Merge branch 'master' of https://github.molgen.mpg.de/EditionOpenAcce…

…ss/EOASkripts

.gitignore

@@ -1,7 +1,5 @@
-/input/
-/output/
+/runtime/
 /dependencies/
-examples
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.init-container.sh

@@ -1,10 +1,7 @@
 #!/bin/bash
 
 
-echo 'export PATH="$EOA_SCRIPTS_DIR:$PATH"' >> ~/.bashrc
-
-ln -s $INPUT_DIR input
-ln -s $OUTPUT_DIR output
+echo 'export PATH="$EOA_SCRIPTS_DIR:$PATH"' > ./.bashrc
 
 # wait, keep container running:
 bash -c 'while :; do :; done & kill -STOP $! && wait $!'

Dockerfile

@@ -104,12 +104,5 @@ RUN echo '#!/bin/bash' > $UTILS_BIN_DIR/saxon
 RUN echo 'java -jar $UTILS_BIN_DIR/saxon9he.jar "$@"' >> $UTILS_BIN_DIR/saxon
 RUN chmod ugo+x $UTILS_BIN_DIR/saxon
 
-# create a HOME and reasonable environment settings for the user:
-ENV HOME /home/user
-RUN useradd --create-home user
-WORKDIR ${HOME}
-
-COPY ".init-container.sh" "$HOME/init_container.sh"
-RUN chmod ugo+x "$HOME/init_container.sh"
-
-USER user
+COPY ".init-container.sh" "$UTILS_BIN_DIR/init_container.sh"
+RUN chmod ugo+x "$UTILS_BIN_DIR/init_container.sh"

README.md

@@ -55,11 +55,11 @@ Docker images are not deleted though.
 
 # General Usage Information
 
-The `input` directory is for unprocessed publications as you might have received them from authors or editors.
-The `output` directory is for processed publications and intermediate data.
+The `runtime/input` directory is for unprocessed publications as you might have received them from authors or editors.
+The `runtime/output` directory is for processed publications and intermediate data.
 When entering the docker container conversion scripts are in your $PATH, and can executed like any other executable.
-In your `HOME` directory you'll find `input` and `output` directories, which are docker volumes mirroring the directories of the same name outside of the container.
-In order to compile a publication, just copy them into `./input`, enter the docker container, and call the necessary scripts.
+In your `HOME` directory you'll find `input` and `output` directories, which are docker volumes mirroring the directories in `runtime/` outside of the container.
+In order to compile a publication, just copy them into `runtime/input`, enter the docker container, and call the necessary scripts.
 For an example, see chapter "Workflows".
 
 ## Configuration
@@ -83,8 +83,8 @@ Compiling your documents involves following a workflow which can consist of seve
 
 ## The LaTeX workflow (eoatex -> pdf, django, epub)
 
-The following description uses the example publication in `input/example` (from the `eoa-publication-model` repository).
-In order to apply the workflow to any other publication copy it into the `input/` directory and adjust paths in the description accordingly.
+The following description uses the example publication in `runtime/input/example` (copied from the `eoa-publication-model` repository).
+In order to apply the workflow to any other publication copy it into the `runtime/input/` directory and adjust paths in the description accordingly.
 
 1. enter the docker container
 

docker-compose.yaml

@@ -6,16 +6,19 @@ services:
     build: .
     image: ${IMAGE_NAME}
     container_name: ${CONTAINER_NAME}
-    command: "/home/user/init_container.sh"
+    command: "/eoa/bin/init_container.sh"
     volumes:
       - ./${SRC_DIR}:${SRC_DIR_IN_CONTAINER}
+      - ./${HOME_DIR}:${HOME_DIR_IN_CONTAINER}
       - ./${INPUT_DIR}:${INPUT_DIR_IN_CONTAINER}
       - ./${OUTPUT_DIR}:${OUTPUT_DIR_IN_CONTAINER}
     environment:
+      - HOME=${HOME_DIR_IN_CONTAINER}
       - INPUT_DIR=${INPUT_DIR_IN_CONTAINER}
       - OUTPUT_DIR=${OUTPUT_DIR_IN_CONTAINER}
       - DEPENDENCIES_DIR=${DEPENDENCIES_DIR_IN_CONTAINER}
       - EOA_SCRIPTS_DIR=${SRC_DIR_IN_CONTAINER}
     ports: []
     user: ${USER}:${GROUP}
+    working_dir: ${HOME_DIR_IN_CONTAINER}
     tty: true

scripts/config/env.conf → scripts/config/env_default.conf

@@ -15,15 +15,20 @@ CONTAINER_NAME=eoa_skripts
 SRC_DIR=src
 SRC_DIR_IN_CONTAINER=/eoa/skripts
 
-INPUT_DIR=input
+DEPENDENCIES_DIR=dependencies
+DEPENDENCIES_DIR_IN_CONTAINER=/eoa/dependencies
+
+RUNTIME_DIR=runtime
+
+HOME_DIR=${RUNTIME_DIR}/work_dir
+HOME_DIR_IN_CONTAINER=/home/work_dir
+
+INPUT_DIR=${RUNTIME_DIR}/input
 INPUT_DIR_IN_CONTAINER=/eoa/input
 
-OUTPUT_DIR=output
+OUTPUT_DIR=${RUNTIME_DIR}/output
 OUTPUT_DIR_IN_CONTAINER=/eoa/output
 
-DEPENDENCIES_DIR=dependencies
-DEPENDENCIES_DIR_IN_CONTAINER=/eoa/dependencies
-
 ###################################################
 # user and group:
 # USER=$(id -u)

scripts/exit.py

@@ -1,56 +1,73 @@
 #!/usr/bin/env python3
 
-from utils.settings import BASE_DIR, load_config
+from utils.settings import env_file, BASE_DIR, load_config, create_docker_env_file
 
 from pathlib import Path
 import shutil
 import os
 
-def rm_dirs( config, rm_deps):
-    path = Path( BASE_DIR, config['DEPENDENCIES_DIR'] )
+def rm_dir(
+        path
+):
     print( "removing dir '{}'".format( path ) )
     shutil.rmtree(
         path,
         ignore_errors=True
     )
 
-def rm_docker_env_file( config ):
-    path = Path(
-        BASE_DIR / ".env"
-    )
-    print( "removing '{}'".format( path ) )
-    path.unlink()
+def rm_file(
+        path
+):
+    if path.is_file():
+        print( "removing file '{}'".format( path ) )
+        path.unlink()
 
 if __name__ == '__main__':
 
     from argparse import ArgumentParser
 
+    if not env_file.exists():
+        create_docker_env_file()
     config = load_config()
 
     parser = ArgumentParser(
         description="clean up the repository"
     )
     parser.add_argument(
-        "--rm-deps",
-        action = "store_true"
+        "-d", "--deps",
+        action = "store_true",
+        help = "remove dependencies",
+    )
+    parser.add_argument(
+        "-r", "--runtime",
+        action = "store_true",
+        help = "remove '{rt_dir}'".format( rt_dir = BASE_DIR / config['RUNTIME_DIR'] ),
     )
     parser.add_argument(
-        "--env-file",
-        action = "store_true"
+        "-e", "--env",
+        action = "store_true",
+        help = "remove existing .env file",
     )
     parser.add_argument(
         "--all",
-        action = "store_true"
+        action = "store_true",
+        help = "purge in every way",
     )
     args = parser.parse_args()
 
     from stop import stop
 
     stop( config )
 
-    rm_dirs(
-            config,
-            rm_deps = args.rm_deps or args.all
-    )
-    if args.env_file or args.all:
-        rm_docker_env_file( config )
+    if args.deps or args.all:
+        rm_dir(
+                path = BASE_DIR / config['DEPENDENCIES_DIR']
+        )
+    if args.runtime or args.all:
+        rm_dir(
+                path = BASE_DIR / config['RUNTIME_DIR']
+        )
+    if args.env or args.all:
+        rm_file(
+                env_file
+        )

scripts/init.py

@@ -37,12 +37,27 @@ def create_dirs( config ):
     create_dir(
         BASE_DIR / config['DEPENDENCIES_DIR']
     )
+    create_dir(
+        BASE_DIR / config['HOME_DIR']
+    )
     create_dir(
         BASE_DIR / config['INPUT_DIR']
     )
     create_dir(
         BASE_DIR / config['OUTPUT_DIR']
     )
+    in_link = Path(BASE_DIR / config['HOME_DIR'] / 'input' )
+    if not(in_link.is_symlink()) and not(in_link.exists()):
+        in_link . symlink_to(
+            config['INPUT_DIR_IN_CONTAINER'],
+            target_is_directory = True,
+        )
+    out_link = Path(BASE_DIR / config['HOME_DIR'] / 'output' )
+    if not(out_link.is_symlink()) and not(out_link.exists()):
+        out_link . symlink_to(
+            config['OUTPUT_DIR_IN_CONTAINER'],
+            target_is_directory = True,
+        )
 
 def install_git_dep(
     repo_name,
@@ -79,12 +94,19 @@ def install_git_dep(
         description="initialize the repository: download git deps, create directories, etc"
     )
     parser.add_argument(
-        "--force-deps",
-        action = "store_true"
+        "-d", "--force-deps",
+        action = "store_true",
+        help = "download dependencies, even if yet existing",
     )
     parser.add_argument(
         "--build",
-        action = "store_true"
+        action = "store_true",
+        help = "rebuild docker image from Dockerfile",
+    )
+    parser.add_argument(
+        "-e", "--env",
+        action = "store_true",
+        help = "overwrite existing .env file",
     )
     args = parser.parse_args()
 
@@ -126,7 +148,7 @@ def install_git_dep(
             env = config,
         )
 
-    # copy example publication to $INPUT_DIR
+    # copy example publication to $INPUT_DIR:
     copy_dir(
         BASE_DIR / config['DEPENDENCIES_DIR'] / 'eoa-publication-model/examples',
         BASE_DIR / config['INPUT_DIR'] / 'example'

scripts/utils/settings.py

@@ -8,7 +8,7 @@
 BASE_DIR = Path( __file__ ).parent.parent.parent
 SCRIPT_DIR = Path( __file__ ).parent.parent
 
-orig_config_file = SCRIPT_DIR / "config" / "env.conf"
+orig_config_file = SCRIPT_DIR / "config" / "env_default.conf"
 env_file = BASE_DIR / ".env"