def generate_docs():
docs = []
#filter for images in the conf that have the generate_docs flag set to true
image_configs = filter(lambda image: image["automated_flags"]["generate_docs"] == True and image["automated_flags"]["include_in_ui"] == True and image["automated_flags"]["build"] == True, config["image_data"])
remote_docs = get_current_versions()
#maps the current documentation to a map of {image_name: version} key values
remote_versions_list = list(map(lambda image_doc: {image_doc["id"]: image_doc["version"]}, remote_docs))
remote_versions = utils.flatten_list_of_dicts(remote_versions_list)
print "current versions detected: " + str(remote_versions)
for image_config in image_configs:
# Here we check first if the remote documentation exists, then if the local version is the same as the remote.
# If the remote documentation exists and the version matches the local, we re-use the old documentation
if image_config["name"] in remote_versions and image_config["version"] == remote_versions[image_config["name"]]:
remote_doc = list(filter(lambda image_doc: image_doc["id"] == image_config["name"], remote_docs))[0]
print "using remote doc: {}".format(remote_doc)
doc = remote_doc
else:
doc = generate_doc_for_image(image_config)
docs.append(doc)
docs.extend(get_other_docs())
return docs
def get_docs(params):
tools = params.image_config["tools"]
doc_builder = get_doc_builder()
docs = {}
for tool in tools:
print "Writing doc for tool {}".format(tool)
#flattens the arrays of objects with packages:version key value pairs into single object with all key value pairs
docs[tool] = utils.flatten_list_of_dicts(doc_builder[tool](params))
return docs
def generate_docs():
docs = []
#filter for images in the conf that have the generate_docs flag set to true
image_configs = filter(
lambda image: image["automated_flags"]["generate_docs"] == True and
image["automated_flags"]["include_in_ui"] == True and image[
"automated_flags"]["build"] == True, config["image_data"])
remote_docs = get_current_versions()
#maps the current documentation to a map of {image_name: version} key values
remote_versions_list = list(
map(lambda image_doc: {image_doc["id"]: image_doc["version"]},
remote_docs))
remote_versions = utils.flatten_list_of_dicts(remote_versions_list)
print "current versions detected: " + str(remote_versions)
legacy_gatk_doc = filter(
lambda remote_doc: remote_doc["id"] == "terra-jupyter-gatk_legacy",
remote_docs)[0]
legacy_bioconductor_doc = utils.read_json_file(static_config_location)[
0] # hard coding this until next bioconductor release (~06/2022)
for image_config in image_configs:
# Here we check first if the remote documentation exists, then if the local version is the same as the remote.
# If the remote documentation exists and the version matches the local, we re-use the old documentation
remote_doc = list(
filter(lambda image_doc: image_doc["id"] == image_config["name"],
remote_docs))[0]
if image_config["name"] in remote_versions and image_config[
"version"] == remote_versions[image_config["name"]]:
print "using remote doc: {}".format(remote_doc)
doc = remote_doc
else:
doc = generate_doc_for_image(image_config)
#Computing legacy images for gatk and bioconductor
if image_config["name"] == "terra-jupyter-gatk":
legacy_gatk_doc = get_legacy_image(image_config["version"],
remote_doc, legacy_gatk_doc)
# TODO: add back in after next bioconductor release (~06/2022)
#if image_config["name"] == "terra-jupyter-bioconductor":
#legacy_bioconductor_doc = get_legacy_image(image_config["version"], doc)
docs.append(doc)
docs.extend(get_other_docs())
docs.extend([legacy_gatk_doc, legacy_bioconductor_doc])
return docs