Merge pull request #78 from i-VRESSE/interactive_apps

Interactive apps

.flake8

@@ -77,6 +77,8 @@ ignore =
   WPS332,
   ; Found protected module import: _runner
   WPS436,
+  ; Found `noqa` comments overuse
+  WPS402,
 
 per-file-ignores =
   ; all tests

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: Install deps
       run: |
         pip install -U pip wheel
@@ -29,7 +29,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: Install deps
       run: |
         pip install -U pip wheel
@@ -48,7 +48,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: Install deps
       run: |
         pip install -U pip wheel
@@ -82,7 +82,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: Install deps
       run: |
         pip install -U pip wheel

.readthedocs.yaml

@@ -7,7 +7,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: '3.9'
+    python: '3.10'
   jobs:
     # https://github.com/readthedocs/readthedocs.org/issues/4912#issuecomment-1143587902
     post_install:

README.md

@@ -23,6 +23,9 @@ moving the input and output files to the right place. To pick where an
 application should be run you can choose from a list of existing Python
 functions or supply your own.
 
+Bartender can run quick interactive applications on completed jobs.
+This is handy if you want to run a quick analysis on the output of a job.
+
 Bartender can be used as the computational backend for a web application, the
 web application should guide visitors into the submission and show the results.
 See <https://github.com/i-VRESSE/haddock3-webapp> for an example.
@@ -44,17 +47,20 @@ at <https://i-vresse-bartender.readthedocs.io> .
     curl -o config.yaml https://raw.githubusercontent.com/i-VRESSE/bartender/main/config-example.yaml
     ```
 
-1. In another terminal, start up a database for storing users and jobs.
+1. In another terminal, start up a database for storing jobs.
 
     ```bash
     docker run \
         -p "5432:5432" \
         -e "POSTGRES_PASSWORD=bartender" \
         -e "POSTGRES_USER=bartender" \
         -e "POSTGRES_DB=bartender" \
+        --mount type=volume,source=bartender-db,target=/var/lib/postgresql/data \
         postgres:15.2-bullseye
     ```
 
+    (Use `docker volume rm bartender-db` to clear the database storage`)
+
 1. Create tables in the database
 
     ```bash
@@ -115,11 +121,10 @@ following steps to run a job:
     4. Use authorize button on top of page to login with username
        `[email protected]` and password `string`.
 4. Submit archive.
-    1. Try out the `POST /api/application/{application}/job` route.
-    2. Use `wc` as application parameter
-    3. Upload the `README.zip` as request body.
-    4. Press execute button
-    5. The response contains a job identifier (`id` property) that can be used
+    1. Try out the `PUT /api/application/wc/job` route.
+    2. Upload the `README.zip` as request body.
+    3. Press execute button
+    4. The response contains a job identifier (`id` property) that can be used
        to fetch the job state.
 5. Fetch job state
     1. Try out the `GET /api/job/{jobid}`

config-example.yaml

@@ -2,12 +2,57 @@ job_root_dir: /tmp/jobs
 destination_picker: bartender.picker:pick_first
 applications:
   wc:
-    command: wc $config
-    config: README.md
+    command_template: wc README.md
+    upload_needs:
+    - README.md
+  count:
+    command_template: >
+      {% set flag = {
+        'lines': '-l',
+        'words': '-w',
+        'chars': '-m',
+        'bytes': '-c',
+      }[what] -%}
+      wc {{ flag|q }} README.md >  count.txt
+    upload_needs:
+    - README.md
+    summary: Count in README.md
+    description: Count the number of lines, words, chars or bytes in a file called README.md in a uploaded zip file.
+    input_schema:
+      additionalProperties: false
+      type: object
+      properties:
+        what:
+          type: string
+          enum: [lines, words, chars, bytes]
+          description: What to count
+          default: lines
+  du:
+    command_template: du -hs . > du.txt
 destinations:
   local:
     scheduler:
       type: memory
       slots: 1
     filesystem:
       type: local
+interactive_applications:
+  count:
+    command_template: >
+      {% set flag = {
+        'lines': '-l',
+        'words': '-w',
+        'chars': '-m',
+        'bytes': '-c',
+      }[what] -%}
+      cat README.md | wc {{ flag|q }} > README.md.count
+    description: Count the number of lines, words, chars or bytes in README.md file.
+    job_application: wc
+    input_schema:
+      additionalProperties: false
+      type: object
+      properties:
+        what:
+          type: string
+          enum: [lines, words, chars, bytes]
+          default: lines

config-haddock3.yaml

@@ -1,28 +1,133 @@
-destination_picker: bartender.config:pick_first
+# Example configuration file for haddock3 and haddock3-re.
+# Expects executables to be in PATH,
+# if not edit this file to use absolute path to executables
+job_root_dir: jobs
+destination_picker: bartender.picker:pick_first
 applications:
   haddock3:
-    command: haddock3 $config
-    config: workflow.cfg
+    command_template: haddock3 workflow.cfg
+    upload_needs:
+    - workflow.cfg
   # Below are other haddock3 commands,
   # that could be hosted by bartender web service.
-  # TODO add support for label and parameters keys
-  haddock3-pp:
-    label: HADDOCK3 preprocess PDB files
-    command: haddock3-pp --output-directory . *.pdb
-  haddock3-analyse:
-    command: haddock3-analyse --run-dir . --modules $modules
-    parameters:
-      modules:
-        type: array
-        items:
-          type: int
-  haddock3-score:
-    command: haddock3-score --outputpdb --outputpsf $config
-    config: complex.pdb
+  # haddock3-pp:
+  #   summary: HADDOCK3 preprocess PDB files
+  #   command_template: haddock3-pp --output-directory . *.pdb
+  # haddock3-analyse:
+  #   command_template: haddock3-analyse --run-dir . -m {{ modules|q }}
+  #   input_schema:
+  #     additionalProperties: false
+  #     type: object
+  #     properties:
+  #       modules:
+  #         type: string
+  #         description: List of module numbers to analyse. Space separated.
 destinations:
   local:
     scheduler:
       type: memory
       slots: 1
     filesystem:
       type: local
+interactive_applications:
+  rescore:
+    command_template: >
+      haddock3-re score
+      --w_elec {{w_elec|q}} --w_vdw {{w_vdw|q}} --w_desolv {{w_desolv|q}} --w_bsa {{w_bsa|q}} --w_air {{w_air|q}}
+      {{ capri_dir|q }}
+      &&
+      haddock3-analyse  --is_cleaned True --inter True -m {{ module_nr|q }} -r output/
+    description: Rescore a HADDOCK run with different weights.
+    job_application: haddock3
+    input_schema:
+      additionalProperties: false
+      properties:
+        module_nr:
+          type: number
+        capri_dir:
+          type: string
+        w_air:
+          type: number
+        w_bsa:
+          type: number
+        w_desolv:
+          type: number
+        w_elec:
+          type: number
+        w_vdw:
+          type: number
+      required:
+      - module_nr
+      - capri_dir
+      - w_elec
+      - w_vdw
+      - w_desolv
+      - w_bsa
+      - w_air
+      type: object
+  reclustrmsd:
+    command_template: >
+      haddock3-re clustrmsd
+      {% if criterion == 'maxclust' -%}
+      --n_clusters {{n_clusters|q}}
+      {% else -%}
+      --clust_cutoff {{clust_cutoff|q}}
+      {% endif -%}
+      {% if min_population -%}
+      --min_population {{min_population|q}}
+      {% endif -%}
+      {{clustrmsd_dir|q}}
+      &&
+      haddock3-analyse --is_cleaned True --inter True -m {{ module_nr|q }} -r output/
+    description: Recluster a HADDOCK run with RSMD and different parameters.
+    job_application: haddock3
+    input_schema:
+      additionalProperties: false
+      properties:
+        module_nr:
+          type: number
+        clustrmsd_dir:
+          type: string
+        criterion:
+          type: string
+          enum: [maxclust, distance]
+        clust_cutoff:
+          type: number
+        n_clusters:
+          type: number
+        min_population:
+          type: number
+      required:
+      - module_nr
+      - criterion
+      - clustrmsd_dir
+      type: object
+  reclustfcc:
+    command_template: >
+      haddock3-re clustfcc
+      --clust_cutoff {{clust_cutoff|q}} --strictness {{strictness|q}} --min_population {{min_population|q}}
+      {{clustfcc_dir|q}}
+      &&
+      haddock3-analyse --is_cleaned True --inter True -m {{ module_nr|q }} -r output/
+    description: Recluster a HADDOCK run with FCC and different parameters.
+    job_application: haddock3
+    input_schema:
+      additionalProperties: false
+      properties:
+        module_nr:
+          type: number
+        clustfcc_dir:
+          type: string
+        clust_cutoff:
+          type: number
+        strictness:
+          type: number
+        min_population:
+          type: number
+      required:
+      - module_nr
+      - clustfcc_dir
+      - clust_cutoff
+      - strictness
+      - min_population
+      type: object