[LAB-577] Plex upgrade to 0.10.0 (#626)

Author: alabdao

infrastructure/ansible/files/colabfold_mini_canary.sh

@@ -3,10 +3,25 @@
 # exit the whole script if any command returns a non-zero exit code
 set -e
 
+# IFPS Custom setup
+export IPFS_PATH=$(mktemp -d)
+export BACALHAU_SERVE_IPFS_PATH=${IPFS_PATH}
+export LOGFILE={{ repo_dir }}/plex_colabfold_out.log
+
+# Ensure there is no port conflict with other canaries
+ipfs init -e
+ipfs bootstrap rm --all
+ipfs config Addresses.API /ip4/127.0.0.1/tcp/8001
+ipfs config Addresses.Gateway /ip4/127.0.0.1/tcp/8002
+ipfs config Addresses.Swarm --json '["/ip4/0.0.0.0/tcp/8000"]'
+export BACALHAU_IPFS_SWARM_ADDRESSES="/dns4/bacalhau.labdao.xyz/tcp/4001/p2p/$(curl -s -X POST bacalhau.labdao.xyz:5001/api/v0/id | jq -r '.ID')"
+
 # plex must run from the same place as tools directory
 cd {{ repo_dir }}
+touch ${LOGFILE}
+echo "$(date) - Running Canary" | tee -a ${LOGFILE}
 
-plex init -t {{ repo_dir }}/tools/colabfold-mini.json -i '{"sequence": ["{{ repo_dir }}/testdata/folding/test.fasta"]}' --scatteringMethod=dotProduct --autoRun=true -a test -a cron | tee plex_colabfold_out.log
+plex init -t {{ repo_dir }}/tools/colabfold-mini.json -i '{"sequence": ["{{ repo_dir }}/testdata/folding/test.fasta"]}' --scatteringMethod=dotProduct --autoRun=true -a test -a cron | tee -a ${LOGFILE}
 # capture the exit status of the plex call
 plex_result_code=${PIPESTATUS[0]}
 # exit immediately if plex exited with an error
@@ -15,7 +30,7 @@ if [ $plex_result_code -gt 0 ]; then
 fi
 
 # parse the output directory from the plex stdout
-result_dir=$(cat plex_colabfold_out.log | grep 'Finished processing, results written to' | sed -n 's/^.*Finished processing, results written to //p' | sed 's/\/io.json//')
+result_dir=$(cat ${LOGFILE} | grep -a 'Finished processing, results written to' | sed -n 's/^.*Finished processing, results written to //p' | sed 's/\/io.json//' | tail -n 1)
 
 # exit if no docked files are found
 cd "$result_dir/entry-0/outputs"
@@ -30,4 +45,6 @@ rm -rf $result_dir
 
 curl -X POST -H "Authorization: Bearer ${HEII_ON_CALL_API_KEY}" https://api.heiioncall.com./triggers/991a6388-5c61-422c-b8cf-202b4c4b55a6/checkin
 
-echo "Colabfold mini canary success"
+echo "$(date) - Colabfold mini canary success" | tee -a ${LOGFILE}
+
+rm -rf ${IPFS_PATH}

infrastructure/ansible/files/equibind_canary.sh

@@ -3,10 +3,26 @@
 # exit the whole script if any command returns a non-zero exit code
 set -e
 
+# IFPS Custom setup
+export IPFS_PATH=$(mktemp -d)
+export BACALHAU_SERVE_IPFS_PATH=${IPFS_PATH}
+export LOGFILE={{ repo_dir }}/plex_equibind_out.log
+
+# Ensure there is no port conflict with other canaries
+ipfs init -e
+ipfs bootstrap rm --all
+ipfs config Addresses.API /ip4/127.0.0.1/tcp/7001
+ipfs config Addresses.Gateway /ip4/127.0.0.1/tcp/7002
+ipfs config Addresses.Swarm --json '["/ip4/0.0.0.0/tcp/7000"]'
+export BACALHAU_IPFS_SWARM_ADDRESSES="/dns4/bacalhau.labdao.xyz/tcp/4001/p2p/$(curl -s -X POST bacalhau.labdao.xyz:5001/api/v0/id | jq -r '.ID')"
+
 # plex must run from the same place as tools directory
 cd {{ repo_dir }}
 
-plex init -t {{ repo_dir }}/tools/equibind.json -i '{"protein": ["{{ repo_dir }}/testdata/binding/abl/7n9g.pdb"], "small_molecule": ["{{ repo_dir }}/testdata/binding/abl/ZINC000003986735.sdf"]}' --scatteringMethod=dotProduct -a test -a cron --autoRun=true 2>&1 | tee plex_equibind_out.log
+touch ${LOGFILE}
+echo "$(date) - Running Canary" | tee -a ${LOGFILE}
+
+plex init -t {{ repo_dir }}/tools/equibind.json -i '{"protein": ["{{ repo_dir }}/testdata/binding/abl/7n9g.pdb"], "small_molecule": ["{{ repo_dir }}/testdata/binding/abl/ZINC000003986735.sdf"]}' --scatteringMethod=dotProduct -a test -a cron --autoRun=true 2>&1 | tee -a ${LOGFILE}
 # capture the exit status of the plex call
 plex_result_code=${PIPESTATUS[0]}
 # exit immediately if plex exited with an error
@@ -15,7 +31,7 @@ if [ $plex_result_code -gt 0 ]; then
 fi
 
 # parse the output directory from the plex stdout
-result_dir=$(cat plex_equibind_out.log | grep 'Finished processing, results written to' | sed -n 's/^.*Finished processing, results written to //p' | sed 's/\/io.json//')
+result_dir=$(cat ${LOGFILE} | grep -a 'Finished processing, results written to' | sed -n 's/^.*Finished processing, results written to //p' | sed 's/\/io.json//' | tail -n 1)
 
 # exit if no docked files are found
 cd "$result_dir/entry-0/outputs"
@@ -30,4 +46,6 @@ rm -rf $result_dir
 
 curl -X POST -H "Authorization: Bearer ${HEII_ON_CALL_API_KEY}" https://api.heiioncall.com./triggers/a7660c2f-5262-4392-918b-d98aee244890/checkin
 
-echo "Canary success"
+echo "$(date) - Canary success" | tee -a ${LOGFILE}
+
+rm -rf ${IPFS_PATH}

infrastructure/ansible/provision_canary.yaml

@@ -6,6 +6,12 @@
     repo_dir: "{{ canary_dir }}/repo"
     binary_dir: "{{ canary_dir }}/binary"
   tasks:
+    # Must provide limit flag to ensure running against current environment
+    - fail:
+        msg: "you must use -l or --limit"
+      when: ansible_limit is not defined
+      run_once: true
+
     - name: Run common tasks
       ansible.builtin.include_tasks: tasks/common_tasks.yaml
 

infrastructure/ansible/tasks/common_tasks.yaml

@@ -1,7 +1,9 @@
 - name: "Gather service facts"
+  become: true
   ansible.builtin.service_facts:
 
 - name: "Disable unattended upgrades service"
+  become: true
   ansible.builtin.systemd:
     name: "unattended-upgrades.service"
     enabled: false
@@ -31,4 +33,6 @@
   become: true
   ansible.builtin.pip:
     name:
+      - pip
       - boto3
+      - pyopenssl

infrastructure/ansible/tasks/install_plex_tasks.yaml

@@ -3,10 +3,13 @@
   become: true
   ansible.builtin.pip:
     name:
-      - pip
-      - pyopenssl
       - github3.py
 
+- name: Print plex_version if provided
+  ansible.builtin.debug:
+    msg: "{{ plex_version }}"
+  when: plex_version is defined
+
 - name: Get the latest plex release
   community.general.github_release:
     repo: plex
@@ -17,8 +20,9 @@
 - name: Download the latest plex binary
   ansible.builtin.get_url:
     #https://github.com/labdao/plex/releases/download/v0.7.0/plex_0.7.0_linux_amd64.tar.gz
-    url: https://github.com/labdao/plex/releases/download/{{ latest_release.tag }}/plex_{{ latest_release.tag | regex_replace('^v([0-9]\.[0-9]\.[0-9])$', '\1') }}_linux_amd64.tar.gz
+    url: https://github.com/labdao/plex/releases/download/{{ latest_release.tag }}/plex_{{ latest_release.tag | regex_replace('^v([0-9]\.[0-9][0-9]\.[0-9])$', '\1') }}_linux_amd64.tar.gz
     dest: /tmp/plex_release.tar.gz
+    force: true
 
 - name: Unzip the plex release
   ansible.builtin.unarchive: