, + {"count": 2, "avg_time": 0, "search": "last-week"} + ] diff --git a/sequence_search/producer/text_search_client.py b/sequence_search/producer/text_search_client.py index 11561720..6210b5d9 100644 --- a/sequence_search/producer/text_search_client.py +++ b/sequence_search/producer/text_search_client.py @@ -10,10 +10,8 @@ See the License for the specific language governing permissions and limitations under the License. """ - -import os - import aiohttp +import socket from .settings import EBI_SEARCH_PROXY_URL, PROJECT_ROOT @@ -93,8 +91,16 @@ async def get_text_search_results(results, job_id, query, start, size, facetcoun except Exception as e: raise ProxyConnectionError() from e - # request facets from ebi text search - url = "http://wwwdev.ebi.ac.uk/ebisearch/ws/rest/rnacentral/seqtoolresults/" \ + # get the hostname of the machine to use the correct URL + hostname = socket.gethostname() + + if hostname == 'default-producer': + ebi_search_url = 'https://www.ebi.ac.uk/ebisearch/ws/rest/rnacentral/seqtoolresults/' + else: + ebi_search_url = 'https://wwwdev.ebi.ac.uk/ebisearch/ws/rest/rnacentral/seqtoolresults/' + + # request facets from ebi text search (dev or prod) + url = "{ebi_search_url}" \ "?toolid=nhmmer" \ "&jobid={job_id}" \ "&query={query}" \ @@ -103,11 +109,13 @@ async def get_text_search_results(results, job_id, query, start, size, facetcoun "&facetfields={facetfields}" \ "&start={start}" \ "&size={size}" \ - .format(job_id=job_id, query=query, fields=','.join(fields), facetcount=facetcount, - facetfields=','.join(facetfields), start=start, size=size) + .format(ebi_search_url=ebi_search_url, job_id=job_id, query=query, fields=','.join(fields), + facetcount=facetcount, facetfields=','.join(facetfields), start=start, size=size) try: - async with aiohttp.ClientSession(timeout=aiohttp.ClientTimeout(total=10)) as session: + # using default timeout. It means that the whole operation should finish in 5 minutes. + # large timeout prevents facet errors + async with aiohttp.ClientSession(timeout=aiohttp.ClientTimeout()) as session: async with session.get(url) as response: if response.status < 400: return await response.json() diff --git a/sequence_search/producer/urls.py b/sequence_search/producer/urls.py index 0b0e0532..69f41302 100644 --- a/sequence_search/producer/urls.py +++ b/sequence_search/producer/urls.py @@ -13,7 +13,7 @@ from aiohttp_swagger import setup_swagger from .views import index, submit_job, job_status, job_result, rnacentral_databases, job_results_urs_list, \ - facets, facets_search, list_rnacentral_ids, post_rnacentral_ids, consumers_statuses, jobs_statuses + facets, facets_search, list_rnacentral_ids, post_rnacentral_ids, consumers_statuses, jobs_statuses, show_searches from . import settings @@ -29,6 +29,7 @@ def setup_routes(app): app.router.add_get('/api/list-rnacentral-ids/{job_id:[A-Za-z0-9_-]+}', list_rnacentral_ids, name='list-rnacentral-ids') app.router.add_post('/api/post-rnacentral-ids/{job_id:[A-Za-z0-9_-]+}', post_rnacentral_ids, name='post-rnacentral-ids') app.router.add_get('/api/consumers-statuses', consumers_statuses, name='consumers-statuses') + app.router.add_get('/api/show-searches', show_searches, name='show-searches') setup_static_routes(app) # setup swagger documentation diff --git a/sequence_search/producer/views/__init__.py b/sequence_search/producer/views/__init__.py index fb5da706..3b5879e7 100644 --- a/sequence_search/producer/views/__init__.py +++ b/sequence_search/producer/views/__init__.py @@ -24,3 +24,4 @@ from .list_rnacentral_ids import list_rnacentral_ids from .post_rnacentral_ids import post_rnacentral_ids from .consumers_statuses import consumers_statuses +from .show_searches import show_searches diff --git a/sequence_search/producer/views/facets_search.py b/sequence_search/producer/views/facets_search.py index baa404c9..e4c064d4 100644 --- a/sequence_search/producer/views/facets_search.py +++ b/sequence_search/producer/views/facets_search.py @@ -12,9 +12,12 @@ """ import logging +import hashlib from aiohttp import web from aiojobs.aiohttp import atomic +from ast import literal_eval +from pymemcache.client import base from ...db.jobs import get_job_results, get_job, job_exists, set_job_ordering from ..text_search_client import get_text_search_results, ProxyConnectionError, EBITextSearchConnectionError, \ @@ -300,13 +303,38 @@ async def facets_search(request): # try to get facets from EBI text search, otherwise stub facets try: ENVIRONMENT = request.app['settings'].ENVIRONMENT - text_search_data = await get_text_search_results(results, job_id, query, start, size, facetcount, ENVIRONMENT) + + # we want to cache the EBI Search result + if ENVIRONMENT == 'PRODUCTION': + client = base.Client(('192.168.0.8', 11211)) + else: + client = base.Client(('localhost', 11211)) + + # create a hash with query parameters + text_search_key = hashlib.md5( + (job_id + query + str(start) + str(size) + str(facetcount) + ordering).encode('utf-8') + ).hexdigest() + + # check if the result is cached + cached_result = client.get(text_search_key) + + if cached_result: + text_search_data = literal_eval(cached_result.decode('utf8')) + logging.debug("Using cache. This is the key used: {}".format(text_search_key)) + else: + text_search_data = await get_text_search_results( + results, job_id, query, start, size, facetcount, ENVIRONMENT + ) + # cache the result + client.set(text_search_key, text_search_data) # if this worked, inject text search results into facets json for entry in text_search_data['entries']: for result in results: if result['rnacentral_id'] == entry['id']: + result['description'] = entry['fields']['description'][0] entry.update(result) + break # sort facets in the same order as in text_search_client text_search_data['facets'].sort(key=lambda el: facetfields.index(el['id'])) @@ -343,4 +371,3 @@ async def facets_search(request): text_search_data['entries'].append(result) return web.json_response(text_search_data) - diff --git a/sequence_search/producer/views/show_searches.py b/sequence_search/producer/views/show_searches.py new file mode 100644 index 00000000..e90e0ea8 --- /dev/null +++ b/sequence_search/producer/views/show_searches.py @@ -0,0 +1,54 @@ +""" +Copyright [2009-2019] EMBL-European Bioinformatics Institute +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + http://www.apache.org/licenses/LICENSE-2.0 +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. +""" +import datetime +from aiohttp import web + + +def convert_average_time(records): + result = [] + for row in records: + item = dict(row.items()) + item['avg_time'] = str(datetime.timedelta(seconds=int(item['avg_time'].seconds))) if item['avg_time'] else 0 + result.append(item) + return result + + +async def show_searches(request): + async with request.app['engine'].acquire() as conn: + all_searches = await conn.execute( + "SELECT count(*), avg(finished - submitted) as avg_time FROM jobs " + "WHERE description !='sequence-search-test' OR description IS NULL" + ) + all_searches_records = await all_searches.fetchall() + all_searches_result = convert_average_time(all_searches_records) + all_searches_result[0].update({'search': 'all'}) + + last_24_hours = await conn.execute( + "SELECT count(*), avg(finished - submitted) as avg_time FROM jobs " + "WHERE (description !='sequence-search-test' OR description IS NULL) AND submitted > %s", + datetime.datetime.now() - datetime.timedelta(days=1) + ) + last_24_hours_records = await last_24_hours.fetchall() + last_24_hours_result = convert_average_time(last_24_hours_records) + last_24_hours_result[0].update({'search': 'last-24-hours'}) + + last_week = await conn.execute( + "SELECT count(*), avg(finished - submitted) as avg_time FROM jobs " + "WHERE (description !='sequence-search-test' OR description IS NULL) AND submitted > %s", + datetime.datetime.now() - datetime.timedelta(days=7) + ) + last_week_records = await last_week.fetchall() + last_week_result = convert_average_time(last_week_records) + last_week_result[0].update({'search': 'last-week'}) + + return web.json_response(all_searches_result + last_24_hours_result + last_week_result) diff --git a/sequence_search/producer/views/submit_job.py b/sequence_search/producer/views/submit_job.py index 64f1af39..7e3028cf 100644 --- a/sequence_search/producer/views/submit_job.py +++ b/sequence_search/producer/views/submit_job.py @@ -16,9 +16,10 @@ from aiohttp import web from aiojobs.aiohttp import atomic +from sequence_search.db.models import JOB_CHUNK_STATUS_CHOICES from ...db.consumers import delegate_job_chunk_to_consumer, find_available_consumers from ...db.jobs import save_job -from ...db.job_chunks import save_job_chunk +from ...db.job_chunks import save_job_chunk, set_job_chunk_status from ...consumer.rnacentral_databases import producer_validator, producer_to_consumers_databases @@ -95,6 +96,10 @@ async def submit_job(request): """ data = await request.json() + # leave databases name in lowercase. + if data['databases']: + data['databases'] = [db.lower() for db in data['databases']] + try: data = serialize(request, data) except (KeyError, TypeError, ValueError) as e: @@ -105,11 +110,15 @@ async def submit_job(request): databases = producer_to_consumers_databases(data['databases']) for database in databases: - job_chunk_id = await save_job_chunk(request.app['engine'], job_id, database) + # save job_chunk with "created" status. This prevents the check_chunks_and_consumers function, + # which runs every 5 seconds, from executing the same job_chunk again. + await save_job_chunk(request.app['engine'], job_id, database) # TODO: what if Job was saved and JobChunk was not? Need transactions? consumers = await find_available_consumers(request.app['engine']) + + # if there are consumers available, delegate job_chunk to consumer for index in range(min(len(consumers), len(databases))): try: await delegate_job_chunk_to_consumer( @@ -123,4 +132,16 @@ async def submit_job(request): except Exception as e: return web.HTTPBadGateway(text=str(e)) + # change job_chunk status to pending if no consumer is available + for index in range(len(consumers), len(databases)): + try: + await set_job_chunk_status( + request.app['engine'], + job_id, + databases[index], + status=JOB_CHUNK_STATUS_CHOICES.pending + ) + except Exception as e: + return web.HTTPBadGateway(text=str(e)) + return web.json_response({"job_id": job_id}, status=201) diff --git a/sequence_search/requirements.txt b/sequence_search/requirements.txt index eec461af..8186b65b 100644 --- a/sequence_search/requirements.txt +++ b/sequence_search/requirements.txt @@ -13,3 +13,4 @@ requests==2.22.0 netifaces==0.10.9 gunicorn==19.9.0 glance==18.0.0 +pymemcache==2.2.2 \ No newline at end of file diff --git a/terraform/hosts.py b/terraform/hosts.py new file mode 100755 index 00000000..2986ad8f --- /dev/null +++ b/terraform/hosts.py @@ -0,0 +1,42 @@ +# terraform-inventory (v0.9) is not working well with terraform (v0.12.6). +# This script creates the hosts file used by ansible. +# First run "terraform show -json > current_state" +import json + + +with open('current_state') as json_file: + data = json.load(json_file) + file = open('../ansible/hosts', 'w') + + file.write('[associate_postgres_floating_ip]\n') + file.write([obj for obj in data['values']['root_module']['resources'] if obj['address'] == 'openstack_compute_floatingip_associate_v2.nfs_server_floating_ip'][0]['values']['floating_ip'] + '\n') + file.write('\n') + + file.write('[nfs_server]\n') + file.write([obj for obj in data['values']['root_module']['resources'] if + obj['address'] == 'openstack_compute_instance_v2.nfs_server'][0]['values']['access_ip_v4'] + '\n') + file.write('\n') + + file.write('[postgres]\n') + file.write([obj for obj in data['values']['root_module']['resources'] if obj['address'] == 'openstack_compute_instance_v2.postgres'][0]['values']['access_ip_v4'] + '\n') + file.write('\n') + + file.write('[sequence_search]\n') + file.write([obj for obj in data['values']['root_module']['resources'] if obj['address'] == 'openstack_compute_floatingip_associate_v2.sequence_search'][0]['values']['floating_ip'] + '\n') + file.write('\n') + + file.write('[producer]\n') + file.write([obj for obj in data['values']['root_module']['resources'] if obj['address'] == 'openstack_compute_instance_v2.producer'][0]['values']['access_ip_v4'] + '\n') + file.write('\n') + + file.write('[monitor]\n') + file.write([obj for obj in data['values']['root_module']['resources'] if + obj['address'] == 'openstack_compute_instance_v2.monitor'][0]['values']['access_ip_v4'] + '\n') + file.write('\n') + + file.write('[consumers]\n') + for obj in data['values']['root_module']['resources']: + if obj['address'] == 'openstack_compute_instance_v2.consumers': + file.write(obj['values']['access_ip_v4'] + '\n') + +# print(json.dumps(output, indent=4)) diff --git a/terraform/main.tf b/terraform/main.tf index 4af64dbe..538b0f1b 100644 --- a/terraform/main.tf +++ b/terraform/main.tf @@ -13,8 +13,8 @@ output "tfstate_file" { value = ["${local.tfstate_file}"] } -resource "null_resource" "pre-flight" { - triggers { +resource "null_resource" "pre_flight" { + triggers = { build_number = "${timestamp()}" } provisioner "local-exec" { @@ -53,7 +53,7 @@ resource "openstack_networking_router_interface_v2" "sequence_search" { resource "openstack_compute_secgroup_v2" "sequence_search" { name = "${terraform.workspace}_sequence_search" - description = "Security group for the sequence_search instances" + description = "Security group for the sequence_search instances (except NFS and monitor)" rule { from_port = 22 to_port = 22 @@ -62,17 +62,17 @@ resource "openstack_compute_secgroup_v2" "sequence_search" { } rule { - from_port = 80 - to_port = 80 + from_port = 5432 + to_port = 5432 ip_protocol = "tcp" - cidr = "0.0.0.0/0" + cidr = "192.168.0.0/24" } rule { from_port = 8000 to_port = 8000 ip_protocol = "tcp" - cidr = "0.0.0.0/0" + cidr = "192.168.0.0/24" } rule { @@ -83,12 +83,76 @@ resource "openstack_compute_secgroup_v2" "sequence_search" { } rule { - from_port = 5432 - to_port = 5432 + from_port = -1 + to_port = -1 + ip_protocol = "icmp" + cidr = "0.0.0.0/0" + } +} + +resource "openstack_compute_secgroup_v2" "sequence_search_nfs_instance" { + name = "${terraform.workspace}_sequence_search_nfs_instance" + description = "Security group for the NFS instance" + rule { + from_port = 22 + to_port = 22 ip_protocol = "tcp" cidr = "0.0.0.0/0" } + rule { + from_port = 2049 + to_port = 2049 + ip_protocol = "tcp" + cidr = "192.168.0.0/24" + } + + rule { + from_port = 2049 + to_port = 2049 + ip_protocol = "udp" + cidr = "192.168.0.0/24" + } + + rule { + from_port = 111 + to_port = 111 + ip_protocol = "tcp" + cidr = "192.168.0.0/24" + } + + rule { + from_port = 111 + to_port = 111 + ip_protocol = "udp" + cidr = "192.168.0.0/24" + } + + rule { + from_port = -1 + to_port = -1 + ip_protocol = "icmp" + cidr = "0.0.0.0/0" + } +} + +resource "openstack_compute_secgroup_v2" "sequence_search_monitor_instance" { + name = "${terraform.workspace}_sequence_search_monitor_instance" + description = "Security group for the monitor instance" + rule { + from_port = 22 + to_port = 22 + ip_protocol = "tcp" + cidr = "0.0.0.0/0" + } + + rule { + from_port = 11211 + to_port = 11211 + ip_protocol = "tcp" + cidr = "192.168.0.0/24" + } + rule { from_port = -1 to_port = -1 @@ -98,7 +162,7 @@ resource "openstack_compute_secgroup_v2" "sequence_search" { } resource "openstack_compute_instance_v2" "producer" { - depends_on = ["openstack_compute_keypair_v2.sequence_search"] + depends_on = ["openstack_compute_keypair_v2.sequence_search", "openstack_networking_subnet_v2.sequence_search"] name = "${terraform.workspace}-producer" image_name = "${var.image}" flavor_name = "${var.flavor}" @@ -111,7 +175,7 @@ resource "openstack_compute_instance_v2" "producer" { } resource "openstack_compute_instance_v2" "postgres" { - depends_on = ["openstack_compute_keypair_v2.sequence_search"] + depends_on = ["openstack_compute_keypair_v2.sequence_search", "openstack_networking_subnet_v2.sequence_search"] name = "${terraform.workspace}-postgres" image_name = "${var.image}" flavor_name = "${var.flavor}" @@ -121,12 +185,37 @@ resource "openstack_compute_instance_v2" "postgres" { uuid = "${openstack_networking_network_v2.sequence_search.id}" fixed_ip_v4 = "192.168.0.6" } +} + +resource "openstack_compute_instance_v2" "nfs_server" { + depends_on = ["openstack_compute_keypair_v2.sequence_search", "openstack_networking_subnet_v2.sequence_search"] + name = "${terraform.workspace}-nfs-server" + image_name = "ubuntu-16.04" + flavor_name = "${var.flavor}" + key_pair = "${openstack_compute_keypair_v2.sequence_search.name}" + security_groups = [ "${openstack_compute_secgroup_v2.sequence_search_nfs_instance.name}" ] + network { + uuid = "${openstack_networking_network_v2.sequence_search.id}" + fixed_ip_v4 = "192.168.0.7" + } +} +resource "openstack_compute_instance_v2" "monitor" { + depends_on = ["openstack_compute_keypair_v2.sequence_search", "openstack_networking_subnet_v2.sequence_search"] + name = "${terraform.workspace}-monitor" + image_name = "${var.image}" + flavor_name = "${var.flavor_monitor}" + key_pair = "${openstack_compute_keypair_v2.sequence_search.name}" + security_groups = [ "${openstack_compute_secgroup_v2.sequence_search_monitor_instance.name}" ] + network { + uuid = "${openstack_networking_network_v2.sequence_search.id}" + fixed_ip_v4 = "192.168.0.8" + } } resource "openstack_compute_instance_v2" "consumers" { count = "${local.count}" - depends_on = ["openstack_compute_keypair_v2.sequence_search"] + depends_on = ["openstack_compute_keypair_v2.sequence_search", "openstack_networking_subnet_v2.sequence_search"] name = "${terraform.workspace}-consumer-${count.index + 1}" image_name = "${var.image}" flavor_name = "${var.flavor}" @@ -134,32 +223,18 @@ resource "openstack_compute_instance_v2" "consumers" { security_groups = [ "${openstack_compute_secgroup_v2.sequence_search.name}" ] network { uuid = "${openstack_networking_network_v2.sequence_search.id}" - fixed_ip_v4 = "192.168.0.${count.index + 7}" + fixed_ip_v4 = "192.168.0.${count.index + 9}" } } -resource "openstack_blockstorage_volume_v2" "sequence_search_consumer_databases" { - count = "${local.count}" - size = 12 - name = "${terraform.workspace}-sequence-search-consumer-databases-${count.index + 1}" - image_id = "sequence_search_databases" -} - -resource "openstack_compute_volume_attach_v2" "attach_databases_to_consumers" { - count = "${local.count}" - instance_id = "${openstack_compute_instance_v2.consumers.*.id[count.index]}" - volume_id = "${openstack_blockstorage_volume_v2.sequence_search_consumer_databases.*.id[count.index]}" -} - -resource "openstack_blockstorage_volume_v2" "sequence_search_producer_databases" { - size = 12 - name = "${terraform.workspace}-sequence-search-producer-databases" - image_id = "sequence_search_databases" +resource "openstack_blockstorage_volume_v2" "nfs_volume" { + name = "${terraform.workspace}-nfs-volume" + size = 100 } -resource "openstack_compute_volume_attach_v2" "attach_databases_to_producer" { - instance_id = "${openstack_compute_instance_v2.producer.id}" - volume_id = "${openstack_blockstorage_volume_v2.sequence_search_producer_databases.id}" +resource "openstack_compute_volume_attach_v2" "attached" { + instance_id = "${openstack_compute_instance_v2.nfs_server.id}" + volume_id = "${openstack_blockstorage_volume_v2.nfs_volume.id}" } resource "openstack_compute_floatingip_associate_v2" "sequence_search" { @@ -168,17 +243,23 @@ resource "openstack_compute_floatingip_associate_v2" "sequence_search" { instance_id = "${openstack_compute_instance_v2.producer.id}" } -resource "openstack_compute_floatingip_associate_v2" "associate_postgres_floating_ip" { - depends_on = ["openstack_compute_instance_v2.postgres", "openstack_networking_router_interface_v2.sequence_search"] +resource "openstack_compute_floatingip_associate_v2" "nfs_server_floating_ip" { + depends_on = ["openstack_compute_instance_v2.nfs_server", "openstack_networking_router_interface_v2.sequence_search"] floating_ip = "${local.postgres_floating_ip}" - instance_id = "${openstack_compute_instance_v2.postgres.id}" + instance_id = "${openstack_compute_instance_v2.nfs_server.id}" } -resource "null_resource" "post-flight" { - triggers { - build_number = "${timestamp()}" - } - provisioner "local-exec" { - command = "terraform-inventory -inventory ${local.tfstate_file} > ../ansible/hosts" - } -} +# resource "openstack_compute_floatingip_associate_v2" "associate_postgres_floating_ip" { +# depends_on = ["openstack_compute_instance_v2.postgres", "openstack_networking_router_interface_v2.sequence_search"] +# floating_ip = "${local.postgres_floating_ip}" +# instance_id = "${openstack_compute_instance_v2.postgres.id}" +# } + +# resource "null_resource" "post_flight" { +# triggers = { +# before = "${null_resource.pre_flight.id}" +# } +# provisioner "local-exec" { +# command = "terraform-inventory -inventory ${local.tfstate_file} > ../ansible/hosts" +# } +# } diff --git a/terraform/providers.tf.template b/terraform/providers.tf.template index 4ae3732b..b98ebb7f 100644 --- a/terraform/providers.tf.template +++ b/terraform/providers.tf.template @@ -5,4 +5,9 @@ provider "openstack" { password = "" auth_url = "https://extcloud05.ebi.ac.uk:13000/v2.0" region = "regionOne" + version = "~> 1.21.1" +} + +provider "null" { + version = "~> 2.1" } diff --git a/terraform/terraform.tfstate b/terraform/terraform.tfstate index 6e6db6f0..54d6992d 100644 --- a/terraform/terraform.tfstate +++ b/terraform/terraform.tfstate @@ -1,2205 +1,2382 @@ { - "version": 3, - "terraform_version": "0.11.13", - "serial": 28, - "lineage": "b3e8e88c-53d9-e061-7720-e7f72e33bfaf", - "modules": [ + "version": 4, + "terraform_version": "0.12.6", + "serial": 1898, + "lineage": "b3e8e88c-53d9-e061-7720-e7f72e33bfaf", + "outputs": { + "floating_ip": { + "value": [ + "193.62.55.44" + ], + "type": [ + "tuple", + [ + "string" + ] + ] + }, + "tfstate_file": { + "value": [ + "terraform.tfstate" + ], + "type": [ + "tuple", + [ + "string" + ] + ] + } + }, + "resources": [ + { + "mode": "managed", + "type": "null_resource", + "name": "pre_flight", + "provider": "provider.null", + "instances": [ { - "path": [ - "root" - ], - "outputs": { - "floating_ip": { - "sensitive": false, - "type": "list", - "value": [ - "193.62.55.44" - ] - }, - "tfstate_file": { - "sensitive": false, - "type": "list", - "value": [ - 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"delete": 600000000000 - } - }, - "tainted": false - }, - "deposed": [], - "provider": "provider.openstack" - } - }, - "depends_on": [] + "enable_dhcp": true, + "gateway_ip": "192.168.0.1", + "host_routes": [], + "id": "07529431-2c9b-489a-b718-a1620a79f161", + "ip_version": 4, + "ipv6_address_mode": "", + "ipv6_ra_mode": "", + "name": "test_sequence_search", + "network_id": "d57738f6-c3f9-4cb6-b732-70b6a0a42e0f", + "no_gateway": false, + "prefix_length": null, + "region": "regionOne", + "subnetpool_id": "", + "tags": null, + "tenant_id": "bd631be0b7e641a7bd0c187493e7104e", + "timeouts": null, + "value_specs": null + }, + "private": "eyJlMmJmYjczMC1lY2FhLTExZTYtOGY4OC0zNDM2M2JjN2M0YzAiOnsiY3JlYXRlIjo2MDAwMDAwMDAwMDAsImRlbGV0ZSI6NjAwMDAwMDAwMDAwfX0=", + "depends_on": [ + "openstack_networking_network_v2.sequence_search" + ] } - ] + ] + } + ] } diff --git a/terraform/variables.tf b/terraform/variables.tf index 68f52e99..2afcdd90 100644 --- a/terraform/variables.tf +++ b/terraform/variables.tf @@ -3,7 +3,11 @@ variable "image" { } variable "flavor" { - default = "s1.jumbo" + default = "s1.capacious" +} + +variable "flavor_monitor" { + default = "s1.small" } variable "ssh_key_file" { @@ -35,11 +39,11 @@ variable "test_postgres_floating_ip" { } variable "default_instances" { - default = 15 + default = 30 } variable "test_instances" { - default = 5 + default = 10 } variable "default_tfstate" {