The Kitchin Research Group

import requests
import os
import xml.etree.ElementTree as ET

from my_scopus import MY_API_KEY

def get_abstract_info(EID, refresh=False):
    'Get and save the json data for EID.'
    base = 'scopus-xml/get_abstract_info'
    if not os.path.exists(base):
        os.makedirs(base)

    fname = '{0}/{1}'.format(base, EID)
    if os.path.exists(fname) and not refresh:
        with open(fname) as f:
            return ET.fromstring(f.read())

    # Otherwise retrieve and save results
    url = ("http://api.elsevier.com/content/abstract/eid/" + EID + '?view=META_ABS')
    resp = requests.get(url,
                    headers={'Accept':'application/xml',
                             'X-ELS-APIKey': MY_API_KEY})
    with open(fname, 'w') as f:
        f.write(resp.text.encode('utf-8'))

    results = ET.fromstring(resp.text.encode('utf-8'))

    return results

from scopus_xml import *
#results = get_abstract_info('2-s2.0-84896759135')
#results = get_abstract_info('2-s2.0-84924911828')
results = get_abstract_info('2-s2.0-84901638552')
for el in results:
    print el.tag
    for el1 in el:
        print '  -->',el1.tag
    print

from scopus_xml import *

results = get_abstract_info('2-s2.0-84901638552')

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

print coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}srctype').text
print coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}source-id').text

#authors = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}authors')
#for author in results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}authors'):
#    print author.find('{http://www.elsevier.com/xml/ani/common}indexed-name').text

for creator in coredata.find('{http://purl.org/dc/elements/1.1/}creator'):
    print creator.attrib

print coredata.find('{http://purl.org/dc/elements/1.1/}title').text
print coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}publicationName').text
print coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}volume').text
print coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}pageRange').text
print coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}coverDate').text
print coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}citedby-count').text
print coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}doi').text

for link in coredata.findall('{http://www.elsevier.com/xml/svapi/abstract/dtd}link'):
    if link.attrib['rel'] == 'scopus':
        print link.attrib['href']
    else:
        print link.attrib['href']

# alternative xpath to get the link
print coredata.find("./{http://www.elsevier.com/xml/svapi/abstract/dtd}link/[@rel='scopus']").attrib['href']

from scopus import *

print '<ol>', get_html('2-s2.0-84901638552'), '</ol>'

import requests
import json, os
from my_scopus import MY_API_KEY

def get_abstract_info(EID, refresh=False):
    'Get and save the json data for EID.'
    base = 'scopus-data/get_abstract_info'
    if not os.path.exists(base):
        os.makedirs(base)

    fname = '{0}/{1}'.format(base, EID)
    if os.path.exists(fname) and not refresh:
        with open(fname) as f:
            return json.loads(f.read())

    # Otherwise retrieve and save results
    url = ("http://api.elsevier.com/content/abstract/eid/" + EID)
    resp = requests.get(url,
                    headers={'Accept':'application/json',
                             'X-ELS-APIKey': MY_API_KEY})
    results = json.loads(resp.text.encode('utf-8'))
    with open(fname, 'w') as f:
        f.write(json.dumps(results))

    return results

import requests
import json

resp = requests.get("http://pub.orcid.org/0000-0003-2625-9232",
                    headers={'Accept':'application/orcid+json'})

print json.dumps(resp.json(),
                 sort_keys=True,
                 indent=4, separators=(',', ': '))

import requests
import json

resp = requests.get("http://pub.orcid.org/0000-0003-2625-9232/orcid-works",
                    headers={'Accept':'application/orcid+json'})

results = resp.json()
for i, result in enumerate( results['orcid-profile']['orcid-activities']
                            ['orcid-works']['orcid-work']):
    print result['work-citation']['citation'].encode('utf-8') + '\n'
    if i == 2:
        break

import requests
import json

resp = requests.get("http://pub.orcid.org/0000-0003-2625-9232/orcid-works",
                    headers={'Accept':'application/orcid+json'})
results = resp.json()

data = []
TITLES, DOIs = [], []

for i, result in enumerate( results['orcid-profile']['orcid-activities']
                            ['orcid-works']['orcid-work']):
    title = str(result['work-title']['title']['value'].encode('utf-8'))
    doi = 'None'

    for x in result.get('work-external-identifiers', []):
        for eid in result['work-external-identifiers']['work-external-identifier']:
            if eid['work-external-identifier-type'] == 'DOI':
                doi = str(eid['work-external-identifier-id']['value'].encode('utf-8'))

    # AIP journals tend to have a \n in the DOI, and the doi is the second line. we get
    # that here.
    if len(doi.split('\n')) == 2:
        doi = doi.split('\n')[1]

    pub_date = result.get('publication-date', None)
    if pub_date:
        year = pub_date.get('year', None).get('value').encode('utf-8')
    else:
        year = 'Unknown'

    # Try to minimize duplicate entries that are found
    dup = False
    if title.lower() in TITLES:
        dup = True
    if (doi != 'None'
        and doi.lower() in DOIs):
        dup = True

    if not dup:
        # truncate title to first 50 characters
        print('| {3} | {0}  | {1} | [[doi:{2}]]|'.format(title[0:50], year, doi, result['work-type']))

    TITLES.append(title.lower())
    DOIs.append(doi.lower())

| JOURNAL_ARTICLE  | A Linear Response DFT+ U Study of Trends in the Ox | 2015 | doi:10.1021/jp511426q                                |
| JOURNAL_ARTICLE  | Relationships between the surface electronic and c | 2015 | doi:10.1063/1.4914093                                |
| JOURNAL_ARTICLE  | Core level shifts in Cu–Pd alloys as a function    | 2015 | doi:10.1016/j.susc.2015.02.011                       |
| JOURNAL_ARTICLE  | Estimating bulk-composition-dependent H2 adsorptio | 2015 | doi:10.1021/cs501585k                                |
| JOURNAL_ARTICLE  | Probing the Coverage Dependence of Site and Adsorb | 2014 | doi:10.1021/jp508805h                                |
| JOURNAL_ARTICLE  | Relating the electronic structure and reactivity o | 2014 | doi:10.1016/j.catcom.2013.10.028                     |
| JOURNAL_ARTICLE  | Electrocatalytic Oxygen Evolution with an Immobili | 2014 | doi:10.1021/ja5015986                                |
| JOURNAL_ARTICLE  | Identifying Potential BO 2 Oxide Polymorphs for Ep | 2014 | doi:10.1021/am4059149                                |
| JOURNAL_ARTICLE  | Simulating temperature programmed desorption of ox | 2014 | doi:10.1007/s11244-013-0166-3                        |
| JOURNAL_ARTICLE  | Probing the effect of electron donation on CO2 abs | 2014 | doi:10.1039/c3ra47097k                               |
| JOURNAL_ARTICLE  | Effects of concentration, crystal structure, magne | 2014 | doi:10.1021/jp507957n                                |
| JOURNAL_ARTICLE  | Effects of O 2 and SO 2 on the Capture Capacity of | 2013 | doi:10.1021/ie400582a                                |
| JOURNAL_ARTICLE  | Number of outer electrons as descriptor for adsorp | 2013 | doi:None                                             |
| JOURNAL_ARTICLE  | Interactions in 1-ethyl-3-methyl imidazolium tetra | 2013 | doi:https://doi.org/10.1016/j.molstruc.2013.01.046 |
| JOURNAL_ARTICLE  | Comparisons of amine solvents for post-combustion  | 2013 | doi:https://doi.org/10.1016/j.ijggc.2013.06.020    |
| JOURNAL_ARTICLE  | Chemical and Molecular Descriptors for the Reactiv | 2012 | doi:10.1021/ie301419q                                |
| JOURNAL_ARTICLE  | Spectroscopic Characterization of Mixed Fe–Ni Ox   | 2012 | doi:10.1021/cs3002644                                |
| REPORT           | Modeling Coverage Dependence in Surface Reaction N | 2012 | doi:10.2172/1149701                                  |
| CONFERENCE_PAPER | Vibrational spectroscopy characterization of CO2-i | 2012 | doi:None                                             |
| CONFERENCE_PAPER | The role of electrolytes in the oxygen evolution r | 2012 | doi:None                                             |
| JOURNAL_ARTICLE  | The outlook for improved carbon capture technology | 2012 | doi:10.1016/j.pecs.2012.03.003                       |
| JOURNAL_ARTICLE  | Structure and Relative Thermal Stability of Mesopo | 2012 | doi:10.1111/j.1551-2916.2012.05236.x                 |
| JOURNAL_ARTICLE  | Preface: Trends in computational catalysis         | 2012 | doi:10.1007/s11244-012-9808-0                        |
| CONFERENCE_PAPER | Exergetic analysis of chemical looping reforming   | 2012 | doi:None                                             |
| JOURNAL_ARTICLE  | Evaluation of a Primary Amine-Functionalized Ion-E | 2012 | doi:10.1021/ie300452c                                |
| CONFERENCE_PAPER | Electrocatalytic water oxidation using iron-center | 2012 | doi:None                                             |
| JOURNAL_ARTICLE  | Effects of strain, d-band filling, and oxidation s | 2012 | doi:10.1063/1.4746117                                |
| BOOK             | Coverage dependent adsorption properties of atomic | 2012 | doi:10.1039/9781849734776-00083                      |
| CONFERENCE_PAPER | Comparisons of solvents for post-combustion CO2 ca | 2012 | doi:None                                             |
| CONFERENCE_PAPER | Characterization of an ion exchange resin for CO2  | 2012 | doi:None                                             |
| CONFERENCE_PAPER | Assessing the ability of using first principles to | 2012 | doi:None                                             |
| JOURNAL_ARTICLE  | Universality in Oxygen Evolution Electrocatalysis  | 2011 | doi:10.1002/cctc.201000397                           |
| CONFERENCE_PAPER | The effect of CO 2 partial pressure on capture wit | 2011 | doi:None                                             |
| CONFERENCE_PAPER | Preparation of Mesoporous La 0.8Sr 0.2MnO 3 infilt | 2011 | doi:10.1149/1.3570235                                |
| JOURNAL_ARTICLE  | Identification of sulfur-tolerant bimetallic surfa | 2011 | doi:10.1021/cs200039t                                |
| JOURNAL_ARTICLE  | Effects of strain, d-band filling, and oxidation s | 2011 | doi:10.1063/1.3631948                                |
| CONFERENCE_PAPER | Determining the conditions necessary for optimal C | 2011 | doi:None                                             |
| JOURNAL_ARTICLE  | Configurational correlations in the coverage depen | 2011 | doi:10.1063/1.3561287                                |
| CONFERENCE_PAPER | An electronic structure based understanding of ami | 2011 | doi:None                                             |
| JOURNAL_ARTICLE  | CO2 Adsorption on Supported Molecular Amidine Syst | 2010 | doi:10.1002/cssc.201000056                           |
| JOURNAL_ARTICLE  | Separation of CO2 from flue gas using electrochemi | 2010 | doi:10.1016/j.fuel.2009.11.036                       |
| JOURNAL_ARTICLE  | New solid-state table: estimating d-band character | 2010 | doi:10.1080/08927022.2010.481794                     |
| JOURNAL_ARTICLE  | Simple model explaining and predicting coverage-de | 2010 | doi:10.1103/PhysRevB.82.045414                       |
| CONFERENCE_PAPER | Intrinsic and extrinsic factors associated with CO | 2010 | doi:None                                             |
| JOURNAL_ARTICLE  | Electrochemical concentration of carbon dioxide fr | 2010 | doi:10.1149/1.3432440                                |
| CONFERENCE_PAPER | Catalyzing the catalyst: Hydrogen dissociation and | 2010 | doi:None                                             |
| JOURNAL_ARTICLE  | Uncertainty and figure selection for DFT based clu | 2009 | doi:10.1080/08927020902833137                        |
| JOURNAL_ARTICLE  | Sulphur poisoning of water-gas shift catalysts: Si | 2009 | doi:10.1080/08927020902833129                        |
| JOURNAL_ARTICLE  | Step decoration of chiral metal surfaces           | 2009 | doi:10.1063/1.3096964                                |
| JOURNAL_ARTICLE  | Relating the coverage dependence of oxygen adsorpt | 2009 | doi:10.1016/j.susc.2009.01.021                       |
| JOURNAL_ARTICLE  | Hydrogen Dissociation and Spillover on Individual  | 2009 | doi:10.1103/PhysRevLett.103.246102                   |
| JOURNAL_ARTICLE  | Correlations in coverage-dependent atomic adsorpti | 2009 | doi:10.1103/PhysRevB.79.205412                       |
| CONFERENCE_PAPER | Catalyzing the catalyst: Novel pathways to hydroge | 2009 | doi:None                                             |
| JOURNAL_ARTICLE  | Atomistic thermodynamics study of the adsorption a | 2009 | doi:10.1016/j.jcat.2008.11.020                       |
| CONFERENCE_PAPER | Ancillary oxygen-fired combustion using electroche | 2009 | doi:None                                             |
| CONFERENCE_PAPER | Adsorbate Cu interactions and catalyst morphologie | 2009 | doi:None                                             |
| CONFERENCE_PAPER | <title>Rotational isomeric state theory applied to | 2008 | doi:10.1117/12.776303                                |
| CONFERENCE_PAPER | The effect of hydration on the adsorption of carbo | 2008 | doi:None                                             |
| CONFERENCE_PAPER | Pt-decorated electrocatalysts for direct alcohol f | 2008 | doi:None                                             |
| CONFERENCE_PAPER | PEM-based electrochemical separation of gases      | 2008 | doi:None                                             |
| CONFERENCE_PAPER | First principles, atomistic thermodynamics for sul | 2008 | doi:None                                             |
| CONFERENCE_PAPER | Evaluating uncertainty in Ab initio phase diagrams | 2008 | doi:None                                             |
| JOURNAL_ARTICLE  | ENVR 1-Basic research needs to assure a secure ene | 2008 | doi:None                                             |
| OTHER            | Density functional theory studies of alloys in het | 2008 | doi:10.1039/b608782p                                 |
| JOURNAL_ARTICLE  | Alloy surface segregation in reactive environments | 2008 | doi:10.1103/PhysRevB.77.075437                       |
| CONFERENCE_PAPER | A first principles evaluation of the role of subst | 2008 | doi:None                                             |
| CONFERENCE_PAPER | Pt nanoparticle electrocatalyst synthesis for dire | 2007 | doi:None                                             |
| CONFERENCE_PAPER | Pt nanoparticle anode electrocatalysts for direct  | 2007 | doi:None                                             |
| JOURNAL_ARTICLE  | Response to &quot;comment on 'Trends in the exchan | 2006 | doi:10.1149/1.2358292                                |
| JOURNAL_ARTICLE  | Trends in the exchange current for hydrogen evolut | 2005 | doi:10.1149/1.1856988                                |
| JOURNAL_ARTICLE  | Trends in the chemical properties of early transit | 2005 | doi:10.1016/j.cattod.2005.04.008                     |
| CONFERENCE_PAPER | Alloy surface segregation in reactive environments | 2005 | doi:None                                             |
| JOURNAL_ARTICLE  | The role of adsorbate-adsorbate interactions in th | 2004 | doi:None                                             |
| JOURNAL_ARTICLE  | Role of strain and ligand effects in the modificat | 2004 | doi:10.1103/PhysRevLett.93.156801                    |
| JOURNAL_ARTICLE  | Origin of the overpotential for oxygen reduction a | 2004 | doi:10.1021/jp047349j                                |
| JOURNAL_ARTICLE  | Modification of the surface electronic and chemica | 2004 | doi:10.1063/1.1737365                                |
| JOURNAL_ARTICLE  | Elucidation of the active surface and origin of th | 2003 | doi:10.1016/j.susc.2003.09.007                       |
| JOURNAL_ARTICLE  | A four-point probe correlation of oxygen sensitivi | 2003 | doi:10.1016/j.susc.2003.08.041                       |
| JOURNAL_ARTICLE  | A comparison of gold and molybdenum nanoparticles  | 2003 | doi:10.1016/s0039-6028(02)02679-1                    |
| JOURNAL_ARTICLE  | H3PW12O40-functionalized tip for scanning tunnelin | 2002 | doi:10.1073/pnas.072514399                           |
| JOURNAL_ARTICLE  | Preparation of paramagnetic ligands for coordinati | 1997 | doi:None                                             |
| JOURNAL_ARTICLE  | Preparation and Characterization of a Bis-Semiquin | 1995 | doi:10.1021/jo00117a004                              |
| JOURNAL_ARTICLE  | SYNTHESIS AND CHARACTERIZATION OF TRISEMIQUINONE L | 1995 | doi:None                                             |

print 8

(defun org-babel-python-strip-session-chars ()
  "Remove >>> and ... from a Python session output."
  (when (and (string=
              "python"
              (org-element-property :language (org-element-at-point)))
             (string-match
              ":session"
              (org-element-property :parameters (org-element-at-point))))

    (save-excursion
      (when (org-babel-where-is-src-block-result)
        (goto-char (org-babel-where-is-src-block-result))
        (end-of-line 1)
        ;(while (looking-at "[\n\r\t\f ]") (forward-char 1))
        (while (re-search-forward
                "\\(>>> \\|\\.\\.\\. \\|: $\\|: >>>$\\)"
                (org-element-property :end (org-element-at-point))
                t)
          (replace-match "")
          ;; this enables us to get rid of blank lines and blank : >>>
          (beginning-of-line)
          (when (looking-at "^$")
            (kill-line)))))))

(add-hook 'org-babel-after-execute-hook 'org-babel-python-strip-session-chars)

import matplotlib.pyplot as plt
plt.plot([3, 4, 5])
plt.show()

def f(s):
    x = 2 * s
    # blank lines look like indentation errors
    return x

print f(4)

print f(9)

plt.figure()
plt.plot([3, 4.5, 5])
plt.savefig('images/session-fig.png')
'images/session-fig.png'

print 6

a = 2
b = 3
c = 4
print
print 'a=      ', a
print 'b =     ', b
print 'a + b = ', a+b