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retorquere / zotero-better-bibtex

Make Zotero effective for us LaTeX holdouts
https://retorque.re/zotero-better-bibtex/
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Prob with cite-keys when used with Eratosthenes #83

Closed RustyRiley closed 10 years ago

RustyRiley commented 10 years ago

got following comment from developer of Eratosthenes app for Android --

"It looks like this is not an eratosthenes problem though. It appears that Better BibTeX is putting spaces in the cite-keys in your bibtex output, which is not valid. It is also putting ' characters in the cite-keys, which I believe is also not valid under the BibTeX standard.

You'll need to contact the dev for better bibtex about this issue. In the mean time, I've fixed your .bib file. It is attached. The next version of eratosthenes will ignore these errors, but you will lose the affected entries. -Matt Matlock P.S. I did find an incidental bug when the last ; is missing from the groupstree, I have fixed this in your file, but I will need to publish an update to the play store to prevent future problems with this."

retorquere commented 10 years ago

Could you export a reference that exhibits this problem using the "Zotero TestCase" exporter and put it in a gist, and add the citekeyformat you use to this issue here?

RustyRiley commented 10 years ago

tried to respond by sending the .bib file -- but it's 4 Mb in size so got error message saying the message couldn't be sent -- not sure what exactly I can do -- I could send a screenshot of what happens when I try to open the database in Eratosthenes, but that would just give some indication of the first error -- Paredes2013 was what came up as the first BUT without the file that tells you nothing? Ideas?

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Sunday, 6 July 2014 12:12 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Could you export a reference that exhibits this problem using the "Zotero TestCase" exporter and put it in a gist, and add the citekeyformat you use to this issue here? — Reply to this email directly or view it on GitHub.

RustyRiley commented 10 years ago

sorry, had never heard of "Zotero Test Case Exporter" till your email but it's for this reference --

http://www.ncbi.nlm.nih.gov/pubmed/24292965

but again, don't know if I can enter JSON files into "this page"

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Sunday, 6 July 2014 12:12 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Could you export a reference that exhibits this problem using the "Zotero TestCase" exporter and put it in a gist, and add the citekeyformat you use to this issue here? — Reply to this email directly or view it on GitHub.

RustyRiley commented 10 years ago

these things are not "the format you use" -- but as generated by the plugin from the file I've got -- figured, in hindsight, the json file might be viewable as a text file --- if so:

[     {         "itemID": "PadillaParedes2013",         "itemType": "journalArticle",         "url": "",         "rights": "",         "series": "",         "volume": "",         "issue": "",         "pages": "",         "publicationTitle": "Journal of abnormal child psychology",         "ISSN": "1573-2835",         "date": "Nov 29, 2013",         "callNumber": "",         "archiveLocation": "",         "extra": "PMID: 24292965",         "journalAbbreviation": "J Abnorm Child Psychol",         "DOI": "10.1007/s10802-013-9828-7",         "accessDate": "",         "seriesTitle": "",         "seriesText": "",         "libraryCatalog": "NCBI PubMed",         "language": "ENG",         "abstractNote": "This study tested whether childhood parental emotional abuse and peer emotional bullying serve as antecedents of depression in adolescence and identified the cognitive mechanisms involved in this process. It was hypothesized that the experience of emotional abuse would predict depressive symptoms via development of rumination and negative inferences. A 3-wave longitudinal study was carried out with 998 adolescents (471 girls and 526 boys) between 13 and 17 years of age. Results showed that emotional abuse by parents and peers at Time 1 predicted a worsening of several cognitive vulnerabilities at Time 2. In addition, brooding mediated between the experiences of abuse and the increase of depressive symptoms at Time 3. Thus, findings suggest that the experiences of childhood emotional abuse by parents and peers serve as antecedents to develop a negative cognitive style, vulnerability that, once developed, is a risk factor for the onset of depressive symptoms in adolescence.",         "title": "Cognitive Vulnerabilities as Mediators between Emotional Abuse and Depressive Symptoms",         "shortTitle": "",         "archive": "",         "creators": [             {                 "creatorType": "author",                 "firstName": "Patricia",                 "lastName": "Padilla Paredes",                 "fieldMode": ""             },             {                 "creatorType": "author",                 "firstName": "Esther",                 "lastName": "Calvete",                 "fieldMode": ""             }         ],         "notes": [],         "attachments": [             {                 "title": "PubMed entry",                 "mimeType": "text/html"             }         ],         "tags": [],         "related": [],         "seeAlso": []     } ]

the citekey  is as produced by the Zotero BetterBibTex plugin -- hence the enquiry

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Sunday, 6 July 2014 12:12 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Could you export a reference that exhibits this problem using the "Zotero TestCase" exporter and put it in a gist, and add the citekeyformat you use to this issue here? — Reply to this email directly or view it on GitHub.

retorquere commented 10 years ago

OK, and what is the citekey format from the better bibtex preferences? On Jul 6, 2014 5:24 AM, "RustyRiley" notifications@github.com wrote:

these things are not "the format you use" -- but as generated by the plugin from the file I've got -- figured, in hindsight, the json file might be viewable as a text file --- if so:

[ { "itemID": "PadillaParedes2013", "itemType": "journalArticle", "url": "", "rights": "", "series": "", "volume": "", "issue": "", "pages": "", "publicationTitle": "Journal of abnormal child psychology", "ISSN": "1573-2835", "date": "Nov 29, 2013", "callNumber": "", "archiveLocation": "", "extra": "PMID: 24292965", "journalAbbreviation": "J Abnorm Child Psychol", "DOI": "10.1007/s10802-013-9828-7", "accessDate": "", "seriesTitle": "", "seriesText": "", "libraryCatalog": "NCBI PubMed", "language": "ENG", "abstractNote": "This study tested whether childhood parental emotional abuse and peer emotional bullying serve as antecedents of depression in adolescence and identified the cognitive mechanisms involved in this process. It was hypothesized that the experience of emotional abuse would predict depressive symptoms via development of rumination and negative inferences. A 3-wave longitudinal study was carried out with 998 adolescents (471 girls and 526 boys) between 13 and 17Â years of age. Results showed that emotional abuse by parents and peers at Time 1 predicted a worsening of several cognitive vulnerabilities at Time 2. In addition, brooding mediated between the experiences of abuse and the increase of depressive symptoms at Time 3. Thus, findings suggest that the experiences of childhood emotional abuse by parents and peers serve as antecedents to develop a negative cognitive style, vulnerability that, once developed, is a risk factor for the onset of depressive symptoms in adolescence.", "title": "Cognitive Vulnerabilities as Mediators between Emotional Abuse and Depressive Symptoms", "shortTitle": "", "archive": "", "creators": [ { "creatorType": "author", "firstName": "Patricia", "lastName": "Padilla Paredes", "fieldMode": "" }, { "creatorType": "author", "firstName": "Esther", "lastName": "Calvete", "fieldMode": "" } ], "notes": [], "attachments": [

    {
            "title": "PubMed entry",
            "mimeType": "text/html"
        }
    ],
    "tags": [],
    "related": [],
    "seeAlso": []
}

]

the citekey is as produced by the Zotero BetterBibTex plugin -- hence the enquiry

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com

Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Sunday, 6 July 2014 12:12 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Could you export a reference that exhibits this problem using the "Zotero TestCase" exporter and put it in a gist, and add the citekeyformat you use to this issue here? — Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48102068 .

RustyRiley commented 10 years ago

That's probably specified in the plugin description - - it's not one of the Zotero export options to output it separately from what I can see

Russell J. Wilson Dunedin Aotearoa / New Zealand Sent from my android device.

-----Original Message----- From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Sun, 06 Jul 2014 6:11 pm Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

OK, and what is the citekey format from the better bibtex preferences? On Jul 6, 2014 5:24 AM, "RustyRiley" notifications@github.com wrote:

these things are not "the format you use" -- but as generated by the plugin from the file I've got -- figured, in hindsight, the json file might be viewable as a text file --- if so:

[ { "itemID": "PadillaParedes2013", "itemType": "journalArticle", "url": "", "rights": "", "series": "", "volume": "", "issue": "", "pages": "", "publicationTitle": "Journal of abnormal child psychology", "ISSN": "1573-2835", "date": "Nov 29, 2013", "callNumber": "", "archiveLocation": "", "extra": "PMID: 24292965", "journalAbbreviation": "J Abnorm Child Psychol", "DOI": "10.1007/s10802-013-9828-7", "accessDate": "", "seriesTitle": "", "seriesText": "", "libraryCatalog": "NCBI PubMed", "language": "ENG", "abstractNote": "This study tested whether childhood parental emotional abuse and peer emotional bullying serve as antecedents of depression in adolescence and identified the cognitive mechanisms involved in this process. It was hypothesized that the experience of emotional abuse would predict depressive symptoms via development of rumination and negative inferences. A 3-wave longitudinal study was carried out with 998 adolescents (471 girls and 526 boys) between 13 and 17Â years of age. Results showed that emotional abuse by parents and peers at Time 1 predicted a worsening of several cognitive vulnerabilities at Time 2. In addition, brooding mediated between the experiences of abuse and the increase of depressive symptoms at Time 3. Thus, findings suggest that the experiences of childhood emotional abuse by parents and peers serve as antecedents to develop a negative cognitive style, vulnerability that, once developed, is a risk factor for the onset of depressive symptoms in adolescence.", "title": "Cognitive Vulnerabilities as Mediators between Emotional Abuse and Depressive Symptoms", "shortTitle": "", "archive": "", "creators": [ { "creatorType": "author", "firstName": "Patricia", "lastName": "Padilla Paredes", "fieldMode": "" }, { "creatorType": "author", "firstName": "Esther", "lastName": "Calvete", "fieldMode": "" } ], "notes": [], "attachments": [

    {
            "title": "PubMed entry",
            "mimeType": "text/html"
        }
    ],
    "tags": [],
    "related": [],
    "seeAlso": []
}

]

the citekey is as produced by the Zotero BetterBibTex plugin -- hence the enquiry

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com

Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Sunday, 6 July 2014 12:12 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Could you export a reference that exhibits this problem using the "Zotero TestCase" exporter and put it in a gist, and add the citekeyformat you use to this issue here? — Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48102068 .

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48103928

retorquere commented 10 years ago

Ah no, I mean: if you go into Preferences -> Better Bib(La)TeX, what does it say in the "Citation key format" field.

RustyRiley commented 10 years ago

Sorry - you're dealing a real novice here

[auth] [year]

Russell J. Wilson Dunedin Aotearoa / New Zealand Sent from my android device.

-----Original Message----- From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Sun, 06 Jul 2014 6:25 pm Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Ah no, I mean: if you go into Preferences -> Better Bib(La)TeX, what does it say in the "Citation key format" field.

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48104151

RustyRiley commented 10 years ago

Haven't checked individual records yet, but the most recent update to Eratosthenes has "fixed" the problem - no errors encountered in opening a new file - same database, with additional references

Russell J. Wilson Dunedin Aotearoa / New Zealand Sent from my android device.

-----Original Message----- From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Sun, 06 Jul 2014 6:25 pm Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Ah no, I mean: if you go into Preferences -> Better Bib(La)TeX, what does it say in the "Citation key format" field.

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48104151

retorquere commented 10 years ago

That's OK - I just want to have this fixed.

retorquere commented 10 years ago

I'm sorry the process of submitting an issue is so esoteric; I have some ideas on making that better, but that's still a little bit out. In the interim, could you let the plugin update itself to 0.5.46, then select one or more entries that exhibit the problem you describe, and export those with the (updated) Zotero TestCase exporter. If you could then upload the resulting file to https://gist.github.com/ and paste the resulting link here, I think I will have enough information to solve it. Unfortunately, the github issue tracker where we are having this discussion tries to style the text, so the entry you pasted in usually altered in subtle ways so as to no longer being what you actually posted, which makes bug tracking harder.

RustyRiley commented 10 years ago

did you get my last email?

Matthew Matlock, the developer of Eratosthenes, released an update a few hours ago -- that successfully addressed the problem, at least as far as the Zotero-BetterBibTex-Eratosthenes link goes

I've updated the extension -- for some reason, i had to click "Check for Updates" in the Zotero Add-ons Manager -- now, the import process (Zotero-BetterBibTex-Eratosthenes) -- works with both the update to the extension and to the app -- but "most people" won't "need' to update the extension to get the process to work "successfully" -- no errors come up, but there are clearly some errors somewhere -- the overall process imported 2334 items into Eratosthenes, but Zotero shows there are 2359 items in the Zotero file -- no difference in number of items imported before/after installing the .46 update

-- but, no way of telling which items are missing -- no errors come up -- probably some "errors" in the original Zotero file independent of extensions, apps etc

thanks for your continued attention to the issues

Russell J. Wilson Dunedin, New Zealand

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Sunday, 6 July 2014 9:41 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

I'm sorry the process of submitting an issue is so esoteric; I have some ideas on making that better, but that's still a little bit out. In the interim, could you let the plugin update itself to 0.5.46, then select one or more entries that exhibit the problem you describe, and export those with the (updated) Zotero TestCase exporter. If you could then upload the resulting file to https://gist.github.com/ and paste the resulting link here, I think I will have enough information to solve it. Unfortunately, the github issue tracker where we are having this discussion tries to style the text, so the entry you pasted in usually altered in subtle ways so as to no longer being what you actually posted, which makes bug tracking harder. — Reply to this email directly or view it on GitHub.

retorquere commented 10 years ago

I didn't see that last massage before you resubmitted it, no. Like the developer of Eratosthenes. I adhere to the creed "be liberal in what you accept, be strict in what you send out". So while I'm happy the Eratosthenes developer managed to work around the error my plugin is generating, I'd rather not be generating it, so I would be hugely appreciative if you could still upload a new testcase to https://gist.github.com/ for any of the entries that generate these faulty keys. I really do want to get this sorted -- thank you for your patience in that regard.

Do you have any idea which of these entries are not picked up by Eratosthenes? I'd also love to get a testcase of one of those.

retorquere commented 10 years ago

Ah, could those extra entries possibly be standalone notes or attachments? The BibTeX exporters don't export those at all.

RustyRiley commented 10 years ago

sorry, I respect what you're trying to do, truly, but don't understand exactly  --- as I tried to explain in my last email   -- there are NO errors currently presenting, so a testcase of WHAT?        --  if the new version of Eratosthenes is not presenting with any errors?       -- as mentioned, before when the "errors" were showing up, Eratosthenes would list a signal error and then abort -- do you want a "testcase" of the single entry of the one that was causing a problem before -- won't that be exactly the same "testcase" as I've already sent?

Separate Issue:

currently I have no idea what entries are not being picked up by Eratosthenes, or for that matter which might not be being exported by Zotero, but as you suggest in your other email, that's a possibility -- see attached PNG file -- clearly, I've on occasion been "too  hasty" with some downloads, and haven't gone back to correct the missing details, or simply haven't deleted those PDF files you can see, if I've created "duplicate entries" with additional details  -- not sure how I get a listing of those from Zotero -- and 25 out of 2000+ ?

Thanks again R

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Sunday, 6 July 2014 11:07 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

I didn't see that last massage before you resubmitted it, no. Like the developer of Eratosthenes. I adhere to the creed "be liberal in what you accept, be strict in what you send out". So while I'm happy the Eratosthenes developer managed to work around the error my plugin is generating, I'd rather not be generating it, so I would be hugely appreciative if you could still upload a new testcase to https://gist.github.com/ for any of the entries that generate these faulty keys. I really do want to get this sorted -- thank you for your patience in that regard. Do you have any idea which of these entries are not picked up by Eratosthenes? I'd also love to get a testcase of one of those. — Reply to this email directly or view it on GitHub.

retorquere commented 10 years ago

sorry, I respect what you're trying to do, truly, but don't understand exactly

That's OK, I'm not always clear enough when I express myself.

--- as I tried to explain in my last email -- there are NO errors currently presenting, so a testcase of WHAT?

A testcase of an entry that used to cause errors in Eratosthenes before you updated it.

  --  if the new version of Eratosthenes is not presenting with any

errors? -- as mentioned, before when the "errors" were showing up, Eratosthenes would list a signal error and then abort -- do you want a "testcase" of the single entry of the one that was causing a problem before -- won't that be exactly the same "testcase" as I've already sent?

Yes; It is nice that the Eratosthenes developer added a workaround for the error I generate, but I'd rather not generate the error at all. The testcase will probably be, but the github formatter modifies what is pasted in here, which I'd rather avoid, and the new testcase exporter includes the export-relevant settings, so we avoid copy-paste errors there too if uploaded to gist.guthub.com. The gist system is careful to not modify what is pasted here, where the issue tracker here does modify things.

Separate Issue:

currently I have no idea what entries are not being picked up by Eratosthenes, or for that matter which might not be being exported by Zotero, but as you suggest in your other email, that's a possibility -- see attached PNG file

Ah, these mails are going through the github issue tracker, which strips attachments, so the PNG isn't there.

-- clearly, I've on occasion been "too hasty" with some downloads, and haven't gone back to correct the missing details, or simply haven't deleted those PDF files you can see, if I've created "duplicate entries" with additional details -- not sure how I get a listing of those from Zotero -- and 25 out of 2000+ ?

If you want me to look, you can create an export of those 2000+ with the Zotero TestCase exporter, and the .bib file that results after saving in Eratosthenes (if that can be done, I don't know), and drop them into http://dbinbox.com/allthatisthecase/ (you can also drop the testcase file above there instead of uploading it to a gist). I'd be happy to look into it.

RustyRiley commented 10 years ago

Can I back to you tomorrow? - - bit late here in New Zealand - - after midnight And need more time to "digest" the procedure - - never done this before

Russell J. Wilson Dunedin Aotearoa / New Zealand Sent from my android device.

-----Original Message----- From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Mon, 07 Jul 2014 12:09 am Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

sorry, I respect what you're trying to do, truly, but don't understand exactly

That's OK, I'm not always clear enough when I express myself.

--- as I tried to explain in my last email -- there are NO errors currently presenting, so a testcase of WHAT?

A testcase of an entry that used to cause errors in Eratosthenes before you updated it.

  --  if the new version of Eratosthenes is not presenting with any

errors? -- as mentioned, before when the "errors" were showing up, Eratosthenes would list a signal error and then abort -- do you want a "testcase" of the single entry of the one that was causing a problem before -- won't that be exactly the same "testcase" as I've already sent?

Yes; It is nice that the Eratosthenes developer added a workaround for the error I generate, but I'd rather not generate the error at all. The testcase will probably be, but the github formatter modifies what is pasted in here, which I'd rather avoid, and the new testcase exporter includes the export-relevant settings, so we avoid copy-paste errors there too if uploaded to gist.guthub.com. The gist system is careful to not modify what is pasted here, where the issue tracker here does modify things.

Separate Issue:

currently I have no idea what entries are not being picked up by Eratosthenes, or for that matter which might not be being exported by Zotero, but as you suggest in your other email, that's a possibility -- see attached PNG file

Ah, these mails are going through the github issue tracker, which strips attachments, so the PNG isn't there.

-- clearly, I've on occasion been "too hasty" with some downloads, and haven't gone back to correct the missing details, or simply haven't deleted those PDF files you can see, if I've created "duplicate entries" with additional details -- not sure how I get a listing of those from Zotero -- and 25 out of 2000+ ?

If you want me to look, you can create an export of those 2000+ with the Zotero TestCase exporter, and the .bib file that results after saving in Eratosthenes (if that can be done, I don't know), and drop them into http://dbinbox.com/allthatisthecase/ (you can also drop the testcase file above there instead of uploading it to a gist). I'd be happy to look into it.

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48110276

retorquere commented 10 years ago

No problem whatsoever. If there's anything else I can help with, I'll be glad to do it. I have been trying to reproduce the error without success so far.

RustyRiley commented 10 years ago

Files uploaded to dbinbox

Important point - - when importing Eratosthenes first scans for compatibility - - it prompts if it thinks it comes from JabRef, BibDesk or if it should be left in native Eratosthenes format - - file uploaded has been set to JabRef during this import process

Russell J. Wilson Dunedin Aotearoa / New Zealand Sent from my android device.

-----Original Message----- From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Mon, 07 Jul 2014 12:09 am Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

sorry, I respect what you're trying to do, truly, but don't understand exactly

That's OK, I'm not always clear enough when I express myself.

--- as I tried to explain in my last email -- there are NO errors currently presenting, so a testcase of WHAT?

A testcase of an entry that used to cause errors in Eratosthenes before you updated it.

  --  if the new version of Eratosthenes is not presenting with any

errors? -- as mentioned, before when the "errors" were showing up, Eratosthenes would list a signal error and then abort -- do you want a "testcase" of the single entry of the one that was causing a problem before -- won't that be exactly the same "testcase" as I've already sent?

Yes; It is nice that the Eratosthenes developer added a workaround for the error I generate, but I'd rather not generate the error at all. The testcase will probably be, but the github formatter modifies what is pasted in here, which I'd rather avoid, and the new testcase exporter includes the export-relevant settings, so we avoid copy-paste errors there too if uploaded to gist.guthub.com. The gist system is careful to not modify what is pasted here, where the issue tracker here does modify things.

Separate Issue:

currently I have no idea what entries are not being picked up by Eratosthenes, or for that matter which might not be being exported by Zotero, but as you suggest in your other email, that's a possibility -- see attached PNG file

Ah, these mails are going through the github issue tracker, which strips attachments, so the PNG isn't there.

-- clearly, I've on occasion been "too hasty" with some downloads, and haven't gone back to correct the missing details, or simply haven't deleted those PDF files you can see, if I've created "duplicate entries" with additional details -- not sure how I get a listing of those from Zotero -- and 25 out of 2000+ ?

If you want me to look, you can create an export of those 2000+ with the Zotero TestCase exporter, and the .bib file that results after saving in Eratosthenes (if that can be done, I don't know), and drop them into http://dbinbox.com/allthatisthecase/ (you can also drop the testcase file above there instead of uploading it to a gist). I'd be happy to look into it.

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48110276

retorquere commented 10 years ago

Thanks so much. I have run tests on that entry, and the key consistently comes out as "PadillaParedes2013"; no spaces, and no single quotes. I'm at a loss to explain what happened; the entry you submitted doesn't have any single quotes at all, so I don't know where it would come from. Do you think the Eratosthenes dev still has the sample you submitted to him or her?

The screenshots do indeed show standalone attachments, and these could account for the missing entries. If you want, I can verify by matching the json file you put in dbinbox with the resulting bib file if exported with better bibtex, and uploaded to dbinbox.

I want to thank you again for your patience.

RustyRiley commented 10 years ago

Thanks, can that be done "easily"

Another issue - can file paths be specified relatively instead of absolutely? The current method is not supported by Eratosthenes - - so far I've not bothered with attachments since I'm using it on my phone - - database with files is 4 Gb +, but...

Russell J. Wilson Dunedin Aotearoa / New Zealand Sent from my android device.

-----Original Message----- From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Mon, 07 Jul 2014 4:20 am Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Thanks so much. I have run tests on that entry, and the key consistently comes out as "PadillaParedes2013"; no spaces, and no single quotes. I'm at a loss to explain what happened; the entry you submitted doesn't have any single quotes at all, so I don't know where it would come from. Do you think the Eratosthenes dev still has the sample you submitted to him or her?

The screenshots do indeed show standalone attachments, and these could account for the missing entries. If you want, I can verify by matching the json file you put in dbinbox with the resulting bib file if exported with better bibtex, and uploaded to dbinbox.

I want to thank you again for your patience.

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48116034

retorquere commented 10 years ago

I hope so... You'd just have to export the items you previously exported with "Zotero TestCase" with "Better BibTeX", and drop that into dbinbox.

The paths are relative to the .bib file if you export files... I think I could force Zotero to use relative paths even when not exporting files (I'd have to check), but why not skip the file attachments entirely if you're not going to export them? That can be done in the preferences, by adding "file" to the skip fields.

RustyRiley commented 10 years ago

I got this comment in an email from the Eratosthenes developer, Matt Matlock:

"In the mean time, you'll have to come up with a way to export

your file attachments with relative paths.

Currently I can see that better bibtex is outputting absolute paths,

which will only be usable on one device (namely the computer you

originally downloaded the attachment on).

Ideally, all your attachments should be stored with,

or in a subdirectory of, the .bib file.

Then all paths can be specified relative to the .bib file,

and eratosthenes will be able to recognize and open them. -Matt Matlock"

library file uploaded to dbinbox

I'm interested in exporting the files as well since then I can have the library on both my phone, for "immediate reference", but without the files, and on a new device, a tablet -- the phone's memory, and processing capacity is limited, even importing and searching is pretty slow (but for most things it's better than many newer phones, at least with a custom ROM installed -- wouldn't use it at all with the stock ROM - Samsung Galaxy Ace 2 -- rates better than the Ace 3 on PhoneRocket.com on the things I want, like graphic display--  just haven't decided WHICH tablet to buy yet, Samsung Note 10 etc or "Nexus"

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Monday, 7 July 2014 10:08 AM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

I hope so... You'd just have to export the items you previously exported with "Zotero TestCase" with "Better BibTeX", and drop that into dbinbox. The paths are relative to the .bib file if you export files... I think I could force Zotero to use relative paths even when not exporting files (I'd have to check), but why not skip the file attachments entirely if you're not going to export them? That can be done in the preferences, by adding "file" to the skip fields. — Reply to this email directly or view it on GitHub.

retorquere commented 10 years ago

I've looked at those two files, and that is worrying; if the exact same entries were selected for these exports, a whopping 129 entries are missing from the bib file, all of which should have been there. I'll look into it further.

As to the file path export, it's conceptually difficult to export relative paths for non-existent files, and Zotero doesn't offer relative paths to the translators such as better bibtex unless you're exporting the files. What I could do is add an option to exclude the file paths entirely if you're not exporting files; I think that would accomplish what you need. Right?

RustyRiley commented 10 years ago

re paths -- I'll share this with the Eratosthenes developer and get his opinion, OK?

don't understand about the numbers  -- faulty hypothesis about source of discrepancy / "missing items"

see graphics -- Zotero shows 2359, Eratosthenes shows 2334, so my hypothesis must have been wrong, if you  used the pdf files to count "missing items" -- pretty sure the same files were used for both TestCase and .bib files - date of creation would indicate if I did / didn't -- haven't entered that many new items in last couple of days

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Monday, 7 July 2014 7:39 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

I've looked at those two files, and that is worrying; if the exact same entries were selected for these exports, a whopping 129 entries are missing from the bib file, all of which should have been there. I'll look into it further. As to the file path export, it's conceptually difficult to export relative paths for non-existent files, and Zotero doesn't offer relative paths to the translators such as better bibtex unless you're exporting the files. What I could do is add an option to exclude the file paths entirely if you're not exporting files; I think that would accomplish what you need. Right? — Reply to this email directly or view it on GitHub.

retorquere commented 10 years ago

Yeah, I was counting mismatches that simply had unicode translated to LaTeX. There was no mismatch. I'll wait about the paths, would also still like to know what faulty key Eratosthenes received -- I can't reproduce the original problem.

RustyRiley commented 10 years ago

this is what I got from the Eratosthenes dev at the time, but don't  have original file that caused the problem

"It looks like this is not an eratosthenes problem though. It appears that Better BibTeX is putting spaces in the cite-keys in your bibtex output, which is not valid. It is also putting ' characters in the cite-keys, which I believe is also not valid under the BibTeX standard."

from memory, the error  message that first presented indicated a problem with entrt "Paredes2013" (not exact, just remembering some of the details)   -- whereas the last name of the author was "Padilla Paredes" (Priscilla, from memory)   --- so if it attempted to create a citekey like "Padilla Paredes2013"  that would have created the error (I'm guessing)  -- damn those women keeping their maiden names when marrying !!!      --   just joking ;-D

haven't heard anything about the paths yet

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Monday, 7 July 2014 9:09 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Yeah, I was counting mismatches that simply had unicode translated to LaTeX. There was no mismatch. I'll wait about the paths, would also still like to know what faulty key Eratosthenes received -- I can't reproduce the original problem. — Reply to this email directly or view it on GitHub.

retorquere commented 10 years ago

Do you still have the bibfile that had that error? The bib file you put in dbinbox doesn't have that error -- the citekey is clean.

RustyRiley commented 10 years ago

no, sorry -- been watching some movies over the weekend, and cleaning up afterwards to save space, including deleting that old, problematic, file

if you're not concerned about possible ethical problem -- have a look at TV Portal in Google Play

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Monday, 7 July 2014 9:37 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Do you still have the bibfile that had that error? The bib file you put in dbinbox doesn't have that error -- the citekey is clean. — Reply to this email directly or view it on GitHub.

retorquere commented 10 years ago

Without that file I'm afraid I have no entry into the issue. Do you think Matt still has a copy?

RustyRiley commented 10 years ago

I'll send him another email

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Monday, 7 July 2014 9:43 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Without that file I'm afraid I have no entry into the issue. Do you think Matt still has a copy? — Reply to this email directly or view it on GitHub.

RustyRiley commented 10 years ago

Checking the time of email from the Eratosthenes dev, he's got back to me "in the early morning", my time, 6-8 hours away, if "we" are lucky

Russell J. Wilson Dunedin Aotearoa / New Zealand Sent from my android device.

-----Original Message----- From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Mon, 07 Jul 2014 9:43 pm Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Without that file I'm afraid I have no entry into the issue. Do you think Matt still has a copy?

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48158896

RustyRiley commented 10 years ago

Just remembered - - have to upload that file to dbinbox - - will do so later, but at least you know it's on its way 😃

Russell J. Wilson Dunedin Aotearoa / New Zealand Sent from my android device.

-----Original Message----- From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Mon, 07 Jul 2014 9:43 pm Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Without that file I'm afraid I have no entry into the issue. Do you think Matt still has a copy?

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48158896

RustyRiley commented 10 years ago

Did you get the file -- I uploaded it to dbinbox

did you work out the problem -- darre say I;ll be trying to use  BetterBibtex again

best Russell

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Monday, 7 July 2014 9:43 PM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

Without that file I'm afraid I have no entry into the issue. Do you think Matt still has a copy? — Reply to this email directly or view it on GitHub.

retorquere commented 10 years ago

I did get it, but I don't get notifications for dbinbox -- thanks. That file does have a whole load of faulty keys, but I can't re-generate them with Better BibTeX -- for example, that bib file has a key "@article{D'Andrea2012,", but if I pick the corresponding entry from the JSON file you put up and generate BibTeX from that using Better BibTex, I get "@article{DAndrea2012,", as I would have expected... are you sure you generated that My Library JULY 4.bib using Better BibTeX?

RustyRiley commented 10 years ago

Pretty darn sure - - you say it has lots of errors - - how about the Padilla Paredes item, that prompted the most initial failure to load in Eratosthenes? Russell J. Wilson Dunedin Aotearoa / New Zealand

Sent with AquaMail for Android http://www.aqua-mail.com

On 9 July 2014 11:54:28 pm AllThatIsTheCase notifications@github.com wrote:

I did get it, but I don't get notifications for dbinbox -- thanks. That file does have a whole load of faulty keys, but I can't re-generate them with Better BibTeX -- for example, that bib file has a key "@article{D'Andrea2012,", but if I pick the corresponding entry from the JSON file you put up and generate BibTeX from that using Better BibTex, I get "@article{DAndrea2012,", as I would have expected... are you sure you generated that My Library JULY 4.bib using Better BibTeX?

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48460240

retorquere commented 10 years ago

That generates "@article{PadillaParedes2013,".

RustyRiley commented 10 years ago

Is that right? Looks right - - but what would I know? 😊

Trouble is, that's all Matt sent, And, as I said, I deleted the original file

And Matt's altered his app to deal with the original problem

Sorry, don't know what more I can do

Russell J. Wilson Dunedin Aotearoa / New Zealand

Sent with AquaMail for Android http://www.aqua-mail.com

On 10 July 2014 12:03:40 am AllThatIsTheCase notifications@github.com wrote:

That generates "@article{PadillaParedes2013,".

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48461043

retorquere commented 10 years ago

That key is correct, yes. I don't think there's more we can do -- whatever produced those faulty keys, Better BibTeX currently doesn't.

Are you still interested in an option to omit paths if you're not exporting files?

RustyRiley commented 10 years ago

Sure

Russell J. Wilson Dunedin Aotearoa / New Zealand

Sent with AquaMail for Android http://www.aqua-mail.com

On 10 July 2014 12:23:55 am AllThatIsTheCase notifications@github.com wrote:

That key is correct, yes. I don't think there's more we can do -- whatever produced those faulty keys, Better BibTeX currently doesn't.

Are you still interested in an option to omit paths if you're not exporting files?

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48462744

RustyRiley commented 10 years ago

Just a thought - - would a file from BB be altered to produce the error if it was imported "wrongly" by adjusting it to make it suit JabRef - - remember , Eratosthenes varies its import procedures depending on its "assumed source" - - know what I mean - - you using Eratosthenes?

Russell J. Wilson Dunedin Aotearoa / New Zealand

Sent with AquaMail for Android http://www.aqua-mail.com

On 10 July 2014 12:23:55 am AllThatIsTheCase notifications@github.com wrote:

That key is correct, yes. I don't think there's more we can do -- whatever produced those faulty keys, Better BibTeX currently doesn't.

Are you still interested in an option to omit paths if you're not exporting files?

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48462744

retorquere commented 10 years ago

I understand what you're saying; I can't exclude that such might have happened, but it seems unlikely to me that E. would have produced keys itself deems invalid. I'm not an E. user, although I do have it on my tablet for testing.

RustyRiley commented 10 years ago

What if I could get an old copy of Eratosthenes - - do You have an old copy of it? IF that file Matt sent Was the original, problem causing file, wouldn't we then be back where we were at the start? For testing purposes? Russell J. Wilson Dunedin Aotearoa / New Zealand

Sent with AquaMail for Android http://www.aqua-mail.com

On 10 July 2014 12:58:09 am AllThatIsTheCase notifications@github.com wrote:

I understand what you're saying; I can't exclude that such might have happened, but it seems unlikely to me that E. would have produced keys itself deems invalid. I'm not an E. user, although I do have it on my tablet for testing.

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48465995

retorquere commented 10 years ago

I don't think that'd do it. You tried to import a BibTeX file into E., right? It is at that import that E. complained. For E. to have generated a file with faulty keys, it would have had to be able to import it first. The file with the errors has Better BibTex comments in it, so it would have to be either:

  1. BBT created the file with the errors -- but I cannot reproduce this, or
  2. BBT created a file that was OK, but another app then mangled it, which is unlikely as the mangling is so specific

Really the only way I can think of that such keys were generated is by using a very specific key formatter using the advanced functions, but even then I'm at a loss how you got to the unfiltered Author fields.

RustyRiley commented 10 years ago

You're more familiar with the options than I am - - could selecting any of those options right at the start have altered things - - the only one that I could have selected differently though is "Notes" -- I started but cancelled exporting all, but stopped when it was taking so long - -

It does seem to be a form of "rule governed behaviour" operating on a "system" - - either the rules, or the system differed - - rules = program version; system = (largely) input (data), procedures selected (options), processing (errors?) - - but this wouldn't produce consistent output

BUT what does "unfiltered author fields" mean? To get an error with "Padilla Paredes" doesn't that imply some sort of "filtering" ? Does this suggest, as you did, that what Matt sent wasn't the first file I sent him?

Russell J. Wilson Dunedin Aotearoa / New Zealand

Sent with AquaMail for Android http://www.aqua-mail.com

On 10 July 2014 1:17:36 am AllThatIsTheCase notifications@github.com wrote:

I don't think that'd do it. You tried to import a BibTeX file into E., right? It is at that import that E. complained. For E. to have generated a file with faulty keys, it would have had to be able to import it first. The file with the errors has Better BibTex comments in it, so it would have to be either:

  1. BBT created the file with the errors -- but I cannot reproduce this, or
  2. BBT created a file that was OK, but another app then mangled it, which is unlikely as the mangling is so specific

Really the only way I can think of that such keys were generated is by using a very specific key formatter using the advanced functions, but even then I'm at a loss how you got to the unfiltered Author fields.

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-48468017

retorquere commented 10 years ago

Not really - this behavior would always have been considered a bug.

I think we'll have to close this one for now - if it re-emerges just open a new issue.

The advanced functions allow access to all zotero reference fields, except author data.

retorquere commented 10 years ago

The new version (to be released somewhere next week will have a hidden option to enable the export you want: you can set extensions.zotero.translators.better-bibtex.attachmentRelativePath in about:config to true, and it will export relative paths even if you're not saving files.

RustyRiley commented 10 years ago

Marvelous --thank you very much Best regards Russell J. Wilson Dunedin, New Zealand

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On July 26, 2014 11:54:25 AM AllThatIsTheCase notifications@github.com wrote:

The new version (to be released somewhere next week will have a hidden option to enable the export you want: you can set extensions.zotero.translators.better-bibtex.attachmentRelativePath in about:config to true, and it will export relative paths even if you're not saving files.

Reply to this email directly or view it on GitHub: https://github.com/ZotPlus/zotero-better-bibtex/issues/83#issuecomment-50216330

RustyRiley commented 10 years ago

Hi, how's it going, maybe I'm looking in the wrong place, but the description of the extension refers to the latest version being July 6th --- been able to get it out?

Regards Russell J. Wilson Dunedin, New Zealand

From: AllThatIsTheCase notifications@github.com To: ZotPlus/zotero-better-bibtex zotero-better-bibtex@noreply.github.com Cc: RustyRiley russwilsonau@yahoo.com.au Sent: Saturday, 26 July 2014 11:54 AM Subject: Re: [zotero-better-bibtex] Prob with cite-keys when used with Eratosthenes (#83)

The new version (to be released somewhere next week will have a hidden option to enable the export you want: you can set extensions.zotero.translators.better-bibtex.attachmentRelativePath in about:config to true, and it will export relative paths even if you're not saving files. — Reply to this email directly or view it on GitHub.

retorquere commented 10 years ago

No, I'm going to release the 11th. I'll be offline for a full week starting this afternoon, I don't like to put out new stuff when I'll be unreachable.