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[release] Regular merge of develop

Merged [release] Regular merge of develop
develop into master
Merged cylon-x requested to merge develop into master
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.ci/generateIndex.py
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import os, re
from os import path
from os.path import exists
from natsort import natsorted
from pathlib import Path
import yaml
from generator import core, save
def line_prepender(filename, line):
with open(filename, 'r+') as f:
content = f.read()
f.seek(0, 0)
f.write(line.rstrip('\r\n') + '\n' + content)
# walk through the folders with all the cards
ind, wl = core.core(["external"])
def get_subdirs(p):
for fname in os.listdir(p):
if os.path.isdir(os.path.join(p, fname)):
yield os.path.join(p, fname)
def has_subdirs(p):
folders = list(get_subdirs(p))
return len(folders) != 0
def build_link(title, href):
# strip the number of the title
if ('handbook' in href):
title = re.sub('[0-9.]', '', title).strip()
# add relative url
href = "{{ '" + href + "' | relative_url }}"
return f'\t\t\t<li><a href="{href}">{title}</a></li>\n'
def root_href(href):
# remove sym link reference in href
if ('handbook-additional' in href):
href = href.replace('handbook-additional', 'handbook').strip()
elif ('handbook-annexes' in href):
href = href.replace('handbook-annexes', 'handbook').strip()
# remove sym link reference in href
if ('lab-software' in href):
href = href.replace('lab-software', 'lab').strip()
elif ('lab-equipment' in href):
href = href.replace('lab-equipment', 'lab').strip()
elif ('lab-hsa' in href):
href = href.replace('lab-hsa', 'lab').strip()
elif ('lab-integrity' in href):
href = href.replace('lab-integrity', 'lab').strip()
# remove sym link reference in href
if ('qms-policies' in href):
href = href.replace('qms-policies', 'qms').strip()
elif ('qms-sops' in href):
href = href.replace('qms-sops', 'qms').strip()
return href
def build_section_start(title, shortcut):
title = title.replace("Gdpr", "GDPR")
title = title.replace("Handbook additional", "Handbook: PI/Supervisor specifics")
title = title.replace("Handbook annexes", "Handbook: Annexes")
title = title.replace("Covid 19", "COVID-19")
title = title.replace("Ppc", "PPC")
title = title.replace("Lab software", "Lab: Software")
title = title.replace("Lab equipment", "Lab: Equipment")
title = title.replace("Lab hsa", "Lab: Health & Safety, Access")
title = title.replace("Lab integrity", "Lab: Integrity")
title = title.replace("Qms sops", "QMS: Standard Operating Procedures (SOPS)")
title = title.replace("Qms policies", "QMS: Policies")
return f'\n\t<div class="index-box noborderbox" id="{shortcut}-card">\n\t\t<h3>{title}</h3>\n\t\t<ul>\n'
def build_section_end():
return "\t\t</ul>\n\t</div>"
def save_tag(localroot, root, filename, tag):
return_tag = ""
os.chdir(root)
length_tag = len(tag)
if "yml" in filename:
with open(filename, "r") as stream:
try:
metadata = list(yaml.load_all(stream, Loader=yaml.FullLoader))
except yaml.YAMLError as exc:
print(exc)
return_tag = metadata[0][tag]
else:
with open(filename, 'r') as f:
for line in f:
# check for the start of the section
if line[0:length_tag+1] == tag + ":":
return_tag = line[length_tag+2:]
return_tag = return_tag.replace('"', '')
break
# change back to the local root
os.chdir(localroot)
return return_tag.rstrip()
def get_ignore():
return ["404.html",
"Gemfile",
"Gemfile.lock",
"README.md",
"_config.yml",
"_site",
"assets",
"help.md",
"index.md",
"pagination.md",
".gitkeep",
]
def save_legacy_from(localroot, root, filename):
legacy_from = []
os.chdir(root)
count = 0
legacy_from_flag = False
with open(filename, 'r') as f:
for line in f:
count += 1
# check for the start of the section
if line[0:12] == "legacy_from:":
legacy_from_flag = True
# append lines from the legacy section
if legacy_from_flag:
legacy_from.append(line)
# check for the end of the header
if legacy_from_flag and line[0:3] == "---":
legacy_from_flag = False
break
# change back to the local root
os.chdir(localroot)
return legacy_from
def remove_header(localroot, root, filename):
nfirstlines = []
os.chdir(root)
# count the number of lines
count = 0
n = 0
headerCheck = False
with open(filename, 'r') as f:
for line in f:
count += 1
# check if the header is actually a header
if count > 1 and line[0:3] == "---":
headerCheck = True
n = count
# remove the header
if headerCheck:
with open(filename) as f, open("tmp"+filename, "w") as out:
for _ in range(n):
nfirstlines.append(next(f))
for line in f:
out.write(line)
os.remove(filename)
os.rename("tmp"+filename, filename)
print(" - Old header removed.")
# change back to the local root
os.chdir(localroot)
return n
def element_header(prefix, permalink, element):
if (
("handbook-annexes" in permalink or "handbook-additional" in permalink) or
("lab-software" in permalink or "lab-equipment" in permalink or "lab-hsa" in permalink) or
("qms-policies" in permalink or "qms-sops" in permalink)
):
element += prefix + "/cards/" + root_href(shortcut) + "\n"
element += prefix + "/" + folder + "/cards/" + root_href(shortcut) + "\n"
return element
def generate_header(folder, permalink, shortcut, order, legacy_from, title, description, qms_yml):
header = "---\n"
if len(order) > 0:
header += "card_order: " + str(order) + "\n"
header += "layout: page\n"
header += "permalink: " + permalink + "\n"
header += "shortcut: " + root_href(shortcut) + "\n"
header += "redirect_from:\n"
header += " - /cards/" + shortcut + "\n"
header += " - /" + folder + "/cards/" + shortcut + "\n"
# generate specific redirects
header = element_header(" - ", shortcut, header)
# include the legacy section in the redirect_from section
if len(legacy_from) > 0:
for item in legacy_from[1:-1]:
header += str(item)
# add the title and description
if len(title) > 0:
header += "title: " + title + "\n"
if len(description) > 0:
header += "description: " + description + "\n"
# include the legacy section
if len(legacy_from) > 0:
for item in legacy_from:
header += str(item)
else:
header += "---"
# add title for QMS documents
if "qms" in shortcut and qms_yml:
header += "\n# " + title
return header
def generate_whitelist_entry(folder, permalink, shortcut):
wl_entry = permalink + "\n"
wl_entry += "/?" + shortcut + "\n"
wl_entry += "/cards/" + shortcut + "\n"
wl_entry += "/" + folder + "/cards/" + shortcut + "\n"
wl_entry = element_header("", permalink, wl_entry)
return wl_entry
def prepare_qms(localroot, root, filename):
os.chdir(root)
filedata = ""
with open(filename, 'r') as file :
for line in file:
filedata += line
# shift the subtitles by 1 level down
filedata = filedata.replace("# ", "## ")
# replace latex command for titles
filedata = filedata.replace("{-}", "##")
# deal with img location
filedata = filedata.replace("policies/"+filename[:-3]+"/", "")
filedata = filedata.replace("sops/"+filename[:-3]+"/", "")
# replace img attributes
filedata = filedata.replace("{ width=50% }", "")
# Write the file out again
with open(filename, 'w') as file:
file.write(filedata)
# change back to the local root
os.chdir(localroot)
# loop through the entire internal tree
localroot = os.getcwd()
# retrieve ignore list
ignore = get_ignore()
# generate the index properly speaking
cardDirs = ["internal", "external"]
sections = []
# determine first the directories
for direct in cardDirs:
if path.isdir(direct) and has_subdirs(direct):
dirs = os.listdir(direct)
dirs = natsorted(dirs)
for d in dirs:
if d[0] != "." and d not in ignore and has_subdirs(direct + "/" + d):
sections.append(d)
sections = list(set(sections))
sections = natsorted(sections)
# Index contains the generated content, init it with an empty container
index = ''
index += '\n<div class="index-box-container">\n'
whiteList = ''
localIndexArr = {k: [] for k in range(len(sections))}
orderArr = {k: [] for k in range(len(sections))}
for folder in cardDirs:
# FolderFlag gets set to true at the first iteration
folderFlag = True
# check if folder exists
if path.isdir(folder) and folder not in ignore:
dirs = os.listdir(folder)
dirs = natsorted(dirs)
for d in dirs:
if d[0] != "." and d not in ignore and has_subdirs(folder + "/" + d):
# set the header of the section
#index += "\n### " + d.replace("-", " ").capitalize() + "\n"
# get the index of the section
indexS = sections.index(d)
maxOrder = 0
if len(localIndexArr[indexS]) == 0:
localIndexArr[indexS] = ["\n"]
# walk through the folders with all the cards
for root, dirs, files in os.walk(folder+"/"+d):
for file in files:
if file.endswith(".md"):
fileName = os.path.join(root, file)
# ignore subsections (.md files that start with _)
if file[0] != "_":
print(" > Generating header for: " + fileName)
# save order and legacy section
order = save_tag(localroot, root, file, "card_order")
legacy_from = save_legacy_from(localroot, root, file)
title = save_tag(localroot, root, file, "title")
description = save_tag(localroot, root, file, "description")
# extract the title from the QMS metadata
qms_yml = False
if "qms" in root:
if exists(os.path.join(root, file[:-3] + ".yml")):
title = save_tag(localroot, root, file[:-3] + ".yml", "title")
prepare_qms(localroot, root, file)
qms_yml = True
else:
print("QMS document is not formatted properly.")
# remove the previous header
n = remove_header(localroot, root, file)
# generate a permalink
permalink = "/" + root + "/"
# generate the shortcut
shortcut = re.sub(folder, '', root)
# remove the first /
shortcut = shortcut[1:]
# replace the / with a :
shortcut = re.sub('/', ':', shortcut)
if len(order) > 0:
# find the maximum of existing orders
if folderFlag:
if len(orderArr[indexS]) > 0:
maxOrder = max(orderArr[indexS])
else:
maxOrder = 0
# after determining the max order, set the folder flag to False to avoid another entry into the same block of code
folderFlag = False
tmp = orderArr[indexS].copy()
tmp.append(maxOrder + int(order))
orderArr[indexS] = tmp
else:
orderArr[indexS] = []
# generate the header for each card
header = generate_header(folder, permalink, shortcut, order, legacy_from, title, description, qms_yml)
# add autogenerated links to whitelist
whiteList += generate_whitelist_entry(folder, permalink, shortcut)
# add the header properly speaking
line_prepender(fileName, header)
# open file and get the title after the header
if "qms" in root:
header_offset = 3
else:
header_offset = 1
if not qms_yml:
count = 0
title = ""
bp = n + header_offset
with open(fileName, 'r') as f:
for line in f:
count += 1
if count == bp:
if len(line) > 2:
title = line
break
else:
bp += 1
# remove first and last chars
title = title.rstrip("\n\r")
title = title[2:]
localIndexArr[indexS].append(build_link(title, root))
# output
print(" + New header added.")
print("-----------------------")
# ordering of cards
for d in sections:
indexS = sections.index(d)
# join all subcategories to the index
# if all subcategories have a predefined order
if len(orderArr[indexS]) == len(localIndexArr[indexS])-1 and len(orderArr[indexS]) > 0:
print("")
X = localIndexArr[indexS][1:]
Y = orderArr[indexS]
localIndexArr[indexS] = [x for _, x in sorted(zip(Y, X))]
# natural sorting otherwise
else:
localIndexArr[indexS] = natsorted(localIndexArr[indexS])
print(localIndexArr)
# determine the index
k = 0
for s in sections:
index += build_section_start(s.replace("-", " ").capitalize(), s)
index += ''.join(localIndexArr[k])
index += build_section_end()
k += 1
# close the container
index += "\n</div>"
## add link to return to main index
index += """<br><center><a href="{{ '/' | relative_url }}">go back</a></center>"""
index += """<br><center><a href="{{ '/cards' | relative_url }}">Overview of all HowTo cards</a></center>"""
# output the index
#print(index)
# Read in the file
indexFile = "cards.md"
filedata = ""
with open(indexFile, 'r') as file :
for line in file:
filedata += line
# stop reading once the index place holder has been reached
if re.search("<!-- index -->", line):
filedata += "[[ index ]]"
break
# Replace the target string
filedata = filedata.replace('[[ index ]]', index)
# Write the file out again
with open(indexFile, 'w') as file:
file.write(filedata)
print("\n > New index generated and saved in " + indexFile)
# write link whitelist out
whiteListFile = ".ci/whitelist.txt"
if Path(whiteListFile).exists():
with open(whiteListFile, 'r') as file :
for line in file:
whiteList += line
with open(whiteListFile, 'w') as file:
file.write(whiteList)
save.save_index(ind, "cards.md")
save.save_whitelist(wl, ".ci/whitelist.txt")