gummy.utils.journal_utils module

Utility programs for journals

gummy.utils.journal_utils.DOMAIN2JOURNAL = {'aacrjournals.org': 'AACRPublications', 'academic.oup.com': 'OxfordAcademic', 'advances.sciencemag.org': 'ScienceAdvances', 'agupubs.onlinelibrary.wiley.com': 'AGUPublications', 'aip.scitation.org': 'Scitation', 'ajp.amjpathol.org': 'ASIP', 'anatomypubs.onlinelibrary.wiley.com': 'AnatomyPubs', 'arxiv.org': 'arXiv', 'bio.biologists.org': 'Biologists', 'biologydirect.biomedcentral.com': 'BioMedCentral', 'biomedgrid.com': 'BiomedGrid', 'bloodcancerdiscov.aacrjournals.org': 'AACRPublications', 'bmcbioinformatics.biomedcentral.com': 'BioMedCentral', 'bmcevolbiol.biomedcentral.com': 'BioMedCentral', 'bmcgenomics.biomedcentral.com': 'BioMedCentral', 'bmcmedicine.biomedcentral.com': 'BioMedCentral', 'cancerdiscovery.aacrjournals.or': 'AACRPublications', 'cancerimmunolres.aacrjournals.org': 'AACRPublications', 'cancerpreventionresearch.aacrjournals.org': 'AACRPublications', 'cancerres.aacrjournals.org': 'AACRPublications', 'cebp.aacrjournals.or': 'AACRPublications', 'chemrxiv.org': 'ChemRxiv', 'clincancerres.aacrjournals.org': 'AACRPublications', 'dev.biologists.org': 'Biologists', 'dl.acm.org': 'ACM', 'eymj.org': 'YMJ', 'faseb.onlinelibrary.wiley.com': 'WileyOnlineLibrary', 'febs.onlinelibrary.wiley.com': 'WileyOnlineLibrary', 'genesdev.cshlp.org': 'GeneDev', 'genomebiology.biomedcentral.com': 'BioMedCentral', 'ieeexplore.ieee.org': 'ieeexplore', 'iopscience.iop.org': 'IOPScience', 'iovs.arvojournals.org': 'ARVOJournals', 'jamanetwork.com': 'JAMANetwork', 'jcs.biologists.org': 'Biologists', 'jkms.org': 'JKMS', 'journals.ametsoc.org': 'AMS', 'journals.aps.org': 'APS', 'journals.lww.com': 'LWWJournals', 'journals.physiology.org': 'RenalPhysiology', 'journals.plos.org': 'PLOSONE', 'journals.sagepub.com': 'SAGEjournals', 'jov.arvojournals.org': 'ARVOJournals', 'keio.pure.elsevier.com': 'UniKeio', 'learnmem.cshlp.org': 'LearningMemory', 'link.springer.com': 'Springer', 'linkinghub.elsevier.com': 'ScienceDirect', 'mcb.asm.org': 'MolCellBio', 'mcr.aacrjournals.org': 'AACRPublications', 'mct.aacrjournals.org': 'AACRPublications', 'onlinelibrary.wiley.com': 'WileyOnlineLibrary', 'psycnet.apa.org': 'PsycNet', 'pubmed.ncbi.nlm.nih.gov': 'PubMed', 'pubs.acs.org': 'ACSPublications', 'pubs.rsc.org': 'RSCPublishing', 'pubs.rsna.org': 'RadioGraphics', 'retrovirology.biomedcentral.com': 'BioMedCentral', 'rnajournal.cshlp.org': 'RNAjournal', 'science.sciencemag.org': 'ScienceMag', 'stemcellsjournals.onlinelibrary.wiley.com': 'StemCells', 'tvst.arvojournals.org': 'ARVOJournals', 'www.aclweb.org': 'ACLAnthology', 'www.biorxiv.org': 'bioRxiv', 'www.bioscience.org': 'Bioscience', 'www.cell.com': 'CellPress', 'www.e-ce.org': 'ClinicalEndoscopy', 'www.embopress.org': 'EMBOPress', 'www.frontiersin.org': 'frontiers', 'www.future-science.com': 'FutureScience', 'www.genetics.org': 'Genetics', 'www.hindawi.com': 'Hindawi', 'www.intechopen.com': 'IntechOpen', 'www.jbc.org': 'JBC', 'www.jkms.org': 'JKMS', 'www.jkns.or.kr': 'JKNS', 'www.jneurosci.org': 'JNeurosci', 'www.jpedsurg.org': 'PediatricSurgery', 'www.jsse.org': 'JSSE', 'www.jstage.jst.go.jp': 'JSTAGE', 'www.lungcancerjournal.info': 'LungCancer', 'www.mdpi.com': 'MDPI', 'www.medrxiv.org': 'medRxiv', 'www.minervamedica.it': 'MinervaMedica', 'www.nature.com': 'Nature', 'www.ncbi.nlm.nih.gov': 'NCBI', 'www.nejm.org': 'NEJM', 'www.nrcresearchpress.com': 'NRCResearchPress', 'www.nrronline.org': 'NRR', 'www.oncotarget.com': 'Oncotarget', 'www.ou.edu': 'UniOKLAHOMA', 'www.plantphysiol.org': 'ASPB', 'www.pnas.org': 'PNAS', 'www.psychiatrist.com': 'PsyChiArtist', 'www.sciencedirect.com': 'ScienceDirect', 'www.scitation.org': 'Scitation', 'www.spandidos-publications.com': 'Spandidos', 'www.tandfonline.com': 'TaylorandFrancisOnline', 'www.thelancet.com': 'TheLancet'}

A dictionary that describes the correspondence between URL domain and the crawler of GummyCrawler.

How to write in a file when adding a new domain.

>>> from gummy.utils.journal_utils import DOMAIN2JOURNAL
>>> digit = max([len(e) for e in DOMAIN2JOURNAL.keys()])+2
>>> for k,v in sorted(DOMAIN2JOURNAL.items(), key=lambda x: x[0]):
...     k = f'"{k}"'
...     print(f'    {k:<{digit}} : "{v}",')
Type

dict

gummy.utils.journal_utils.canonicalize(url, driver=None, sleep_for_loading=1)[source]

canonicalize the URL by accessing the URL once.

Parameters

  • url (str) – URL of the paper.

  • driver (WebDriver) – Selenium WebDriver. (default= None)

  • sleep_for_loading (int) – Number of seconds to wait for a web page to load (default= 1 )

Returns

canonized URL.

Return type

str

gummy.utils.journal_utils.whichJournal(url, driver=None, verbose=True)[source]

Decide which journal from the domain of the url

If the journal_type cannot be determined, Twitter DM twitter badge will open automatically, so please feel free to request it to the developer.

Parameters

  • url (str) – URL of the paper.

  • driver (WebDriver) – Selenium WebDriver. (default= None)

  • verbose (bool) – Whether to print message or not. (default= True)

Returns

journal_type

Return type

str

Examples

>>> journal_type = whichJournal("https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1573881/")
Estimated Journal Type : NCBI
>>> journal_type
'ncbi'