.github/workflows/canary.yml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -3,7 +3,7 @@ name: Canary Run Equibind Tool
  
    on:

      workflow_dispatch:

      schedule:

        - cron: '*/10 * * * *'

        - cron: '23 * * * *'

    jobs:

      canary:

    @@ -50,4 +50,4 @@ jobs:
  
            run: |

              curl -X POST -H 'Authorization: Bearer ${{ secrets.HEII_ON_CALL_API_KEY }}' https://api.heiioncall.com./triggers/${HEII_ON_CALL_INBOUND_TRIGGER_ID}/checkin

            env:

              HEII_ON_CALL_INBOUND_TRIGGER_ID: e720588c-35cd-4392-9d02-bec350aa34e9

              HEII_ON_CALL_INBOUND_TRIGGER_ID: df86b926-d9c1-4584-8c91-28ffde7af8c2

infrastructure/ansible/files/equibind_canary.sh

-Original file line number
+Diff line change
@@ -0,0 +1,33 @@
+    #!/bin/bash
+    # exit the whole script if any command returns a non-zero exit code
+    set -e
+    # plex must run from the same place as tools directory
+    cd {{ repo_dir }}
+    plex -tool equibind -input-dir {{ repo_dir }}/testdata/binding/abl 2>&1 | tee plex_out.log
+    # capture the exit status of the plex call
+    plex_result_code=${PIPESTATUS[0]}
+    # exit immediately if plex exited with an error
+    if [ $plex_result_code -gt 0 ]; then
+      exit $plex_result_code
+    fi
+    # parse the output directory from the plex stdout
+    result_dir=$(cat plex_out.log | grep 'Finished processing, results written to' | sed -n 's/^.*Finished processing, results written to //p' | sed 's/\/io.json//')
+    # exit if no docked files are found
+    cd "$result_dir/entry-0/outputs"
+    if [ "$(find . -name '*docked.sdf' | grep 'docked.sdf')" == "" ]; then
+      echo "No docked files found"
+      exit 1
+    else
+      echo "Docked files found"
+    fi
+    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"

infrastructure/ansible/install_plex_tasks.yaml

-Original file line number
+Diff line change
@@ -0,0 +1,36 @@
+    # {{ plex_dir }} must be writable by the user
+    - name: Install required pip packages
+      become: yes
+      ansible.builtin.pip:
+        name:
+          - pip
+          - pyopenssl
+          - github3.py
+        state: latest
+    - name: Get the latest plex release
+      community.general.github_release:
+        repo: plex
+        user: labdao
+        action: latest_release
+      register: latest_release
+    - 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
+        dest: /tmp/plex_release.tar.gz
+    - name: Unzip the plex release
+      ansible.builtin.unarchive:
+        src: /tmp/plex_release.tar.gz
+        remote_src: true
+        include: plex
+        dest: "{{ plex_dir }}"
+    - name: Link the plex binary to the system path
+      become: yes
+      ansible.builtin.file:
+        src: "{{ plex_dir }}/plex"
+        dest: /usr/local/bin/plex
+        state: link

infrastructure/ansible/jupyter_deploy_plex.yaml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -4,40 +4,22 @@
  
      vars:

        plex_dir: /opt/local/plex

      tasks:

        - name: Pull the plex repository

        - name: Create plex dir, writable by user

          become: yes

          ansible.builtin.file:

            path: "{{ plex_dir }}"

            owner: ubuntu

            group: ubuntu 

            state: directory

        - name: Pull the plex repository

          ansible.builtin.git:

            repo: https://github.com/labdao/plex.git

            dest: "{{ plex_dir }}/"

        - name: Get the latest plex release

          community.general.github_release:

            repo: plex

            user: labdao

            action: latest_release

          register: latest_release

        - name: Download the latest plex binary

          become: yes

          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

            dest: /tmp/plex_release.tar.gz

        - name: Unzip the plex release

          become: yes

          ansible.builtin.unarchive:

            src: /tmp/plex_release.tar.gz

            remote_src: true

            include: plex

            dest: "{{ plex_dir }}"

        - name: Link the plex binary to the system path

          become: yes

          ansible.builtin.file:

            src: "{{ plex_dir }}/plex"

            dest: /usr/local/bin/plex

            state: link

        - name: Install Plex

          ansible.builtin.include_tasks:

            file: install_plex_tasks.yaml

        - name: Add plex python wrapper to the conda path

          become: yes

infrastructure/ansible/provision_canary.yaml

-Original file line number
+Diff line change
@@ -0,0 +1,54 @@
+    - name: Provision Canary
+      remote_user: ubuntu
+      hosts: tag_Type_compute
+      vars:
+        canary_dir: /opt/local/canary
+        repo_dir: "{{ canary_dir }}/repo"
+        binary_dir: "{{ canary_dir }}/binary"
+      tasks:
+        - name: Install aptitude
+          become: yes
+          ansible.builtin.apt:
+            name: aptitude
+            state: latest
+            update_cache: true
+        - name: Install required system packages
+          become: yes
+          ansible.builtin.apt:
+            pkg:
+              - pip
+        - name: Ensure directories exist, writable by user
+          become: yes
+          ansible.builtin.file:
+            path: "{{ item }}"
+            owner: ubuntu
+            group: ubuntu
+            state: directory
+          loop:
+            - "{{ repo_dir }}"
+            - "{{ binary_dir }}"
+        - name: Pull the plex repository
+          ansible.builtin.git:
+            repo: https://github.com/labdao/plex.git
+            dest: "{{ repo_dir }}/"
+        - name: Install Plex
+          ansible.builtin.include_tasks:
+            file: install_plex_tasks.yaml
+          vars:
+            plex_dir: "{{ binary_dir }}"
+        - name: Place canary srcript
+          ansible.builtin.template:
+            src: files/equibind_canary.sh
+            dest: "{{ canary_dir }}/equibind_canary.sh"
+            mode: 'u+x'
+        - name: Set a cron job to run canary
+          ansible.builtin.cron:
+            name: "Run equibind canary"
+            job: "{{ canary_dir }}/equibind_canary.sh"
+            minute: "*/5"

Move canary to compute box #369

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Merged

hevans66 merged 3 commits into main from ops/dial-back-canary

Jun 6, 2023

-Original file line number
+Diff line change
@@ -0,0 +1,33 @@
+    #!/bin/bash
+    # exit the whole script if any command returns a non-zero exit code
+    set -e
+    # plex must run from the same place as tools directory
+    cd {{ repo_dir }}
+    plex -tool equibind -input-dir {{ repo_dir }}/testdata/binding/abl 2>&1 | tee plex_out.log
+    # capture the exit status of the plex call
+    plex_result_code=${PIPESTATUS[0]}
+    # exit immediately if plex exited with an error
+    if [ $plex_result_code -gt 0 ]; then
+      exit $plex_result_code
+    fi
+    # parse the output directory from the plex stdout
+    result_dir=$(cat plex_out.log | grep 'Finished processing, results written to' | sed -n 's/^.*Finished processing, results written to //p' | sed 's/\/io.json//')
+    # exit if no docked files are found
+    cd "$result_dir/entry-0/outputs"
+    if [ "$(find . -name '*docked.sdf' | grep 'docked.sdf')" == "" ]; then
+      echo "No docked files found"
+      exit 1
+    else
+      echo "Docked files found"
+    fi
+    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"

-Original file line number
+Diff line change
@@ -0,0 +1,36 @@
+    # {{ plex_dir }} must be writable by the user
+    - name: Install required pip packages
+      become: yes
+      ansible.builtin.pip:
+        name:
+          - pip
+          - pyopenssl
+          - github3.py
+        state: latest
+    - name: Get the latest plex release
+      community.general.github_release:
+        repo: plex
+        user: labdao
+        action: latest_release
+      register: latest_release
+    - 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
+        dest: /tmp/plex_release.tar.gz
+    - name: Unzip the plex release
+      ansible.builtin.unarchive:
+        src: /tmp/plex_release.tar.gz
+        remote_src: true
+        include: plex
+        dest: "{{ plex_dir }}"
+    - name: Link the plex binary to the system path
+      become: yes
+      ansible.builtin.file:
+        src: "{{ plex_dir }}/plex"
+        dest: /usr/local/bin/plex
+        state: link

-Original file line number
+Diff line change
@@ -0,0 +1,54 @@
+    - name: Provision Canary
+      remote_user: ubuntu
+      hosts: tag_Type_compute
+      vars:
+        canary_dir: /opt/local/canary
+        repo_dir: "{{ canary_dir }}/repo"
+        binary_dir: "{{ canary_dir }}/binary"
+      tasks:
+        - name: Install aptitude
+          become: yes
+          ansible.builtin.apt:
+            name: aptitude
+            state: latest
+            update_cache: true
+        - name: Install required system packages
+          become: yes
+          ansible.builtin.apt:
+            pkg:
+              - pip
+        - name: Ensure directories exist, writable by user
+          become: yes
+          ansible.builtin.file:
+            path: "{{ item }}"
+            owner: ubuntu
+            group: ubuntu
+            state: directory
+          loop:
+            - "{{ repo_dir }}"
+            - "{{ binary_dir }}"
+        - name: Pull the plex repository
+          ansible.builtin.git:
+            repo: https://github.com/labdao/plex.git
+            dest: "{{ repo_dir }}/"
+        - name: Install Plex
+          ansible.builtin.include_tasks:
+            file: install_plex_tasks.yaml
+          vars:
+            plex_dir: "{{ binary_dir }}"
+        - name: Place canary srcript
+          ansible.builtin.template:
+            src: files/equibind_canary.sh
+            dest: "{{ canary_dir }}/equibind_canary.sh"
+            mode: 'u+x'
+        - name: Set a cron job to run canary
+          ansible.builtin.cron:
+            name: "Run equibind canary"
+            job: "{{ canary_dir }}/equibind_canary.sh"
+            minute: "*/5"

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