diff --git a/.ci/generateIndex.py b/.ci/generateIndex.py
index b09107308449bb917b322e95a5c8edb901ccf3e9..b60cac50d05d2ca84d52ab2c06884907f365b7a0 100644
--- a/.ci/generateIndex.py
+++ b/.ci/generateIndex.py
@@ -1,7 +1,9 @@
import os, re
from os import path
+from os.path import exists
from natsort import natsorted
from pathlib import Path
+import yaml
def line_prepender(filename, line):
with open(filename, 'r+') as f:
@@ -9,6 +11,16 @@ def line_prepender(filename, line):
f.seek(0, 0)
f.write(line.rstrip('\r\n') + '\n' + content)
+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
@@ -20,16 +32,13 @@ def build_link(title, href):
return f'\t\t\t<li><a href="{href}">{title}</a></li>\n'
-def root_handbook(href):
+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()
- return href
-
-def root_lab(href):
# remove sym link reference in href
if ('lab-software' in href):
href = href.replace('lab-software', 'lab').strip()
@@ -37,6 +46,14 @@ def root_lab(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
@@ -50,6 +67,9 @@ def build_section_start(title, shortcut):
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'
@@ -62,12 +82,23 @@ def save_tag(localroot, root, filename, tag):
length_tag = len(tag)
- 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:]
- break
+ 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)
@@ -84,7 +115,8 @@ def get_ignore():
"assets",
"help.md",
"index.md",
- "pagination.md"
+ "pagination.md",
+ ".gitkeep",
]
def save_legacy_from(localroot, root, filename):
@@ -149,7 +181,19 @@ def remove_header(localroot, root, filename):
return n
-def generate_header(folder, permalink, shortcut, order, legacy_from, title, description):
+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:
@@ -157,18 +201,13 @@ def generate_header(folder, permalink, shortcut, order, legacy_from, title, desc
header += "layout: page\n"
header += "permalink: " + permalink + "\n"
- header += "shortcut: " + root_handbook(shortcut) + "\n"
+ header += "shortcut: " + root_href(shortcut) + "\n"
header += "redirect_from:\n"
header += " - /cards/" + shortcut + "\n"
header += " - /" + folder + "/cards/" + shortcut + "\n"
- # special case of handbook
- if "handbook-annexes" in permalink or "handbook-additional" in permalink:
- header += " - /cards/" + root_handbook(shortcut) + "\n"
- header += " - /" + folder + "/cards/" + root_handbook(shortcut) + "\n"
- # separate lab section
- if "lab-software" in permalink or "lab-equipment" in permalink or "lab-hsa" in permalink:
- header += " - /cards/" + root_lab(shortcut) + "\n"
- header += " - /" + folder + "/cards/" + root_lab(shortcut) + "\n"
+
+ # generate specific redirects
+ header = element_header(" - ", shortcut, header)
# include the legacy section in the redirect_from section
if len(legacy_from) > 0:
@@ -188,6 +227,10 @@ def generate_header(folder, permalink, shortcut, order, legacy_from, title, desc
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):
@@ -195,16 +238,40 @@ def generate_whitelist_entry(folder, permalink, shortcut):
wl_entry += "/?" + shortcut + "\n"
wl_entry += "/cards/" + shortcut + "\n"
wl_entry += "/" + folder + "/cards/" + shortcut + "\n"
- if "handbook-annexes" in permalink or "handbook-additional" in permalink:
- wl_entry += "/cards/" + root_handbook(shortcut) + "\n"
- wl_entry += "/" + folder + "/cards/" + root_handbook(shortcut) + "\n"
- # separate lab section
- if "lab-software" in permalink or "lab-equipment" in permalink or "lab-hsa" in permalink:
- wl_entry += "/cards/" + root_lab(shortcut) + "\n"
- wl_entry += "/" + folder + "/cards/" + root_lab(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()
@@ -212,17 +279,17 @@ localroot = os.getcwd()
ignore = get_ignore()
# generate the index properly speaking
-cardDirs = ["internal", "external", "policies"]
+cardDirs = ["internal", "external"]
sections = []
# determine first the directories
for direct in cardDirs:
- if path.isdir(direct):
+ 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:
+ if d[0] != "." and d not in ignore and has_subdirs(direct + "/" + d):
sections.append(d)
sections = list(set(sections))
@@ -246,7 +313,7 @@ for folder in cardDirs:
dirs = natsorted(dirs)
for d in dirs:
- if d[0] != "." and d not in ignore:
+ 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"
@@ -273,6 +340,16 @@ for folder in cardDirs:
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)
@@ -305,7 +382,7 @@ for folder in cardDirs:
orderArr[indexS] = []
# generate the header for each card
- header = generate_header(folder, permalink, shortcut, order, legacy_from, title, description)
+ 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)
@@ -314,23 +391,29 @@ for folder in cardDirs:
line_prepender(fileName, header)
# open file and get the title after the header
- count = 0
- title = ""
- bp = n + 1
-
- 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:]
+ 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))
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d960dae7c6d6b4728082dda94b7aae702a061a09..01a1a01873a9091267c14a74e8ea92a102680140 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -24,7 +24,7 @@ prepare:index:
- if: $CI_COMMIT_REF_NAME
- if: '$CI_PIPELINE_SOURCE == "merge_request_event" && $CI_COMMIT_MESSAGE !~ /tmpBranch/ && $CI_COMMIT_MESSAGE !~ /Update index/'
before_script:
- - pip install natsort
+ - pip install -r requirements.txt
script:
- python .ci/generateIndex.py
- mkdir .tmp
diff --git a/assets/js/box_hider.js b/assets/js/box_hider.js
index 48aa48bdb0009749a279c59ef4143a08cc858af6..bd20a7d4b6f34bac94d7a42bc5e398620a1c4805 100644
--- a/assets/js/box_hider.js
+++ b/assets/js/box_hider.js
@@ -24,7 +24,7 @@ window.boxHider = (function() {
function GetSelectedBoxElement(id) {
var allBoxesArray = GetAllBoxElementsArray();
// note: handbook and lab are actually grouped sections
- if (id.startsWith('handbook') || id.startsWith('lab')) {
+ if (id.startsWith('handbook') || id.startsWith('lab') || id.startsWith('qms')) {
return true;
} else {
var element = document.getElementById(id);
@@ -96,6 +96,14 @@ window.boxHider = (function() {
ShowElement(box);
}
});
+ } else if (boxId.startsWith('qms')) {
+ allBoxes.map(function(box) {
+ if (!box.id.startsWith('qms')) {
+ HideElement(box);
+ } else {
+ ShowElement(box);
+ }
+ });
} else {
allBoxes.map(function(box) {
if (box != selectedBox) {
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000000000000000000000000000000000000..594a2568e1ee92ed7e0e59b474401de45016b358
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,15 @@
+appnope~=0.1.2
+backcall~=0.2.0
+decorator~=5.1.0
+jedi~=0.18.1
+matplotlib-inline~=0.1.3
+natsort~=7.1.1
+parso~=0.8.3
+pexpect~=4.8.0
+pickleshare~=0.7.5
+prompt-toolkit~=3.0.24
+ptyprocess~=0.7.0
+Pygments~=2.10.0
+PyYAML~=6.0
+traitlets~=5.1.1
+wcwidth~=0.2.5