Merge pull request #40 from INCATools/allow-docker

Allow docker to be used in builds of sqlite

Author: cmungall

src/semsql/builder/builder.py

@@ -1,19 +1,51 @@
+import logging
+import os
 import subprocess
+from dataclasses import field
 from pathlib import Path
+from typing import Optional
 
 from sqlalchemy import create_engine
 from sqlalchemy.orm import sessionmaker
 import requests
 
 this_path = Path(__file__).parent
 
-def make(target: str):
+
+class DockerConfig:
+    """
+    Configuration for running ODK Docker image
+    """
+    odk_version: str = None  ## not used yet
+    memory: str = None
+
+
+def make(target: str, docker_config: Optional[DockerConfig] = None):
     """
     Builds a target such as a SQLite file using the build.Makefile
 
     :param target: Make target
+    :param docker_config: if passed, use ODK docker with the specific config
     """
-    subprocess.run(['make', '-f', this_path / 'build.Makefile', target])
+    path_to_makefile = str(this_path / 'build.Makefile')
+    if docker_config is not None:
+        mem = docker_config.memory
+        if mem is None:
+            mem = '4g'
+        pwd = os.getcwd()
+        pre = ['docker', 'run',
+               '-m', mem,
+               '-v', f'{pwd}/:/work',
+               '-v', f'{this_path}/:/builder',
+               '-w', '/work',
+               '--rm', '-ti', 'obolibrary/odkfull']
+        path_to_makefile = '/builder/build.Makefile'
+    else:
+        pre = []
+    cmd = pre + ['make', target, '-f', path_to_makefile]
+    logging.info(f'CMD={cmd}')
+    subprocess.run(cmd)
+
 
 def db_from_owl(input: str) -> str:
     """
@@ -29,6 +61,7 @@ def db_from_owl(input: str) -> str:
     else:
         raise ValueError(f'Path must be an OWL file')
 
+
 def download_obo_sqlite(ontology: str, destination: str):
     """
     Downloads pre-made SQLite file
@@ -41,6 +74,7 @@ def download_obo_sqlite(ontology: str, destination: str):
     r = requests.get(url, allow_redirects=True)
     open(destination, 'wb').write(r.content)
 
+
 def connect(owl_file: str):
     """
     Generates a SQLite connection to an OWL file
@@ -52,4 +86,4 @@ def connect(owl_file: str):
     engine = create_engine(f'sqlite:///{db}')
     Session = sessionmaker(bind=engine)
     session = Session()
-    return session
+    return session

src/semsql/builder/cli.py

@@ -26,7 +26,12 @@ def main(verbose: int, quiet: bool):
 
 @main.command()
 @click.argument('path')
-def make(path):
+@click.option('--docker/--no-docker',
+              default=False,
+              show_default=True,
+              help="Uses ODK docker image"
+              )
+def make(path, docker):
     """
     Makes a specified target, such as a db file
 
@@ -36,7 +41,11 @@ def make(path):
 
     (assumes envo.owl is in the same folder)
     """
-    builder.make(path)
+    if docker:
+        docker_config = builder.DockerConfig()
+    else:
+        docker_config = None
+    builder.make(path, docker_config=docker_config)
 
 
 @main.command()