The Kitchin Research Group

(org-add-link-type
 "comment"
 ;;  follow function
(lambda (linkstring)
   (let ((elm (org-element-context))
         (use-dialog-box nil))
     (when (y-or-n-p "Delete comment? ")
       (setf (buffer-substring
              (org-element-property :begin elm)
              (org-element-property :end elm))
             (cond
              ((org-element-property :contents-begin elm)
               (buffer-substring
                (org-element-property :contents-begin elm)
                (org-element-property :contents-end elm)))
              (t
               ""))))))
 ;; format function
 (lambda (path description format)
   (let* ((data (read (concat "(" path ")")))
          (head (car data))
          (plist (cdr data)))
     (cond
      ((eq format 'html)
       (format "<font color=\"red\"><abbr title=\"%s\" color=\"red\">COMMENT</abbr></font> %s" path (or description "")))
      ((eq format 'latex)
       (format "\\todo%s{%s}%s"
               (if (-contains? data :inline) "[inline]" "")
               (mapconcat (lambda (s)
                            (format "%s" s))
                          (-remove-item :inline data) " ")
               (if description (format "{%s}" description) "")))))))

(defun add-comment (begin end &optional arg)
  "Comment the region. With a prefix ARG, make the comment inline."
  (interactive (list (region-beginning)
                     (region-end)
                     current-prefix-arg))
  (let ((inline (if arg ":inline " "")))
        (if (region-active-p)
            (let ((selected-text (buffer-substring begin end)))
              (setf (buffer-substring begin end)
                    (format
                     "[[comment:%s%s][%s]]"
                     inline
                     (read-input "Comment: ") selected-text)))
          (insert (format
                   "[[comment:%s%s]]"
                   inline
                   (read-input "Comment: "))))))

def get_author_link(EID):
    results = get_abstract_info(EID)
    authors = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}authors')
    if authors is None:
        return 'No authors found'
    s = []

    for author in authors:
        name = author.find('{http://www.elsevier.com/xml/ani/common}indexed-name').text
        auid = author.attrib['auid']
        s += ['<a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId={0}">{1}</a>'.format(auid, name)]

    return ', '.join(s)

from scopus_xml import *
print get_author_link('2-s2.0-84896759135')
print get_author_link('2-s2.0-84901638552')

def get_journal_link(EID):
    results = get_abstract_info(EID)
    coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')

    journal = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}publicationName').text
    sid = coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}source-id').text
    s = '<a href="http://www.scopus.com/source/sourceInfo.url?sourceId={sid}">{journal}</a>'

    return s.format(sid=sid, journal=journal)

from scopus_xml import *
print get_journal_link('2-s2.0-84901638552')

def get_doi_link(EID):
    results = get_abstract_info(EID)
    coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')
    doi = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}doi')
    if doi is not None: doi = doi.text
    s = '<a href="https://doi.org/{doi}">doi:{doi}</a>'
    return s.format(doi=doi)

from scopus_xml import *
print get_doi_link('2-s2.0-84901638552')

def get_abstract_link(EID):
    results = get_abstract_info(EID)
    coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')

    data = get_abstract_info(EID)

    title = coredata.find('{http://purl.org/dc/elements/1.1/}title').text.encode('utf-8')
    link = coredata.find("./{http://www.elsevier.com/xml/svapi/abstract/dtd}link/[@rel='scopus']").attrib['href'].encode('utf-8')
    s = '<a href="{link}">{title}</a>'
    return s.format(link=link, title=title)

from scopus_xml import *
print get_abstract_link('2-s2.0-84901638552')

def get_cite_img_link(EID):
    results = get_abstract_info(EID)
    coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')
    doi = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}doi')
    if doi is not None: doi = doi.text
    s = '<img src="http://api.elsevier.com/content/abstract/citation-count?doi={doi}&httpAccept=image/jpeg&apiKey={apikey}"></img>'

    return s.format(doi=doi, apikey=MY_API_KEY, cite_link=None)

from scopus_xml import *
print get_cite_img_link('2-s2.0-84901638552')

def get_html_citation(EID):
    results = get_abstract_info(EID)
    coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')
    s = '{authors}, <i>{title}</i>, {journal}, <b>{volume}{issue}</b>, {pages}, ({year}), {doi}, {cites}.'

    issue = ''
    if coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}issueIdentifier') is not None:
        issue = '({})'.format(    coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}issueIdentifier').text)

    volume = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}volume')
    if volume is not None:
        volume = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}volume').text
    else:
        volume = 'None'

    pages = ''
    if coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}pageRange') is not None:
        pages = 'p. ' + coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}pageRange').text
    elif coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}article-number') is not None:
        pages = coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}article-number').text
    else:
        pages = 'no pages found'


    year = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}coverDate').text

    return s.format(authors=get_author_link(EID),
                    title=get_abstract_link(EID),
                    journal=get_journal_link(EID),
                    volume=volume,
                    issue=issue,
                    pages=pages,
                    year=year,
                    doi=get_doi_link(EID),
                    cites=get_cite_img_link(EID))

from scopus_xml import *
print '<ol>'
print '<li>',get_html_citation('2-s2.0-84896759135'),'</li>'
print
print '<li>',get_html_citation('2-s2.0-84924911828'),'</li>'
print
print '<li>',get_html_citation('2-s2.0-84901638552'),'</li>'
print '</ol>'

import requests
import json
from my_scopus import MY_API_KEY
resp = requests.get("http://api.elsevier.com/content/search/scopus?query=AU-ID(7004212771)&field=eid,aggregationType&count=100",
                    headers={'Accept':'application/json',
                             'X-ELS-APIKey': MY_API_KEY})

results = resp.json()

return [[str(r['eid']), str(r['prism:aggregationType'])] for r in results['search-results']["entry"] if str(r['prism:aggregationType']) == 'Journal']

from scopus_xml import *

import requests
import json
from my_scopus import MY_API_KEY
resp = requests.get("http://api.elsevier.com/content/search/scopus?query=AU-ID(7004212771)&field=eid,aggregationType&count=100",
                    headers={'Accept':'application/json',
                             'X-ELS-APIKey': MY_API_KEY})

results = resp.json()

data = [[str(r['eid']), str(r['prism:aggregationType'])] for r in
        results['search-results']["entry"] if str(r['prism:aggregationType']) == 'Journal']


with open('../publications.html.mako', 'w') as f:
    f.write('''<%inherit file="_templates/site.mako" />
<article class="page_box">
<%self:filter chain="markdown">

<h1>Online collections of our work</h1>
Pick your favorite:
<ul>
<li><a href="http://orcid.org/0000-0003-2625-9232">orcid:0000-0003-2625-9232</a></li>

<li><a href="http://www.researcherid.com/rid/A-2363-2010">researcherid:A-2363-2010</a></li>

<li><a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=7004212771">scopusid:7004212771</a></li>

<li><a href="https://scholar.google.com/citations?user=jD_4h7sAAAAJ">Google Scholar</a></li>

<li><a href="https://www.researchgate.net/profile/John_Kitchin">Research Gate</a></li>

<li><a href="https://www.growkudos.com/profiles/40205">Kudos</a></li>
</ul>

<h1>Publications</h1>
The authors are linked to their Scopus page, the title linked to the Scopus abstract, the journal linked to the Scopus journal page, and the DOI is linked to https://doi.org which normally redirects you to the journal page.

<ol reversed="reversed">
''')

    for eid,type in data:
        f.write('<li>{}</li>'.format(get_html_citation(eid)))
    f.write('''</ol>

</%self:filter>
</article>
''')

def get_author_link(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']
    html = '<a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId={0}">{1}</a>'
    authors = [html.format(auid, name) for auid, name in
               zip([x['@auid'] for x in result['authors']['author']],
                   [x['ce:indexed-name'] for x in result['authors']['author']])]

    return ','.join(authors)

from scopus import *
print get_author_link('2-s2.0-84901638552')

from scopus import *
EID = '2-s2.0-84901638552'
data = get_abstract_info(EID)
result = data['abstracts-retrieval-response']
print result['coredata']['source-id']
print result['coredata']['prism:publicationName']

def get_journal_link(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']
    sid = result['coredata']['source-id']
    journal = result['coredata']['prism:publicationName']
    s = '<a href="http://www.scopus.com/source/sourceInfo.url?sourceId={sid}">{journal}</a>'

    return s.format(sid=sid, journal=journal)

from scopus import *
print get_journal_link('2-s2.0-84901638552')

from scopus import *
EID = '2-s2.0-84901638552'
data = get_abstract_info(EID)
result = data['abstracts-retrieval-response']
print result['coredata']['prism:doi']

def get_doi_link(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']
    s = '<a href="https://doi.org/{doi}">doi:{doi}</a>'
    return s.format(doi=result['coredata']['prism:doi'])

from scopus import *
print get_doi_link('2-s2.0-84901638552')

def get_cite_img_link(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']
    s = '<img src="http://api.elsevier.com/content/abstract/citation-count?doi={doi}&httpAccept=image/jpeg&apiKey={apikey}"></img>'
    return s.format(doi=result['coredata']['prism:doi'].strip(), apikey=MY_API_KEY)

from scopus import *
print get_cite_img_link('2-s2.0-84901638552')

from scopus import *
EID = '2-s2.0-84901638552'
data = get_abstract_info(EID)
result = data['abstracts-retrieval-response']

print result['coredata']['dc:title']
for ref in result['coredata']['link']:
    if ref['@rel'] == 'scopus':
        print ref['@href'].replace('&', '&')
        break

def get_abstract_link(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']
    title = result['coredata']['dc:title']
    for ref in result['coredata']['link']:
        if ref['@rel'] == 'scopus':
            link = ref['@href'].replace('&', '&')

    s = '<a href="{link}">{title}</a>'
    return s.format(link=link, title=title)

from scopus import *
print get_abstract_link('2-s2.0-84901638552')

def get_html(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']

    s = '<li>{authors}, <i>{title}</i>, {journal}, <b>{volume}{issue}</b>, p. {pages}, ({year}), {doi}, {cites}.</li>'

    issue = ''
    if result['coredata'].get('prism:issue'):
        issue = '({})'.format(result['coredata'].get('prism:issue'))
    return s.format(authors=get_author_link(EID),
                    title=get_abstract_link(EID),
                    journal=get_journal_link(EID),
                    volume=result['coredata'].get('prism:volume'),
                    issue=issue,
                    pages=result['coredata'].get('prism:pageRange'),
                    year=result['coredata'].get('prism:coverDate'),
                    doi=get_doi_link(EID),
                    cites=get_cite_img_link(EID))

from scopus import *
print get_html('2-s2.0-84901638552')