Long 'creator name' causes syncing not to work

JM1723 · July 30, 2019

Report ID: 113769211
I exported approximately 600 citations from the PsycINFO database in RIS format and had the "link to external resolver" and URL boxes checked as standard. I then imported this citations into Zotero. I noticed that after all files imported that there was also several hundred blank items that I had to delete. My Zotero then had trouble syncing as many of the citations had put too many names in the Editor field, so I had to manually alter the Editor field to allow syncing. i.e. deleting the editor field if it was not relevant bibliographic information such as e.g. for a journal article. Am hoping this could please be fixed as it was very tedious manually altering several hundred citations!
Cheers,
JM1723

dstillman · July 30, 2019

This is likely just bad data from PsycINFO, but can you provide a link to example record on PsycINFO that imported incorrectly?

JM1723 · July 31, 2019

PsycINFO is a subscription based service so you will not be able to access it from a link I give you as it goes through my institution.

However an example of a record that imported incorrectly is: "Human anxiety-specific "theta" occurs with selective stopping and localizes to right inferior frontal gyrus." If you have access to PsycINFO and look up that record you will see it.

Zotero listed in the editor field: Aron, Baxter, Carver, Chung, Corr, Coxon, Filiou, Floden, Gratton, Gray, Gray, Insel, Kessler, Kessler, Kessler, LeDoux, Logan, MacDonald, Mathew, McNaughton, McNaughton, McNaughton, McNaughton, McNaughton, McNaughton, McNaughton, McNaughton, Mitchell, Nachev, Nachev, Nachev, Neo, Okamoto, Pascual-Marqui, Rubia, Schonbrodt, Shadli, Shadli, Stinear, Verbruggen, Woodnorth, Young, Zhang

In the database it does not list any editors, only the authors of which there are seven and they do not exactly match what is listed in the editor field. Authors: Shadli SM, High O, Byers B, Gibbs P, Steller R, Glue P, McNaughton N.

JM1723 · July 31, 2019

Oh wait I see the issue... Zotero has taken the first author name of the list of cited references under this record and listed them as editors. That is what the error is coming from.

dstillman · July 31, 2019

We'd still want to see the actual URL that you're trying to save. You can x out your institution name.

JM1723 · July 31, 2019

dstillman · July 31, 2019

OK, I can only access that article through either Journals@Ovid or APA PsycNET, neither of which has this problem. Can you download the RIS for a single item that shows this problem and paste it here?

dstillman · July 31, 2019

(But basically, since you're actually importing a RIS file rather than using the Save to Zotero button, it means that the incorrect data is in the RIS file itself. If you provide the RIS we can see exactly what's there, though.)

JM1723 · July 31, 2019

Here is what was in the RIS file:
Part 1

1.
TY - JOUR
ID - 2019-33051-001
DO - http://dx.doi.org/10.1037/bne0000316
T1 - Human anxiety-specific "theta" occurs with selective stopping and localizes to right inferior frontal gyrus.
A1 - Shadli, Shabah M
A1 - High, Olivia
A1 - Byers, Bede
A1 - Gibbs, Polly
A1 - Steller, Rubina
A1 - Glue, Paul
A1 - McNaughton, Neil
A2 - Aron, Aron, Baxter, Carver, Chung, Corr, Coxon, Filiou, Floden, Gratton, Gray, Gray, Insel, Kessler, Kessler, Kessler, LeDoux, Logan, MacDonald, Mathew, McNaughton, McNaughton, McNaughton, McNaughton, McNaughton, McNaughton, McNaughton, McNaughton, Mitchell, Nachev, Nachev, Nachev, Neo, Okamoto, Pascual-Marqui, Rubia, Schonbrodt, Shadli, Shadli, Stinear, Verbruggen, Woodnorth, Young, Zhang
Y1 - 2019//
N1 - International Australasian Winter Conference on Brain Research. 36th. An earlier version of this article was presented at the aforementioned conference.
N2 - Anxiety disorders have high prevalence and generate major disability. But they have poor treatment targeting because psychiatry lacks diagnostic biomarkers. Right frontal goal-conflict-specific-rhythmicity (GCSR) in the simple stop signal task appears homologous to hippocampal "theta" as an anxiety-process biomarker but is weak and transient. An anticipatory response inhibition task (ARIT) elicits strong subjective conflict and so might generate stronger GCSR. Healthy participants provided EEG during an ARIT, which allowed direct comparison of selective (left, SG; right, GS), and nonselective (both, SS) handed stopping. We assessed GCSR as intermediate versus the average of short and long delay stop-specific power. SG produced right frontal 5-12 Hz GCSR that, as in the SST: significantly correlated with trait anxiety and neuroticism; and was sensitive to pregabalin (75 mg), buspirone (10 mg), and perhaps triazolam (0.25 mg). GS and SS produced faster stopping and only 9-10Hz GCSR, which did not correlate significantly with trait anxiety or neuroticism and was sensitive to pregabalin and buspirone but not triazolam. Source localization suggested that GCSR, like stopping, involves multiple right frontal circuits that depend on response speed. Anxiolytic-sensitive GCSR generalizes from the speeded stop signal task to fixed-time anticipatory response inhibition tasks. GCSR, and the circuits engaged, vary with stop signal RTs conditions. Tasks with longer stop times may be optimal to generate GCSR homologous with rodent hippocampal theta as (a) the first direct anchor of a specific neural form of trait anxiety; (b) a single-dose screen in normal humans for novel anxiolytics; and (c) a potential clinical anxiety biomarker. (PsycINFO Database Record (c) 2019 APA, all rights reserved)
KW - *Anxiety
KW - *Biological Markers
KW - *Hippocampus
KW - *Neuroticism
KW - *Response Inhibition
KW - Buspirone
KW - Theta Rhythm
KW - Triazolam
KW - Pregabalin
M3 - Electrophysiology [2530]
JF - Behavioral Neuroscience
SP - No
EP - Specified
CY - US
PB - American Psychological Association
PB - US
SN - 0735-7044

JM1723 · July 31, 2019

Part 2
AD - McNaughton, Neil: Department of Psychology, University of Otago, P.O. Box 56, Dunedin, New Zealand, 9054, neil.mcnaughton@otago.ac.nz
AD - McNaughton, Neil: neil.mcnaughton@otago.ac.nz
M1 - American Psychiatric Association. (2013). Diagnostic and statistical manual of mental disorders (5th ed.). Arlington, VA: Author.2013-14907-000
M1 - Aron, A. R., Robbins, T. W., & Poldrack, R. A. (2004). Inhibition and the right inferior frontal cortex. Trends in Cognitive Sciences, 8, 170-177. http://dx.doi.org/10.1016/j.tics.2004.02.010
M1 - Aron, A. R., Robbins, T. W., & Poldrack, R. A. (2014). Inhibition and the right inferior frontal cortex: One decade on. Trends in Cognitive Sciences, 18, 177-185. http://dx.doi.org/10.1016/j.tics.2013.12.003
M1 - Baxter, A. J., Vos, T., Scott, K. M., Ferrari, A. J., & Whiteford, H. A. (2014). The global burden of anxiety disorders in 2010. Psychological Medicine, 44, 2363-2374. http://dx.doi.org/10.1017/S0033291713003243
M1 - Carver, C. S., & White, T. L. (1994). Behavioral inhibition, behavioral activation, and affective responses to impending reward and punishment: the BIS/BAS scales. Journal of Personality and Social Psychology, 67, 319-333. http://dx.doi.org/10.1037/0022-3514.67.2.319
M1 - Chung, D., Chang, S., Lee, J., Kim, S., Park, H., Ryu, S., & Jeong, J. (2007). EEG source localization analysis for local global visual processing usin sLORETA. IEEE EMBS Conference on Neural Engineering (pp. 568-571). Kohala Coast, Hawaii: IEEE.
M1 - Corr, P. J. (2008). The reinforcement sensitivity theory of personality. Cambridge, England: Cambridge University Press.http://dx.doi.org/10.1017/CBO9780511819384
M1 - Coxon, J. P., Stinear, C. M., & Byblow, W. D. (2007). Selective inhibition of movement. Journal of Neurophysiology, 97, 2480-2489. http://dx.doi.org/10.1152/jn.01284.2006
M1 - Filiou, M. D., & Turck, C. W. (2011). General overview: Biomarkers in neuroscience research. International Review of Neurobiology, 101, 1-17. http://dx.doi.org/10.1016/B978-0-12-387718-5.00001-8

JM1723 · July 31, 2019

Part 3
M1 - Floden, D., & Stuss, D. T. (2006). Inhibitory Control is Slowed in Patients with Right Superior Medial Frontal Damage. Journal of Cognitive Neuroscience, 18, 1843-1849. http://dx.doi.org/10.1162/jocn.2006.18.11.1843
M1 - Gratton, G. (1998). Dealing with artifacts: The EOG contamination of the event-related brain potential. Behavior Research Methods, Instruments, & Computers, 30, 44-53. http://dx.doi.org/10.3758/BF03209415
M1 - Gray, J. A. (1977). Drug effects on fear and frustration: Possible limbic site of action of minor tranquilizers. In L. L. Iversen, S. D. Iversen, & S. H. Snyder (Eds.), Handbook of psychopharmacology. Vol 8: Drugs, neurotransmitters and behaviour (pp. 433-529). New York, NY: Plenum Press.
M1 - Gray, J. A., & McNaughton, N. (2000). The neuropsychology of anxiety: An enquiry into the functions of the septo-hippocampal system (2nd ed.). New York, NY: Oxford University Press.
M1 - Insel, T. (2013). Transforming diagnosis [Web log post]. Bethesda, MD: National Institute of Mental Health. Retrieved from https://www.nimh.nih.gov/about/directors/thomas-insel/blog/2013/transforming-diagnosis.shtml
M1 - Kessler, R. C. (2007). The global burden of anxiety and mood disorders: Putting the European Study of the Epidemiology of Mental Disorders (ESEMeD) findings into perspective. The Journal of Clinical Psychiatry, 68(Suppl. 2), 10-19.172885022008-13135-002
M1 - Kessler, R. C., Berglund, P., Demler, O., Jin, R., Merikangas, K. R., & Walters, E. E. (2005). Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Archives of General Psychiatry, 62, 593-602. http://dx.doi.org/10.1001/archpsyc.62.6.593
M1 - Kessler, R. C., Ruscio, A. M., Shear, K., & Wittchen, H.-U. (2010). Epidemiology of Anxiety Disorders. In M. B. Stein & T. Steckler (Eds.), Behavioral neurobiology of anxiety and its treatment (pp. 21-35). Berlin, Germany: Springer Berlin Heidelberg.2010-13520-002
M1 - LeDoux, J. (2012). Rethinking the emotional brain. Neuron, 73, 653-676. http://dx.doi.org/10.1016/j.neuron.2012.02.004
M1 - Logan, G. D., & Cowan, W. B. (1984). On the Ability to Inhibit Thought and Action: A Theory of an Act of Control. Psychological Review, 91, 295-327. http://dx.doi.org/10.1037/0033-295X.91.3.295
M1 - MacDonald, H. J., Coxon, J. P., Stinear, C. M., & Byblow, W. D. (2014). The fall and rise of corticomotor excitability with cancellation and reinitiation of prepared action. Journal of Neurophysiology, 112, 2707-2717. http://dx.doi.org/10.1152/jn.00366.2014
M1 - Mathew, S. J., Price, R. B., & Charney, D. S. (2008). Recent advances in the neurobiology of anxiety disorders: Implications for novel therapeutics. American Journal of Medical Genetics. Part C, Seminars in Medical Genetics, 148C, 2, 89-98. http://dx.doi.org/10.1002/ajmg.c.30172
M1 - McNaughton, N. (1990). Evolution and anxiety. In N. McNaughton & G. Andrews (Eds.), Anxiety (Vol. 1, pp. 115-121). Dunedin, New Zealand: University of Otago Press.1990-98566-012
M1 - McNaughton, N. (1999). A gene promotes anxiety in mice-and also in scientists. Nature Medicine, 5, 1131-1132. http://dx.doi.org/10.1038/13455
M1 - McNaughton, N. (2018). What do you mean "anxiety"? Developing the first anxiety syndrome biomarker. Journal of the Royal Society of New Zealand, 48, 177-190. http://dx.doi.org/10.1080/03036758.2017.1358184
M1 - McNaughton, N., & Corr, P. J. (2004). A two-dimensional neuropsychology of defense: Fear/anxiety and defensive distance. Neuroscience and Biobehavioral Reviews, 28, 285-305. http://dx.doi.org/10.1016/j.neubiorev.2004.03.005
M1 - McNaughton, N., Kocsis, B., & Hajos, M. (2007). Elicited hippocampal theta rhythm: A screen for anxiolytic and procognitive drugs through changes in hippocampal function?. Behavioural Pharmacology, 18, 5-6, 329-346. http://dx.doi.org/10.1097/FBP.0b013e3282ee82e3
M1 - McNaughton, N., Ruan, M., & Woodnorth, M. A. (2006). Restoring theta-like rhythmicity in rats restores initial learning in the Morris water maze. Hippocampus, 16, 1102-1110. http://dx.doi.org/10.1002/hipo.20235
M1 - McNaughton, N., Swart, C., Neo, P., Bates, V., & Glue, P. (2013). Anti-anxiety drugs reduce conflict-specific "theta"-A possible human anxiety-specific biomarker. Journal of Affective Disorders, 148, 104-111. http://dx.doi.org/10.1016/j.jad.2012.11.057
M1 - McNaughton, N., & Zangrossi, H. (2008). Theoretical approaches to the modeling of anxiety in animals, Handbook of anxiety and fear. New York, NY: Elsevier.17, 11-27. http://dx.doi.org/10.1016/S1569-7339(07)00002-1
M1 - Mitchell, D. J., McNaughton, N., Flanagan, D., & Kirk, I. J. (2008). Frontal-midline theta from the perspective of hippocampal "theta.". Progress in Neurobiology, 86, 156-185. http://dx.doi.org/10.1016/j.pneurobio.2008.09.005
M1 - Nachev, P., Kennard, C., & Husain, M. (2008). Functional role of the supplementary and pre-supplementary motor areas. Nature Reviews Neuroscience, 9, 856-869. http://dx.doi.org/10.1038/nrn2478
M1 - Nachev, P., Rees, G., Parton, A., Kennard, C., & Husain, M. (2005). Volition and conflict in human medial frontal cortex. Current Biology, 15, 122-128. http://dx.doi.org/10.1016/j.cub.2005.01.006
M1 - Nachev, P., Wydell, H., O'neill, K., Husain, M., & Kennard, C. (2007). The role of the pre-supplementary motor area in the control of action. NeuroImage, 36, T155-T163. http://dx.doi.org/10.1016/j.neuroimage.2007.03.034
M1 - Neo, P. S., Thurlow, J. K., & McNaughton, N. (2011). Stopping, goal-conflict, trait anxiety and frontal rhythmic power in the stop-signal task. Cognitive, Affective & Behavioral Neuroscience, 11, 485-493. http://dx.doi.org/10.3758/s13415-011-0046-x
M1 - Okamoto, H., & Aizawa, H. (2013). Fear and anxiety regulation by conserved affective circuits. Neuron, 78, 411-413. http://dx.doi.org/10.1016/j.neuron.2013.04.031
M1 - Pascual-Marqui, R. D. (2002). Standardized low resolution brain electromagnetic tomography (sLORETA): technical details. Methods and Findings in Experimental and Clinical Pharmacology, 24D, 5-12.12575463
M1 - Rubia, K., Smith, A. B., Brammer, M. J., & Taylor, E. (2003). Right inferior prefrontal cortex mediates response inhibition while mesial prefrontal cortex is responsible for error detection. NeuroImage, 20, 351-358. http://dx.doi.org/10.1016/S1053-8119(03)00275-1
M1 - Schonbrodt, F. D., & Perugini, M. (2013). At what sample size do correlations stabilize?. Journal of Research in Personality, 47, 609-612. http://dx.doi.org/10.1016/j.jrp.2013.05.009
M1 - Shadli, S. M., Glue, P., McIntosh, J., & McNaughton, N. (2015). An improved human anxiety process biomarker: Characterization of frequency band, personality and pharmacology. Translational Psychiatry, 5, 12, e699http://dx.doi.org/10.1038/tp.2015.188
M1 - Shadli, S. M., Smith, M. J., Glue, P., & McNaughton, N. (2016). Testing an anxiety process biomarker: Generalisation from an auditory to a visual stimulus. Biological Psychology, 117, 50-55. http://dx.doi.org/10.1016/j.biopsycho.2016.02.011
M1 - Stinear, C. M., Coxon, J. P., & Byblow, W. D. (2009). Primary motor cortex and movement prevention: Where Stop meets Go. Neuroscience and Biobehavioral Reviews, 33, 662-673. http://dx.doi.org/10.1016/j.neubiorev.2008.08.013
M1 - Verbruggen, F., & Logan, G. D. (2008). Response inhibition in the stop-signal paradigm. Trends in Cognitive Sciences, 12, 418-424. http://dx.doi.org/10.1016/j.tics.2008.07.005
M1 - Woodnorth, M. A., & McNaughton, N. (2002). Similar effects of medial supramammillary or systemic injection of chlordiazepoxide on both theta frequency and fixed-interval responding. Cognitive, Affective & Behavioral Neuroscience, 2, 76-83. http://dx.doi.org/10.3758/CABN.2.1.76
M1 - World Health Organization. (2010). International statistical classification of diseases and related health problems (10th revision). Retrieved from http://apps.who.int/classifications/icd10/browse/2010/en

JM1723 · July 31, 2019

Part 4
M1 - Young, C. K., & McNaughton, N. (2009). Coupling of theta oscillations between anterior and posterior midline cortex and with the hippocampus in freely behaving rats. Cerebral Cortex, 19, 24-40. http://dx.doi.org/10.1093/cercor/bhn055
M1 - Zhang, S., McIntosh, J., Shadli, S. M., Neo, P. S., Huang, Z., & McNaughton, N. (2017). Removing eye blink artefacts from EEG-A single-channel physiology-based method. Journal of Neuroscience Methods, 291, 213-220. http://dx.doi.org/10.1016/j.jneumeth.2017.08.031
DO - http://dx.doi.org/10.1037/bne0000316
L2 - http://ovidsp.ovid.com/ovidweb.cgi?T=JS&PAGE=reference&D=psyc16&NEWS=N&AN=2019-33051-001
ER -
NL - Behav Neurosci

Link to the Ovid Full Text or citation: http://ezproxy.lib.xxx.edu.au/login?url=http://ovidsp.ovid.com/ovidweb.cgi?T=JS&CSC=Y&NEWS=N&PAGE=fulltext&D=psyc16&AN=2019-33051-001Link to the External Link Resolver: http://ezproxy.lib.monash.edu.au/login?url=https://monash-hosted-exlibrisgroup-com.ezproxy.lib.monash.edu.au/primo-explore/openurl?institution=MUA&vid=MONUI_SP&lang=en_US&sid=OVID:psycdb&id=pmid:&id=doi:10.1037/bne0000316&issn=0735-7044&isbn=&volume=&issue=&spage=No&pages=No+Pagination+Specified&date=2019&title=Behavioral+Neuroscience&atitle=Human+anxiety-specific+"theta"+occurs+with+selective+stopping+and+localizes+to+right+inferior+frontal+gyrus.&aulast=Shadli&pid=<author>Shadli,+Shabah+M;High,+Olivia;Byers,+Bede;Gibbs,+Polly;Steller,+Rubina;Glue,+Paul;McNaughton,+Neil</author><AN>2019-33051-001</AN><DT>Journal+Article</DT>

dstillman · July 31, 2019

Right, so, as you can see, all those names are in the RIS file as A2 (Secondary Author). Someone else would know the details on why we treat that as Editor for some item types — presumably for compatibility with EndNote or other programs that violate the RIS spec — but the fact that they're listed as authors at all in the RIS file is obviously incorrect.

JM1723 · July 31, 2019

Yes agreed!
So then this is then more a problem with PsycINFO and there isn't anything that can be done to fix this with Zotero unless I manually alter RIS files?

dstillman · July 31, 2019

That's right. If you want, we can help you remove either all the A2 lines (if they're all invalid) or just the ones above a certain length. You'd need to download a text editor like Notepad++ that can do search/replace using regular expressions.

JM1723 · July 31, 2019

Okay. I think I am happy to leave things as they are and know that Notepad++ is an option for the future as I have started using these records in Zotero fir my purposes and altering RIS would mean starting again which would take a substantial amount of time. I will keep this in mean for when I am working with PsycINFO again.

But thanks so much for all your help, dstillman!
Cheers,
JM1723

dstillman · July 31, 2019

Actually, we could also just tell you some code you could run in Zotero to remove all the editors above a certain length…

JM1723 · July 31, 2019

Oh really?
That would be swell if that's the case!

dstillman · July 31, 2019

OK, first temporarily disable auto-sync in the Sync pane of the preferences, close Zotero, and make a backup of the zotero.sqlite file in your Zotero data directory.

Next, enable and open the Run JavaScript window:

https://www.zotero.org/support/dev/client_coding/javascript_api#running_ad_hoc_javascript_in_zotero

Then run this code to see the "Editor" fields that will be removed:

var maxLength = 255;
var items = await Zotero.Items.getAll(Zotero.Libraries.userLibraryID);
var longCreators = [];
for (let item of items) {
    for (let i = 0; i < item.numCreators(); i++) {
        let creator = item.getCreator(i);
        if (creator.creatorTypeID == Zotero.CreatorTypes.getID('editor')) {
            let name = (creator.firstName + ' ' + creator.lastName).trim();
            if (name.length > maxLength) {
                longCreators.push(name);
            }
        }
    }
}
return longCreators;

Finally, to actually remove them, run this code:

var maxLength = 255;
var items = await Zotero.Items.getAll(Zotero.Libraries.userLibraryID);
for (let item of items) {
    let changed = false;
    for (let i = 0; i < item.numCreators(); i++) {
        let creator = item.getCreator(i);
        if (creator.creatorTypeID == Zotero.CreatorTypes.getID('editor')) {
            let name = (creator.firstName + ' ' + creator.lastName).trim();
            if (name.length > maxLength) {
                item.removeCreator(i);
                i--;
                changed = true;
            }
        }
    }
    if (changed) {
        await item.saveTx();
    }
}

If everything looks good — you can sort by Date Modified in the middle pane and review the modified items — then you can re-enable auto-sync.

JM1723 · July 31, 2019

That has worked a treat!
Thanks so much for all your help and time spent dstillman, this has saved me so much time!
Cheers,
JM1723

uklomp1 · August 3, 2020

Hi, we have the same problem, but none of the files return, even if we insert 'maxLength = 3'.
Edit: I think it has to do with the code referring to my main library, as I was now able to retrieve files from my main library (where no sync problem occurs) when inserting something like 'maxLenght = 10'. But the problem is within our Group Libary and my coding skills end here. What would be the adjustment(s) for that?
Thanks!

dstillman · August 4, 2020

@uklomp1: Replace this line:

var items = await Zotero.Items.getAll(Zotero.Libraries.userLibraryID);

with this:

var items = await Zotero.Items.getAll(Zotero.Groups.getAll().filter(x => x.name == 'GROUP NAME')[0].libraryID);

…where GROUP NAME is the name of the group.

uklomp1 · August 10, 2020

That worked great. Thank you very much!