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dsifford / academic-bloggers-toolkit

WordPress plugin providing an all-in-one solution for effective academic blogging.
https://wordpress.org/plugins/academic-bloggers-toolkit/
GNU General Public License v3.0
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Cannot import references from .bib or .ris exported from Endnote #428

Closed LindaEve closed 5 years ago

LindaEve commented 6 years ago

ABT Version: 4.13.3

PHP Version: 5.6.32

Theme: 250 (Rutgers University custom theme)

Plugin List:

Browser: Firefox 57.0.4

Expected behavior: Expected to be able to import a reference list from a RIS or BIB file

Actual behavior: Tried to select file and got a message "Error The selected file could not be processed"

Console messages:

// Paste messages here
dsifford commented 6 years ago

Thanks for the report.

Can you share one or both of the files you're trying to import so I can try and see what's causing the issue?

Thanks

LindaEve commented 6 years ago

Sure, thank you. Both files are attached here.

Linda

From: Derek Sifford notifications@github.com Sent: Thursday, February 1, 2018 10:55:59 AM To: dsifford/academic-bloggers-toolkit Cc: Linda Everett; Author Subject: Re: [dsifford/academic-bloggers-toolkit] Cannot import references from .bib or .ris exported from Endnote (#428)

Thanks for the report.

Can you share one or both of the files you're trying to import so I can try and see what's causing the issue?

Thanks

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdsifford%2Facademic-bloggers-toolkit%2Fissues%2F428%23issuecomment-362309969&data=02%7C01%7Clindaeve%40rutgers.edu%7C445d6ae27633458eb86408d5698c61e3%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636530974023893168&sdata=aACHhS438ne01gcSbdhUMPvpsRwTVqdaYjb%2BJ0MX%2BuA%3D&reserved=0, or mute the threadhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAiXzYs-Kv-1kqb6UQ03VlxGo85fsSi4Cks5tQd6PgaJpZM4R1tBf&data=02%7C01%7Clindaeve%40rutgers.edu%7C445d6ae27633458eb86408d5698c61e3%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636530974023893168&sdata=kEuHlt2zP4qeCXHXKWlZVMR8lwuBJvvia1zrIEpFIJc%3D&reserved=0.

@article{RN1, author = {Bayraktar, M. and Peltier, M. and Vetrano, A. and Arita, Y. and Gurzenda, E. and Joseph, A. and Kazzaz, J. and Sharma, S. and Hanna, N.}, title = {IL-10 modulates placental responses to TLR ligands}, journal = {Am J Reprod Immunol}, volume = {62}, number = {6}, pages = {390-9}, ISSN = {1046-7408}, DOI = {10.1111/j.1600-0897.2009.00756.x}, year = {2009}, type = {Journal Article} }

@article{RN2, author = {Chao, M. W. and Kozlosky, J. and Po, I. P. and Strickland, P. O. and Svoboda, K. K. and Cooper, K. and Laumbach, R. J. and Gordon, M. K.}, title = {Diesel exhaust particle exposure causes redistribution of endothelial tube VE-cadherin}, journal = {Toxicology}, volume = {279}, number = {1-3}, pages = {73-84}, ISSN = {0300-483x}, DOI = {10.1016/j.tox.2010.09.011}, year = {2011}, type = {Journal Article} }

@article{RN3, author = {Chen, X. and Nomani, A. and Patel, N. and Nouri, F. S. and Hatefi, A.}, title = {Bioengineering a non-genotoxic vector for genetic modification of mesenchymal stem cells}, journal = {Biomaterials}, volume = {152}, pages = {1-14}, ISSN = {0142-9612}, DOI = {10.1016/j.biomaterials.2017.10.028}, year = {2018}, type = {Journal Article} }

@article{RN4, author = {Dragomir, A. C. and Sun, R. and Choi, H. and Laskin, J. D. and Laskin, D. L.}, title = {Role of galectin-3 in classical and alternative macrophage activation in the liver following acetaminophen intoxication}, journal = {J Immunol}, volume = {189}, number = {12}, pages = {5934-41}, ISSN = {0022-1767}, DOI = {10.4049/jimmunol.1201851}, year = {2012}, type = {Journal Article} }

@article{RN5, author = {Fong, D. and Yeh, A. and Naftalovich, R. and Choi, T. H. and Chan, M. M.}, title = {Curcumin inhibits the side population (SP) phenotype of the rat C6 glioma cell line: towards targeting of cancer stem cells with phytochemicals}, journal = {Cancer Lett}, volume = {293}, number = {1}, pages = {65-72}, ISSN = {0304-3835}, DOI = {10.1016/j.canlet.2009.12.018}, year = {2010}, type = {Journal Article} }

@article{RN6, author = {Francis, M. and Groves, A. M. and Sun, R. and Cervelli, J. A. and Choi, H. and Laskin, J. D. and Laskin, D. L.}, title = {Editor's Highlight: CCR2 Regulates Inflammatory Cell Accumulation in the Lung and Tissue Injury following Ozone Exposure}, journal = {Toxicol Sci}, volume = {155}, number = {2}, pages = {474-484}, ISSN = {1096-0929}, DOI = {10.1093/toxsci/kfw226}, year = {2017}, type = {Journal Article} }

@article{RN7, author = {Francis, M. and Sun, R. and Cervelli, J. A. and Choi, H. and Mandal, M. and Abramova, E. V. and Gow, A. J. and Laskin, J. D. and Laskin, D. L.}, title = {Editor's Highlight: Role of Spleen-Derived Macrophages in Ozone-Induced Lung Inflammation and Injury}, journal = {Toxicol Sci}, volume = {155}, number = {1}, pages = {182-195}, ISSN = {1096-0929}, DOI = {10.1093/toxsci/kfw192}, year = {2017}, type = {Journal Article} }

@article{RN8, author = {Garbuzenko, O. B. and Saad, M. and Pozharov, V. P. and Reuhl, K. R. and Mainelis, G. and Minko, T.}, title = {Inhibition of lung tumor growth by complex pulmonary delivery of drugs with oligonucleotides as suppressors of cellular resistance}, journal = {Proc Natl Acad Sci U S A}, volume = {107}, number = {23}, pages = {10737-42}, ISSN = {0027-8424}, DOI = {10.1073/pnas.1004604107}, year = {2010}, type = {Journal Article} }

@article{RN9, author = {Jin, F. and Fondell, J. D.}, title = {A novel androgen receptor-binding element modulates Cdc6 transcription in prostate cancer cells during cell-cycle progression}, journal = {Nucleic Acids Res}, volume = {37}, number = {14}, pages = {4826-38}, ISSN = {0305-1048}, DOI = {10.1093/nar/gkp510}, year = {2009}, type = {Journal Article} }

@article{RN10, author = {Kawamura, K. and Yao, K. and Shukaliak-Quandt, J. A. and Huh, J. and Baig, M. and Quigley, L. and Ito, N. and Necker, A. and McFarland, H. F. and Muraro, P. A. and Martin, R. and Ito, K.}, title = {Different development of myelin basic protein agonist- and antagonist-specific human TCR transgenic T cells in the thymus and periphery}, journal = {J Immunol}, volume = {181}, number = {8}, pages = {5462-72}, ISSN = {0022-1767}, year = {2008}, type = {Journal Article} }

@article{RN11, author = {Mandal, M. and Gardner, C. R. and Sun, R. and Choi, H. and Lad, S. and Mishin, V. and Laskin, J. D. and Laskin, D. L.}, title = {The spleen as an extramedullary source of inflammatory cells responding to acetaminophen-induced liver injury}, journal = {Toxicol Appl Pharmacol}, volume = {304}, pages = {110-20}, ISSN = {0041-008x}, DOI = {10.1016/j.taap.2016.04.019}, year = {2016}, type = {Journal Article} }

@article{RN12, author = {Mathew, R. and Karp, C. M. and Beaudoin, B. and Vuong, N. and Chen, G. and Chen, H. Y. and Bray, K. and Reddy, A. and Bhanot, G. and Gelinas, C. and Dipaola, R. S. and Karantza-Wadsworth, V. and White, E.}, title = {Autophagy suppresses tumorigenesis through elimination of p62}, journal = {Cell}, volume = {137}, number = {6}, pages = {1062-75}, ISSN = {0092-8674}, DOI = {10.1016/j.cell.2009.03.048}, year = {2009}, type = {Journal Article} }

@article{RN13, author = {Mathew, R. and Kongara, S. and Beaudoin, B. and Karp, C. M. and Bray, K. and Degenhardt, K. and Chen, G. and Jin, S. and White, E.}, title = {Autophagy suppresses tumor progression by limiting chromosomal instability}, journal = {Genes Dev}, volume = {21}, number = {11}, pages = {1367-81}, ISSN = {0890-9369 (Print) 0890-9369}, DOI = {10.1101/gad.1545107}, year = {2007}, type = {Journal Article} }

@article{RN14, author = {Postel, E. H. and Wohlman, I. and Zou, X. and Juan, T. and Sun, N. and D'Agostin, D. and Cuellar, M. and Choi, T. and Notterman, D. A. and La Perle, K. M.}, title = {Targeted deletion of Nm23/nucleoside diphosphate kinase A and B reveals their requirement for definitive erythropoiesis in the mouse embryo}, journal = {Dev Dyn}, volume = {238}, number = {3}, pages = {775-87}, ISSN = {1058-8388 (Print) 1058-8388}, DOI = {10.1002/dvdy.21887}, year = {2009}, type = {Journal Article} }

@article{RN15, author = {Sunil, V. R. and Francis, M. and Vayas, K. N. and Cervelli, J. A. and Choi, H. and Laskin, J. D. and Laskin, D. L.}, title = {Regulation of ozone-induced lung inflammation and injury by the beta-galactoside-binding lectin galectin-3}, journal = {Toxicol Appl Pharmacol}, volume = {284}, number = {2}, pages = {236-45}, ISSN = {0041-008x}, DOI = {10.1016/j.taap.2015.02.002}, year = {2015}, type = {Journal Article} }

@article{RN16, author = {Venosa, A. and Malaviya, R. and Choi, H. and Gow, A. J. and Laskin, J. D. and Laskin, D. L.}, title = {Characterization of Distinct Macrophage Subpopulations during Nitrogen Mustard-Induced Lung Injury and Fibrosis}, journal = {Am J Respir Cell Mol Biol}, volume = {54}, number = {3}, pages = {436-46}, ISSN = {1044-1549}, DOI = {10.1165/rcmb.2015-0120OC}, year = {2016}, type = {Journal Article} }

@article{RN17, author = {Vetrano, A. M. and Laskin, D. L. and Archer, F. and Syed, K. and Gray, J. P. and Laskin, J. D. and Nwebube, N. and Weinberger, B.}, title = {Inflammatory effects of phthalates in neonatal neutrophils}, journal = {Pediatr Res}, volume = {68}, number = {2}, pages = {134-9}, ISSN = {0031-3998}, DOI = {10.1203/00006450-201011001-00260 10.1203/PDR.0b013e3181e5c1f7}, year = {2010}, type = {Journal Article} }

@article{RN18, author = {Weinberger, B. and Quizon, C. and Vetrano, A. M. and Archer, F. and Laskin, J. D. and Laskin, D. L.}, title = {Mechanisms mediating reduced responsiveness of neonatal neutrophils to lipoxin A4}, journal = {Pediatr Res}, volume = {64}, number = {4}, pages = {393-8}, ISSN = {0031-3998}, DOI = {10.1203/PDR.0b013e318180e4af}, year = {2008}, type = {Journal Article} }

@article{RN19, author = {Weinberger, B. and Vetrano, A. M. and Syed, K. and Murthy, S. and Hanna, N. and Laskin, J. D. and Laskin, D. L.}, title = {Influence of labor on neonatal neutrophil apoptosis, and inflammatory activity}, journal = {Pediatr Res}, volume = {61}, number = {5 Pt 1}, pages = {572-7}, ISSN = {0031-3998 (Print) 0031-3998}, DOI = {10.1203/pdr.0b013e318045be38}, year = {2007}, type = {Journal Article} }

@article{RN20, author = {Zhao, X. and Ren, G. and Liang, L. and Ai, P. Z. and Zheng, B. and Tischfield, J. A. and Shi, Y. and Shao, C.}, title = {Brief report: interferon-gamma induces expansion of Lin(-)Sca-1(+)C-Kit(+) Cells}, journal = {Stem Cells}, volume = {28}, number = {1}, pages = {122-6}, ISSN = {1066-5099}, DOI = {10.1002/stem.252}, year = {2010}, type = {Journal Article} }

dsifford commented 6 years ago

Thanks @LindaEve

If not too much trouble, would you mind dragging and dropping the file into this issue thread on GitHub when you get a chance? Reason being: There are sometimes hidden characters in the file that cause the issue. Just want to be certain the file I'm trying is identical to the one that triggered your issue.

Thanks

LindaEve commented 6 years ago

Hi Derek I had to rename them as .txt files to get them to upload here, but anyway, here they are. FlowCyt.bib.txt FlowCyt.ris.txt

Thanks so much! Linda

glorious1 commented 6 years ago

@LindaEve, Your files have Windows line endings (CR LF). Unless something has changed, you need to change them to Unix (LF) and they will hopefully work.

dsifford commented 6 years ago

@glorious1 Windows line endings should work now to my knowledge. I explicitly went in and fixed that. Let me know if that is not the case.

LindaEve commented 6 years ago

@dsifford It still does not work. @glorious1 I appreciate your input but I have no idea how to change the line endings and I'm not sure it's really worth it.

glorious1 commented 6 years ago

Another issue I noticed with importing files is fields that have multiple lines with line endings within them. I'm not sure it still does, but in my early testing, that prevented import. Try editing your RIS file so it has just a couple of references, and get rid of multiple lines in fields. In your file I see it in the N1 and KW fields. You could just delete those fields.

However, I'm not sure that would explain the BIB file. I'm unfamiliar with them.

If you have the option to select fields to be exported from EndNote into the RIS or BIB file, I would restrict it to just the fields you need to build the reference - it might help avoid problems like this.

Edit: actually, reviewing the documentation, I don't find that there is a feature to import BIB files. Maybe stick with RIS.

LindaEve commented 6 years ago

@glorious1 I tried getting rid of any field with line breaks and that more or less worked. Sadly I am still not finding the plugin really works for me. What I really need is the ability to import a publication list based on a PubMed search (like an author or a serious of PMIDs or a grant number... that sort of thing). And I need just a nice list of publications that is not dependent on in-text citations.

dsifford commented 6 years ago

@glorious1 bibtex import is available. Also, "list-type" fields where there are the same field on mulitple lines (eg, KW )are also supported. If these things are not working, open an issue and provide an example of that here: https://github.com/dsifford/astrocite

@LindaEve What you are describing is also supported. Check out the wiki page for "static publication list"

https://github.com/dsifford/academic-bloggers-toolkit/wiki

glorious1 commented 6 years ago

There is a way to enter a list of pmid’s, from the plus sign. Also you can generate a static reference list (no citations) through the second row of icons.

On Feb 7, 2018, at 9:24 AM, LindaEve notifications@github.com wrote:

@glorious1 I tried getting rid of any field with line breaks and that more or less worked. Sadly I am still not finding the plugin really works for me. What I really need is the ability to import a publication list based on a PubMed search (like an author or a serious of PMIDs or a grant number... that sort of thing). And I need just a nice list of publications that is not dependent on in-text citations.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

dsifford commented 5 years ago

Closing this thread since (I think) this has already been fixed? Reopen if not...