comparison env/lib/python3.7/site-packages/planemo/training/topic.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"

4:79f47841a781

"""Module contains code for the Topic class, dealing with the creation of a training topic."""

import collections
import os

from planemo import templates
from .utils import (
    load_yaml,
    Requirement,
    save_to_yaml
)


INDEX_FILE_TEMPLATE = """---
layout: topic
topic_name: {{ topic }}
---
"""

README_FILE_TEMPLATE = """
{{ topic }}
==========

Please refer to the [CONTRIBUTING.md](../../CONTRIBUTING.md) before adding or updating any material
"""


DOCKER_FILE_TEMPLATE = """
# Galaxy - {{ topic_title }}
#
# to build the docker image, go to root of training repo and
#    docker build -t {{ topic_name }} -f topics/{{ topic_name }}/docker/Dockerfile .
#
# to run image:
#    docker run -p "8080:80" -t {{ topic_name }}
#    use -d to automatically dowload the datalibraries in the container

FROM bgruening/galaxy-stable:latest

MAINTAINER Galaxy Training Material

ENV GALAXY_CONFIG_BRAND "GTN: {{ topic_title }}"

# copy the tutorials directory for your topic
ADD topics/{{ topic_name }}/tutorials/ /tutorials/

# install everything for tutorials
ADD bin/docker-install-tutorials.sh /setup-tutorials.sh
ADD bin/mergeyaml.py /mergeyaml.py
ADD bin/data_libarary_download.sh /data_libarary_download.sh
RUN /setup-tutorials.sh

ENTRYPOINT ["/data_libarary_download.sh"]
"""


INTRO_SLIDES_FILE_TEMPLATE = """---
layout: introduction_slides
logo: "GTN"

title: {{ title }}
type: {{ type }}
contributors:
- contributor
---

### How to fill the slide decks?

Please follow our
[tutorial to learn how to fill the slides]({{ '{{' }} site.baseurl {{ '}}' }}/topics/contributing/tutorials/create-new-tutorial-slides/slides.html)
"""


class Topic(object):
    """Class to describe a training topic."""

    def __init__(self, name="new_topic", target="use", title="The new topic", summary="Summary", parent_dir="topics"):
        """Init a topic instance."""
        self.name = name
        self.type = target
        self.title = title
        self.summary = summary
        self.docker_image = ""
        self.maintainers = ["maintainers"]
        self.parent_dir = parent_dir
        self.set_default_requirement()
        self.set_paths()

    def init_from_kwds(self, kwds):
        """Init a topic instance from a kwds dictionary."""
        self.name = kwds["topic_name"]
        self.type = kwds["topic_target"]
        self.title = kwds["topic_title"]
        self.summary = kwds["topic_summary"]
        self.set_default_requirement()
        self.set_paths()

    def init_from_metadata(self):
        """Init a topic instance from the metadata file."""
        metadata = load_yaml(self.metadata_fp)
        self.name = metadata['name']
        self.type = metadata['type']
        self.title = metadata['title']
        self.summary = metadata['summary']
        self.requirements = []
        if 'requirements' in metadata:
            for r in metadata['requirements']:
                req = Requirement()
                req.init_from_dict(r)
                self.requirements.append(req)
        if 'docker_image' in metadata:
            self.docker_image = metadata['docker_image']
        self.maintainers = metadata['maintainers']
        self.set_paths()

    # GETTERS
    def get_requirements(self):
        """Get the requirements as a list of ordered dictionaries."""
        reqs = []
        for req in self.requirements:
            reqs.append(req.export_to_ordered_dict())
        return reqs

    def export_metadata_to_ordered_dict(self):
        """Export the topic metadata into an ordered dictionary."""
        metadata = collections.OrderedDict()
        metadata['name'] = self.name
        metadata['type'] = self.type
        metadata['title'] = self.title
        metadata['summary'] = self.summary
        metadata['requirements'] = self.get_requirements()
        metadata['docker_image'] = self.docker_image
        metadata['maintainers'] = self.maintainers
        return metadata

    # SETTERS
    def set_default_requirement(self):
        """Set default requirement: Galaxy introduction."""
        self.requirements = []
        if self.type == 'use':
            self.requirements.append(Requirement())

    def set_paths(self):
        """Set the paths to folder and files."""
        self.dir = os.path.join(self.parent_dir, self.name)
        self.img_folder = os.path.join(self.dir, "images")
        self.tuto_folder = os.path.join(self.dir, "tutorials")
        self.index_fp = os.path.join(self.dir, "index.md")
        self.readme_fp = os.path.join(self.dir, "README.md")
        self.metadata_fp = os.path.join(self.dir, "metadata.yaml")
        self.docker_folder = os.path.join(self.dir, "docker")
        self.dockerfile_fp = os.path.join(self.docker_folder, "Dockerfile")
        self.slides_folder = os.path.join(self.dir, "slides")

    # TESTS
    def exists(self):
        """Test if the topic exists."""
        return os.path.isdir(self.dir)

    # OTHER METHODS
    def create_topic_structure(self):
        """Create the skeleton of a new topic.

        1. create the folder and its structure
        2. update the index.md to match your topic's name
        3. fill the metadata
        4. add a symbolic link to the metadata.yaml from the metadata folder
        """
        # create the folder and its structure
        os.makedirs(self.dir)
        self.img_folder = os.path.join(self.dir, "images")
        os.makedirs(self.img_folder)
        self.tuto_folder = os.path.join(self.dir, "tutorials")
        os.makedirs(self.tuto_folder)

        # create the index.md and add the topic name
        self.index_fp = os.path.join(self.dir, "index.md")
        with open(self.index_fp, 'w') as index_f:
            index_f.write(
                templates.render(INDEX_FILE_TEMPLATE, **{'topic': self.name}))

        # create the README file
        self.readme_fp = os.path.join(self.dir, "README.md")
        with open(self.readme_fp, 'w') as readme_f:
            readme_f.write(
                templates.render(README_FILE_TEMPLATE, **{'topic': self.title}))

        # create the metadata file
        self.metadata_fp = os.path.join(self.dir, "metadata.yaml")
        save_to_yaml(self.export_metadata_to_ordered_dict(), self.metadata_fp)

        # create Dockerfile
        self.docker_folder = os.path.join(self.dir, "docker")
        os.makedirs(self.docker_folder)
        self.dockerfile_fp = os.path.join(self.docker_folder, "Dockerfile")
        with open(self.dockerfile_fp, 'w') as dockerfile:
            dockerfile.write(
                templates.render(
                    DOCKER_FILE_TEMPLATE,
                    **{'topic_name': self.name, 'topic_title': self.title}))

        # create empty introduction slides
        self.slides_folder = os.path.join(self.dir, "slides")
        os.makedirs(self.slides_folder)
        self.intro_slide_fp = os.path.join(self.slides_folder, "introduction.html")
        with open(self.intro_slide_fp, 'w') as intro_slide_f:
            intro_slide_f.write(
                templates.render(
                    INTRO_SLIDES_FILE_TEMPLATE,
                    **{'title': "Introduction to %s" % self.title, 'type': "introduction"}))

        # add a symbolic link to the metadata.yaml
        metadata_dir = "metadata"
        if not os.path.isdir(metadata_dir):
            os.makedirs(metadata_dir)
        os.chdir(metadata_dir)
        os.symlink(os.path.join("..", self.metadata_fp), "%s.yaml" % self.name)
        os.chdir("..")