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orcid_cv.py
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import os
import xmltodict
import json
import requests
from copy import deepcopy
from reportlab.pdfgen import canvas
from reportlab.lib.pagesizes import letter
from reportlab.pdfbase.ttfonts import TTFont
from reportlab.pdfbase import pdfmetrics
from reportlab.platypus import Paragraph, Spacer, Table, SimpleDocTemplate, Image
from reportlab.lib.enums import TA_LEFT, TA_RIGHT
from reportlab.lib.styles import ParagraphStyle
from reportlab.lib import colors
from datetime import datetime
package_directory = os.path.dirname(os.path.abspath(__file__))
class HyperlinkedImage(Image, object):
# https://stackoverflow.com/questions/18114820/is-it-possible-to-get-a-flowables-coordinate-position-once-its-rendered-using
def __init__(self, filename, hyperlink=None, width=None, height=None, kind='direct', mask='auto', lazy=1):
super(HyperlinkedImage, self).__init__(filename, width, height, kind, mask, lazy)
self.hyperlink = hyperlink
def drawOn(self, canvas, x, y, _sW=0):
if self.hyperlink: # If a hyperlink is given, create a canvas.linkURL()
x1 = x
y1 = y
x2 = x1 + self._width
y2 = y1 + self._height
canvas.linkURL(url=self.hyperlink, rect=(x1, y1, x2, y2), thickness=0, relative=1)
super(HyperlinkedImage, self).drawOn(canvas, x, y, _sW)
def load_xml(xml_path):
with open(xml_path, encoding='utf-8') as xd:
xml_dict = xmltodict.parse(xd.read())
# Remove top_level
if len(xml_dict.keys()) == 1:
return list(xml_dict.values())[0]
else:
raise Exception('XML dictionary has more than one top-level key')
def list_works(orcid_dir):
work_xml_list = os.listdir(os.path.join(orcid_dir, 'works'))
for (i, w) in enumerate(work_xml_list):
xml_dict = load_xml(os.path.join(orcid_dir, 'works', w))
print(str(i) + ': ' + xml_dict['work:work']['work:title']['common:title'] + ' (' + xml_dict['work:work']['@put-code'] + ')')
def get_recursive_key(input_dict, *keys):
if not isinstance(input_dict, dict):
raise TypeError('first argument must be a dict.')
if len(keys) == 0 or not all([isinstance(k, str) for k in keys]):
raise TypeError('Keys must all be of type "str".')
_dict = input_dict
for key in keys:
if _dict.__contains__(key) and not _dict[key] is None:
_dict = _dict[key]
else:
print('Could not find: ' + '-'.join(keys) + ' in item #' + input_dict['@put-code'])
return ''
return _dict
def load_affiliation(affiliation_path):
# Load and enter top level xml
affiliation_xml = load_xml(affiliation_path)
# Extract common info
affiliation_dict = {'organization': get_recursive_key(affiliation_xml, 'common:organization', 'common:name'),
'department': get_recursive_key(affiliation_xml, 'common:department-name'),
'role': get_recursive_key(affiliation_xml, 'common:role-title'),
'start_date': get_recursive_key(affiliation_xml, 'common:start-date', 'common:year'),
'end_date': get_recursive_key(affiliation_xml, 'common:end-date', 'common:year')}
# Make date str
if affiliation_dict['end_date'] == '':
affiliation_dict['date_range'] = affiliation_dict['start_date'] + ' - present'
else:
affiliation_dict['date_range'] = affiliation_dict['start_date'] + ' - ' + affiliation_dict['end_date']
return affiliation_dict
def load_work(work_path):
# Convert .xml to dictionary. Generically loads fields, styles determine later display
in_work_dict = load_xml(work_path)
out_work_dict = {'type': in_work_dict['work:type'], # This field is used for sorting entries and defines other behavior
'title': get_recursive_key(in_work_dict, 'work:title', 'common:title'),
'subtitle': '',
'journal': get_recursive_key(in_work_dict, 'work:journal-title'),
'doi': get_recursive_key(in_work_dict, 'common:url'),
'year': get_recursive_key(in_work_dict, 'common:publication-date', 'common:year'),
'month': get_recursive_key(in_work_dict, 'common:publication-date', 'common:month'),
'authors': get_recursive_key(in_work_dict, 'work:contributors', 'work:contributor')}
# Check empty date for later sorting
if out_work_dict['year'] == '':
out_work_dict['year'] = 0
if out_work_dict['month'] == '':
out_work_dict['month'] = 0
# Extract authors from list
if not out_work_dict['authors'] == '':
if isinstance(out_work_dict['authors'], dict):
out_work_dict['authors'] = [out_work_dict['authors']['work:credit-name']]
elif isinstance(out_work_dict['authors'], list):
out_work_dict['authors'] = [i['work:credit-name'] for i in out_work_dict['authors']]
# Journal / repository
if out_work_dict['type'] == 'preprint':
if not out_work_dict['doi'] == '':
try:
print('Trying to find host repository for article: ' + out_work_dict['title'])
doi_data = requests.get(out_work_dict['doi'])
url = doi_data.url
start_idx = url.find('www.') + 4
slash_idx = url.find('/', start_idx)
url = url[start_idx:slash_idx]
out_work_dict['journal'] = url[:url.rfind('.')]
if 'rxiv' in out_work_dict['journal']:
out_work_dict['journal'] = out_work_dict['journal'].replace('rxiv', 'Rxiv')
except:
print('Could not lookup preprint: ' + out_work_dict['title'])
elif out_work_dict['type'] == 'software':
out_work_dict['subtitle'] = get_recursive_key(in_work_dict, 'work:title', 'common:subtitle')
return out_work_dict
def load_funding(funding_path):
in_funding_dict = load_xml(funding_path)
out_funding_dict = {'title': get_recursive_key(in_funding_dict, 'funding:title', 'common:title'),
'role': get_recursive_key(in_funding_dict, 'funding:organization-defined-type'),
'org': get_recursive_key(in_funding_dict, 'common:organization', 'common:name'),
'start_year': get_recursive_key(in_funding_dict, 'common:start-date', 'common:year'),
'end_year': get_recursive_key(in_funding_dict, 'common:end-date', 'common:year'),
'value': get_recursive_key(in_funding_dict, 'funding:amount', '#text')}
return out_funding_dict
def load_review(review_path):
in_review_dict = load_xml(review_path)
# Parse IISN
issn = in_review_dict['peer-review:review-group-id'][5:]
r = requests.get(f"https://portal.issn.org/resource/ISSN/{issn}")
potential_name = ''
for l in r.iter_lines():
line = str(l)
if issn in line:
potential_name = line
idx = potential_name.find('|')
potential_name = potential_name[idx+2:-5]
break
if potential_name == '':
print(f"Could not identify ISSN {issn}")
# Make dict
out_review_dict = {'year': get_recursive_key(in_review_dict, 'peer-review:review-completion-date', 'common:year'),
'role': get_recursive_key(in_review_dict, 'peer-review:review-type'),
'org': potential_name.title()}
return out_review_dict
def extract_orcid_info(orcid_dir):
# First check if there is an ORCID.json file
if os.path.isfile(os.path.join(orcid_dir, 'ORCID.json')):
print('Loading ORCID dict from local json.')
with open(os.path.join(orcid_dir, 'ORCID.json')) as f:
return json.load(f)
# Personal info
personal_info = load_xml(os.path.join(orcid_dir, "person.xml"))
personal = {'lastname': get_recursive_key(personal_info, 'person:name', 'personal-details:family-name'),
'givenname': get_recursive_key(personal_info, 'person:name', 'personal-details:given-names'),
'links': {'ORCID': 'https://orcid.org/' + get_recursive_key(personal_info, 'person:name', '@path')}}
# Workout other elements of name
personal['fullname'] = personal['givenname'] + ' ' + personal['lastname']
personal['name-short'] = initalize_name(personal['fullname'])
personal['firstname'] = personal['fullname'][0:personal['fullname'].find(' ')]
# Extract links
if 'researcher-url:researcher-urls' in personal_info.keys():
# Assign so it's not insanely long
link_list = get_recursive_key(personal_info, 'researcher-url:researcher-urls', 'researcher-url:researcher-url')
for i in range(len(link_list)):
personal['links'][link_list[i]['researcher-url:url-name']] = link_list[i]['researcher-url:url']
# Get primary email
personal['email'] = [e['email:email'] for e in personal_info['email:emails']['email:email'] if e['@primary'] == 'true'][0]
# Parse XML folders to make dictionaries
employment_dict = folder_to_dict(os.path.join(orcid_dir, 'affiliations', 'employments'), load_affiliation)
education_dict = folder_to_dict(os.path.join(orcid_dir, 'affiliations', 'educations'), load_affiliation)
work_dict = folder_to_dict(os.path.join(orcid_dir, 'works'), load_work)
funding_dict = folder_to_dict(os.path.join(orcid_dir, 'fundings'), load_funding)
review_dict = folder_to_dict(os.path.join(orcid_dir, 'peer_reviews'), load_review)
# Combine
out_dict = {'personal': personal,
'work': work_dict,
'employment': employment_dict,
'education': education_dict,
'funding': funding_dict,
'reviews': review_dict}
# Write the json
print('Saving local json.')
with open(os.path.join(orcid_dir, 'ORCID.json'), 'w') as fp:
json.dump(out_dict, fp, indent = 4)
return out_dict
def folder_to_dict(path, load_fun: callable) -> dict:
_dict = {}
xml_list = os.listdir(path)
for x in xml_list:
_dict[x[:-4]] = load_fun(os.path.join(path, x))
return _dict
def dict_to_list(input_dict: dict) -> list:
return [input_dict[k] for k in input_dict.keys()]
def initalize_name(input_str):
str_split = input_str.split(' ')
for i in range(len(str_split) - 1):
if '.' in str_split[i] and str_split[i][1] == '.':
continue
else:
str_split[i] = str_split[i][0] + '.'
output_str = ''.join([*str_split[:-1], ' ', str_split[-1]])
return output_str
def embolden_authors(person, author_list):
for (i, a) in enumerate(author_list):
if person['lastname'] in a:
embolden = False
if person['fullname'] in a:
embolden = True
elif person['name-short'] in a:
embolden = True
elif person['firstname'] + ' ' + person['lastname'] in a:
embolden = True
elif person['firstname'][0] + '. ' + person['lastname'] in a:
embolden = True
else:
print('Did not embolden: ' + a)
if embolden:
author_list[i] = ''.join(['<b>', a, '</b>'])
return author_list
def add_equal_author(author_list: list[str], num_first: int = 0, num_last: int = 0):
num_authors = len(author_list)
for i in range(1, len(author_list) + 1):
if i <= num_first:
author_list[i-1] += '*'
if i > num_authors-num_last:
author_list[i-1] += '*'
def get_column_widths(config, section_type):
ratio = 1
table_width = int(config['pagesize'][0] - (config['margin'] * 2))
if config['style'] == 'greenspon-default':
if section_type == 'work':
ratio = 7
elif section_type == 'affiliation':
ratio = 6
elif section_type == 'person':
ratio = 3.5
else:
ValueError('what')
else:
ValueError('Invalid style')
right_col_width = round(table_width / ratio)
return [table_width - right_col_width, right_col_width]
def make_affiliation_table(config, affiliation, section_heading = ''):
if config['style'] == 'greenspon-default':
if section_heading == '':
table_data = [[Paragraph(affiliation['role'], style = config['item_title_style']), Paragraph(affiliation['date_range'], style = config['item_date_style'])],
[Paragraph(affiliation['organization'] + ', ' + affiliation['department'], style = config['item_body_style']), '']]
table_style = [('VALIGN', (0, 0), (-1, -1), 'TOP'),
('NOSPLIT', (0, 0), (-1, -1))] # ('GRID', (0,0), (-1, -1), 0.5, colors.gray)
else:
table_data = [[Paragraph(section_heading, style = config['section_style']), ''],
['', ''], # Padding for large config['section_style']
[Paragraph(affiliation['role'], style = config['item_title_style']), Paragraph(affiliation['date_range'], style = config['item_date_style'])],
[Paragraph(affiliation['organization'] + ', ' + affiliation['department'], style = config['item_body_style']), '']]
table_style = [('SPAN', (0, 0), (-1, 0)),
('LINEBELOW', (0, 1), (-1, 1), 2, colors.gray),
('VALIGN', (0, 0), (-1, -1), 'TOP'),
('NOSPLIT', (0, 0), (-1, -1))]
else:
ValueError('Invalid style')
return table_data, table_style
def make_work_table(config, work_title, work_body, work_date, section_heading = ''):
# Show as empty
if work_date == 0:
work_date = ''
if config['style'] == 'greenspon-default':
if section_heading == '':
table_data = [[Paragraph(work_title, style = config['item_title_style']), Paragraph(work_date, style = config['item_date_style'])],
[work_body, '']]
table_style = [('VALIGN', (0, 0), (-1, -1), 'TOP'),
('NOSPLIT', (0, 0), (-1, -1))] # ('GRID', (0,0), (-1, -1), 0.5, colors.gray)
else:
table_data = [[Paragraph(section_heading, style = config['section_style']), ''],
['', ''], # Padding for large config['section_style']
[Paragraph(work_title, style = config['item_title_style']), Paragraph(work_date, style = config['item_date_style'])],
[work_body, '']]
table_style = [('SPAN', (0, 0), (-1, 0)),
('LINEBELOW', (0, 1), (-1, 1), 2, colors.gray),
('VALIGN', (0, 0), (-1, -1), 'TOP'),
('NOSPLIT', (0, 0), (-1, -1))]
else:
ValueError('Invalid style')
return table_data, table_style
def make_funding_table(config, fund, section_heading = ''):
if config['style'] == 'greenspon-default':
if section_heading == '':
table_data = [[Paragraph(fund['title'], style = config['item_title_style']), Paragraph(fund['start_year'], style = config['item_date_style'])],
[fund['org'], '']]
table_style = [('VALIGN', (0, 0), (-1, -1), 'TOP'),
('NOSPLIT', (0, 0), (-1, -1))] # ('GRID', (0,0), (-1, -1), 0.5, colors.gray)
else:
table_data = [[Paragraph(section_heading, style = config['section_style']), ''],
['', ''], # Padding for large config['section_style']
[Paragraph(fund['title'], style = config['item_title_style']), Paragraph(fund['start_year'], style = config['item_date_style'])],
[fund['org'], '']]
table_style = [('SPAN', (0, 0), (-1, 0)),
('LINEBELOW', (0, 1), (-1, 1), 2, colors.gray),
('VALIGN', (0, 0), (-1, -1), 'TOP'),
('NOSPLIT', (0, 0), (-1, -1))]
else:
ValueError('Invalid style')
return table_data, table_style
def process_external_links(link_dict):
link_list = []
for (k, v) in link_dict.items():
im_path = os.path.join(package_directory, 'external_link_img', k + '.png')
link_list.append(HyperlinkedImage(im_path, hyperlink = v, height = 15, width = 15))
return link_list
def add_person_section(elements, orcid_dict, config):
if config['style'] == 'greenspon-default':
# Format table
column_widths = get_column_widths(config, 'person')
info = dict_to_list(orcid_dict['employment'])
info = sorted(info, key = lambda v: int(v['start_date']), reverse = True)
fullname = orcid_dict['personal']['fullname']
person_summary = ('<br/>' +
info[0]['role'] + '<br/>' +
info[0]['organization'] + '<br/>' +
orcid_dict['personal']['email'])
table_data = [[Paragraph(fullname, style = config['person_title_style']), Paragraph(person_summary, style = config['person_summary_style'])]]
table_style = [('NOSPLIT', (0, 0), (-1, -1)),
('VALIGN', (0, 0), (-1, -1), 'TOP')]
# Convert to table
t = Table(table_data, colWidths = column_widths)
t.setStyle(table_style)
# Append
elements.append(t)
elements.append(Spacer(0, -15))
# Add links
link_list = process_external_links(orcid_dict['personal']['links'])
t = Table([link_list], colWidths = [20] * 1, hAlign='LEFT')
t.setStyle(table_style)
elements.append(t)
elements.append(Spacer(0, config['item_spacing']))
else:
ValueError('Nope')
def add_affiliation_section(elements, orcid_dict: dict, config, heading, affiliation_type):
# Compute column size
column_widths = get_column_widths(config, 'affiliation')
# Get correct affiliation type
if not orcid_dict.__contains__(affiliation_type):
return ValueError('Dict does not contain affiliation type: ' + affiliation_type)
# Sort the affiliations
affiliations = dict_to_list(orcid_dict[affiliation_type])
affiliations = sorted(affiliations, key = lambda v: int(v['start_date']), reverse = True)
# Iterate through affiliations and make tables
is_heading = True
for af in affiliations:
# prepare table
if is_heading:
table_data, table_style = make_affiliation_table(config, af, section_heading = heading)
is_heading = False
else:
table_data, table_style = make_affiliation_table(config, af)
# Convert to table
t = Table(table_data, colWidths = column_widths)
t.setStyle(table_style)
# Append
elements.append(t)
elements.append(Spacer(0, config['item_spacing']))
def add_work_section(elements, orcid_dict, config, heading, search_str):
# Compute column size
column_widths = get_column_widths(config, 'work')
if isinstance(search_str, str):
search_str = [search_str]
# Get subset of publications
works = dict_to_list(orcid_dict['work'])
works = [w for w in works if w['type'] in search_str]
if works == []:
return ValueError('No matching works for: ' + search_str)
works = sorted(works, key = lambda v: int(v['year']) * 1000 + int(v['month']), reverse = True) # Sort by year then month
# Iterate through list and make tables
is_heading = True
for work in works:
work_date = work['year']
work_journal = work['journal']
# Process title
work_title = work['title']
if '‐' in work_title: # Replace bad character
work_title = work_title.replace('‐', '-')
# Swap journal and date for software
if work['type'] == 'software':
work_journal = work['subtitle']
work_date = work['journal']
work['subtitle'] = '' # Prevent duplications from custom subtitle fields
# Process author
author_cat = ''
if not work['authors'] == []:
author_list = work['authors']
if config['initalize_authors']:
author_list = [initalize_name(i) for i in author_list]
if config['embolden_author']:
author_list = embolden_authors(orcid_dict['personal'], author_list)
if len(author_list) > 1:
author_list[-1] = 'and ' + author_list[-1]
if len(author_list) > 2:
author_cat = ', '.join(author_list)
if '‐' in author_cat: # Replace bad character
author_cat = author_cat.replace('‐', '-')
# Process DOI/link
doi_str = work['doi']
if doi_str == '': # Remove "," and go straight to author line
work_str = work_journal
else:
if 'doi.org/' in doi_str:
idx = doi_str.find('doi.org/')
short_doi = doi_str[idx + 8:]
doi_str = '<link href="' + 'https://www.doi.org/' + short_doi + '">' + 'DOI: <u>' + short_doi + ' </u></link>'
elif 'github.com/' in doi_str:
idx = doi_str.find('github.com/')
short_doi = doi_str[idx + 11:]
doi_str = '<link href="' + 'https://www.github.com/' + short_doi + '">' + 'GitHub: <u>' + short_doi + ' </u></link>'
else:
doi_str = '<link href="' + doi_str + '"><u>' + doi_str + ' </u></link>'
work_str = work_journal + ', ' + doi_str
# Add subtitle
if work['subtitle'] != '':
work_str = work_str + ', ' + work['subtitle']
# Add formatting to work str
work_body = Paragraph(work_str + '<br/>' + author_cat, style = config['item_body_style'])
# prepare table
if is_heading:
table_data, table_style = make_work_table(config, work_title, work_body, work_date, section_heading = heading)
is_heading = False
else:
table_data, table_style = make_work_table(config, work_title, work_body, work_date, section_heading = '')
# Convert to table
t = Table(table_data, colWidths = column_widths)
t.setStyle(table_style)
# Append
elements.append(t)
elements.append(Spacer(0, config['item_spacing']))
def add_funding_section(elements, orcid_dict, config, heading):
# Compute column size
column_widths = get_column_widths(config, 'affiliation')
# Sort the fund
fund = dict_to_list(orcid_dict['funding'])
fund = sorted(fund, key = lambda v: int(v['start_year']), reverse = True)
# Iterate through fund and make tables
is_heading = True
for f in fund:
# prepare table
if is_heading:
table_data, table_style = make_funding_table(config, f, section_heading = heading)
is_heading = False
else:
table_data, table_style = make_funding_table(config, f)
# Convert to table
t = Table(table_data, colWidths = column_widths)
t.setStyle(table_style)
# Append
elements.append(t)
elements.append(Spacer(0, config['item_spacing']))
class FooterCanvas(canvas.Canvas):
left_str: str = ""
def __init__(self, *args, **kwargs):
canvas.Canvas.__init__(self, *args, **kwargs)
self.pages = []
def showPage(self):
self.pages.append(dict(self.__dict__))
self._startPage()
def save(self):
page_count = len(self.pages)
for page in self.pages:
self.__dict__.update(page)
self.draw_canvas(page_count)
canvas.Canvas.showPage(self)
canvas.Canvas.save(self)
def draw_canvas(self, page_count):
page = "Page %s of %s" % (self._pageNumber, page_count)
x = 100
self.saveState()
self.setStrokeColorRGB(0, 0, 0)
self.setLineWidth(0.5)
self.line(50, 78, letter[0] - 50, 78)
self.setFont('Helvetica', 9)
self.drawString(letter[0]-x, 65, page)
self.drawString(50, 65, datetime.today().strftime("%d-%b-%Y"))
self.restoreState()
def make_document_config(style):
if style.lower() == 'greenspon-default':
# Enable TTF fonts
# pdfmetrics.registerFont(TTFont('GillSans', 'GIL_____.TTF'))
# pdfmetrics.registerFont(TTFont('GillSansBold', 'GILB____.TTF'))
# pdfmetrics.registerFontFamily('GillSans', normal = 'GillSans', bold = 'GillSansBold')
config = {'style': style.lower(),
'pagesize': letter,
'margin': 50,
'item_spacing': 5,
'initalize_authors': True,
'embolden_author': True,
'initalize_primary_author': True,
'person_title_style': ParagraphStyle('PersonTitle', alignment = TA_LEFT, fontSize = 22, fontName = 'Helvetica-Bold'),
'person_summary_style': ParagraphStyle('PersonSummary', alignment = TA_RIGHT, fontSize = 9, fontName = 'Helvetica'),
'section_style': ParagraphStyle('SectionTitle', alignment = TA_LEFT, fontSize = 18, fontName = 'Helvetica-Bold'),
'item_title_style': ParagraphStyle('ItemTitle', alignment = TA_LEFT, fontSize = 11, fontName = 'Helvetica-Bold'),
'item_date_style': ParagraphStyle('ItemDate', alignment = TA_RIGHT, fontSize = 9, fontName = 'Helvetica-Bold'),
'item_body_style': ParagraphStyle('ItemBody', alignment = TA_LEFT, fontSize = 9, fontName = 'Helvetica', underlineWidth = 1,
underlineOffset = '-0.1*F')}
else:
ValueError('Invalid style')
return config
def quick_build(orcid_dir, output_fname, style = 'greenspon-default'):
orcid_dict = extract_orcid_info(orcid_dir)
config = make_document_config(style)
doc_title = orcid_dict['personal']['fullname'] + ' - CV'
doc = SimpleDocTemplate(output_fname,
pagesize = letter,
leftMargin = config['margin'],
rightMargin = config['margin'],
topMargin = config['margin'],
bottomMargin = config['margin'],
title = doc_title)
elements = []
add_person_section(elements, orcid_dict, config)
add_affiliation_section(elements, orcid_dict, config, 'Employment', 'employment')
add_affiliation_section(elements, orcid_dict, config, 'Education', 'education')
add_work_section(elements, orcid_dict, config, 'Research Publications', 'journal-article')
add_work_section(elements, orcid_dict, config, 'Talks', 'lecture-speech')
add_work_section(elements, orcid_dict, config, 'Preprints', 'preprint')
doc.build(elements)
print('Success!')