Upgrade StorageDuplicates, RIS, PDF, Endnote, File Not Found
I've been using Zotero for about six months now with fairly good results, excluding one or two exceptions: RIS import/export between Endnote and now the duplicate issue.
I'm a former Endnote X1 user. I've been working between Endnote and my new Zotero library but finally decided to try and import my old Endnote library of roughly 1500 references, most with attached PDFs. I was hopeful that I would avoid any problems by using the ris-fix.vbs solution:
http://forums.zotero.org/discussion/70/3/importing-endnote-files-into-zotero/
http://www.zotero.org/support/kb/exporting_from_endnote_with_pdfs
However, when clicking on the attached pdf labeled "Full Text (PDF)" that was imported I ended up getting the "File Not Found" error: "The attached file could not be found. It may have been moved or deleted outside of Zotero." What a disappointment. I was dumb enough to try importing twice (a second time after updating Endnote to the X1.0.2 build) and now I have at least a pair of duplicates for each reference in Zotero. :(
I've searched the forum on the file not found /pdf error and several other people have also reported it. However I'm still unclear about how to fix it. Any suggestions?
Meanwhile here is a simple and temporary fix for finding (some) duplicates if you have Endnote as well: a) export Zotero library to Endnote b) click 'find duplicates' in Endnote "References" menu c) use results as key to (more easily) clean Zotero library. Perhaps this is obvious but at least it's a start.
Thanks, Peter
PS here is an excerpt from my RIS file - one instance that has created the 'full text (pdf)' file leading nowhere (the first RIS export before the X1.0.2 update and after running the 'ris-fix.vb' fix:
[NOTE: for my own privacy I have deleted part of the file location in the L1 line and replaced with '...' (L1 - file://C:\Peter on C\ ... \PDF\Public space as 'context' in assistive information and---.pdf]
TY - JOUR
AB - This paper examines emergent issues of `context' raised by the application of information and communication technologies for people with cognitive impairment. The issue of the development and application of cognitive prostheses for this group provides an opportunity to examine assumptions and issues emerging from this area pertaining to understandings of the term `context' in these applications. In this sense the paper takes these assumptions and issues as a point of departure for the development of a `problematic' that can contribute to the study of the experience of cognitive impairment. The paper specifically addresses recent concerns about the lack of knowledge of these experiences in public spaces such as shopping centres, given that this is a critical site for the civic participation of this group. We argue that this participation should be understood in terms of the `meeting of two histories': the history of contemporary requirements governing participation in public space and the habitus of people with cognitive impairment with regard to this participation. The paper proposes that the salience of cognitive impairment in these spaces turns on what it means for individuals to inhabit them as complex `Container Technologies' (Sofia) and underlines the importance of understanding their efforts to attain a sense of normality (Goffman) in these contexts. We propose that this approach can inform research contributing to the development of a `pattern language', informing applications that make cognition a system property in networks that operate between humans, machines and their contexts.
AD - Australasian CRC for Interaction Design, PO Box 2008, Kelvin Grove, QLD 4059, Australia 2: School of Design, Queensland University of Technology, Brisbane, Australia 3: Centre for Social Change Research, Queensland University of Technology, Brisbane, Australia
AU - Adkins, Barbara
AU - Smith, Dianne
AU - Barnett, Karen
AU - Grant, Eryn
DA - June 2006
KW - cognitive impairment; information and communication technology; ICT; public space; interaction order; habitus; field
L1 - file://C:\Peter on C\ ... \PDF\Public space as 'context' in assistive information and---.pdf
IS - 3
N1 - doi:10.1080/13691180600751330
PY - 2006
SP - 355-372
ST - Public space as 'context' in assistive information and communication technologies for people with cognitive impairment
T2 - Information, Communication and Society
TI - Public space as 'context' in assistive information and communication technologies for people with cognitive impairment
UR - http://www.ingentaconnect.com/content/routledg/rics/2006/00000009/00000003/art00006
http://dx.doi.org/10.1080/13691180600751330
VL - 9
ID - 1085
ER -
I'm a former Endnote X1 user. I've been working between Endnote and my new Zotero library but finally decided to try and import my old Endnote library of roughly 1500 references, most with attached PDFs. I was hopeful that I would avoid any problems by using the ris-fix.vbs solution:
http://forums.zotero.org/discussion/70/3/importing-endnote-files-into-zotero/
http://www.zotero.org/support/kb/exporting_from_endnote_with_pdfs
However, when clicking on the attached pdf labeled "Full Text (PDF)" that was imported I ended up getting the "File Not Found" error: "The attached file could not be found. It may have been moved or deleted outside of Zotero." What a disappointment. I was dumb enough to try importing twice (a second time after updating Endnote to the X1.0.2 build) and now I have at least a pair of duplicates for each reference in Zotero. :(
I've searched the forum on the file not found /pdf error and several other people have also reported it. However I'm still unclear about how to fix it. Any suggestions?
Meanwhile here is a simple and temporary fix for finding (some) duplicates if you have Endnote as well: a) export Zotero library to Endnote b) click 'find duplicates' in Endnote "References" menu c) use results as key to (more easily) clean Zotero library. Perhaps this is obvious but at least it's a start.
Thanks, Peter
PS here is an excerpt from my RIS file - one instance that has created the 'full text (pdf)' file leading nowhere (the first RIS export before the X1.0.2 update and after running the 'ris-fix.vb' fix:
[NOTE: for my own privacy I have deleted part of the file location in the L1 line and replaced with '...' (L1 - file://C:\Peter on C\ ... \PDF\Public space as 'context' in assistive information and---.pdf]
TY - JOUR
AB - This paper examines emergent issues of `context' raised by the application of information and communication technologies for people with cognitive impairment. The issue of the development and application of cognitive prostheses for this group provides an opportunity to examine assumptions and issues emerging from this area pertaining to understandings of the term `context' in these applications. In this sense the paper takes these assumptions and issues as a point of departure for the development of a `problematic' that can contribute to the study of the experience of cognitive impairment. The paper specifically addresses recent concerns about the lack of knowledge of these experiences in public spaces such as shopping centres, given that this is a critical site for the civic participation of this group. We argue that this participation should be understood in terms of the `meeting of two histories': the history of contemporary requirements governing participation in public space and the habitus of people with cognitive impairment with regard to this participation. The paper proposes that the salience of cognitive impairment in these spaces turns on what it means for individuals to inhabit them as complex `Container Technologies' (Sofia) and underlines the importance of understanding their efforts to attain a sense of normality (Goffman) in these contexts. We propose that this approach can inform research contributing to the development of a `pattern language', informing applications that make cognition a system property in networks that operate between humans, machines and their contexts.
AD - Australasian CRC for Interaction Design, PO Box 2008, Kelvin Grove, QLD 4059, Australia 2: School of Design, Queensland University of Technology, Brisbane, Australia 3: Centre for Social Change Research, Queensland University of Technology, Brisbane, Australia
AU - Adkins, Barbara
AU - Smith, Dianne
AU - Barnett, Karen
AU - Grant, Eryn
DA - June 2006
KW - cognitive impairment; information and communication technology; ICT; public space; interaction order; habitus; field
L1 - file://C:\Peter on C\ ... \PDF\Public space as 'context' in assistive information and---.pdf
IS - 3
N1 - doi:10.1080/13691180600751330
PY - 2006
SP - 355-372
ST - Public space as 'context' in assistive information and communication technologies for people with cognitive impairment
T2 - Information, Communication and Society
TI - Public space as 'context' in assistive information and communication technologies for people with cognitive impairment
UR - http://www.ingentaconnect.com/content/routledg/rics/2006/00000009/00000003/art00006
http://dx.doi.org/10.1080/13691180600751330
VL - 9
ID - 1085
ER -
on this thread, follow the discussion between Dan and castellg towards the bottom
http://forums.zotero.org/discussion/70/3/importing-endnote-files-into-zotero/
that might help - this seems to be a windows issue
I'd suggest trying some of the proposed solution with a couple of items instead of the whole library.
As for duplicates - generally duplicate detection should be done, I agree, but in your case this is easy to take care of: You can just sort by date added in the middle panel and then delete all items from the first import. You can use the little table icon next to the + sign to add columns to the middle pane.
I had forgotten about sorting by "date added" (it wasn't checked for viewing). That helps. :)
The suggestion referenced in this thread (http://forums.zotero.org/discussion/70/3/importing-endnote-files-into-zotero/) didn't work for me. Am I doing something wrong? I copied the Endnote library file and its corresponding .data folder (with pdfs) to the desktop as Dan suggested but with no success. To confirm, it is only the Endnote library folders that should be copied to the desktop and no others? I tried with just one reference as you suggested.
The problem I believe is due to the fact that Endnote creates a separate subfolder for each reference pdf with a specific name in the PDF folder. For example the full pdf link in the reference below is: C:\Documents and Settings\plut\Desktop\temp\endnote_library.Data\PDF\Public space as '-0311115776\Public space as 'context' in assistive information and---.pdf
However the L1 line is:
L1 - file://C:\Documents and Settings\plut\Desktop\temp\endnote_library.Data\PDF\Public space as 'context' in assistive information and---.pdf
Hence the folder "Public space as '-0311115776" is missing from the L1 line.
It seems that Zotero does not know to go one level deeper to look for the pdf or the 'ris-fix.vb' fix is not accounting for Endnote's strange folder structure. (Why it just doesn't put all the pdfs directly into the same folder without creating another level of folders is a mystery to me.)
Here is the complete RIS file:
TY - JOUR
AU - Adkins, Barbara
AU - Smith, Dianne
AU - Barnett, Karen
AU - Grant, Eryn
PY - 2006
TI - Public space as 'context' in assistive information and communication technologies for people with cognitive impairment
SP - 355-372
N1 - June 2006
JF - Information, Communication and Society
VL - 9
IS - 3
N1 - Public space as 'context' in assistive information and communication technologies for people with cognitive impairment
N1 - doi:10.1080/13691180600751330
L1 - file://C:\Documents and Settings\plut\Desktop\temp\endnote_library.Data\PDF\Public space as 'context' in assistive information and---.pdf
KW - cognitive impairment; information and communication technology; ICT; public space; interaction order; habitus; field
N2 - This paper examines emergent issues of `context' raised by the application of information and communication technologies for people with cognitive impairment. The issue of the development and application of cognitive prostheses for this group provides an opportunity to examine assumptions and issues emerging from this area pertaining to understandings of the term `context' in these applications. In this sense the paper takes these assumptions and issues as a point of departure for the development of a `problematic' that can contribute to the study of the experience of cognitive impairment. The paper specifically addresses recent concerns about the lack of knowledge of these experiences in public spaces such as shopping centres, given that this is a critical site for the civic participation of this group. We argue that this participation should be understood in terms of the `meeting of two histories': the history of contemporary requirements governing participation in public space and the habitus of people with cognitive impairment with regard to this participation. The paper proposes that the salience of cognitive impairment in these spaces turns on what it means for individuals to inhabit them as complex `Container Technologies' (Sofia) and underlines the importance of understanding their efforts to attain a sense of normality (Goffman) in these contexts. We propose that this approach can inform research contributing to the development of a `pattern language', informing applications that make cognition a system property in networks that operate between humans, machines and their contexts.
AD - Australasian CRC for Interaction Design, PO Box 2008, Kelvin Grove, QLD 4059, Australia 2: School of Design, Queensland University of Technology, Brisbane, Australia 3: Centre for Social Change Research, Queensland University of Technology, Brisbane, Australia
UR - http://www.ingentaconnect.com/content/routledg/rics/2006/00000009/00000003/art00006
http://dx.doi.org/10.1080/13691180600751330
ID - 1085
ER -
But that really shouldn't happen -
how does the L1 line of that item look before you run the script?
BEFORE:
L1 - internal-pdf://Public space as '-0311115776/Public space as 'context' in assistive information and---.pdf
AFTER:
L1 - file://C:\Documents and Settings\plut\Desktop\temp\endnote_library.Data\PDF\Public space as 'context' in assistive information and---.pdf
So it's the script I suspect.
I can't imagine that I'm the first to have this issue with the script, or?
Should I do a manual find & replace?
It works when I manual edit L1 but of course this will take some time with 1500 plus. :( The correct line should read:
L1 - file://C:\Documents and Settings\plut\Desktop\temp\endnote_library.Data\PDF\Public space as '-0311115776\Public space as 'context' in assistive information and---.pdf
search: "internal-pdf://"
replace: "file://C:\Documents and Settings\plut\Desktop\temp\endnote_library.Data\PDF"
As for the script - might have to do something with the input? not sure, I don't read vbs and Windows file systems give me headaches to start with... but maybe noksagt will stop by and clarify.
I'm sure it's just a small hiccup in the script but it's still curious if no one else has come across this earlier.
The only issue now is that Zotero renamed all my linked pdfs to "Full Text (PDF)" in the library which messes with my naming system (Author Date Title). This system made it easier for me to share pdfs with my colleagues. A bit of a disappointment. Is there any way to correct this so the names are left intact?
Still, this is a huge improvement over no pdfs. ;)
Thank you.
First off, I had Endnote 8 on my Mac, and needed a new version in order to convert the PDF files previously inserted as images/figures in the references. This was easily solved by downloading the latest Endnote version as a trial version (30 days).
Then it turned out that my RIS export in Endnote filled in the URL in both the L1 and UR field. So if a reference had a URL it didn't get the File Attachment in the export. I edited the RIS export filter manually and changed the L1 field to File Attachment.
After exporting the RIS TXT-file, I edited it with TextEdit, and replaced the internal-pdf:// with file:///pdf/ (after copying Endnotes PDF subfolder content to /pdf on my computer). I'm not sure whether it is necessary to copy the files, but it makes the file path shorter (and less prone to errors).
Then the import to Zotero worked fine! The PDF files are now stored in Zotero, which is very nice.