Activity for Chris Putnam
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Chris Putnam posted a comment on discussion General Discussion
The latest version (7.2) has this fix in it. Let me know if you see any more issues. Thanks again. Chris.
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history_version7
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history_version7
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history_version7
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Thanks for the report. I found the bug that was preventing titles from being output properly. I will upload a fixed version shortly. I've also solved one problem parsing the names in this file. However, I wonder if the names in the Endnote file aren't entered correctly. The format of the names really confuses my name parsing algorithms and I suspect that Endnote will generate odd names from them as well. For example, in the second reference you have: Alexander A. Samuel and Bruin, De Arie and Kornet...
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I've modified the page parsing code so that it will handle this situation (the end tags will contain "32, 64" in this case). This will come out in the next release.
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Thanks for catching these. They'll be corrected in the next release.
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history_version7
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Sorry about that. Please check the current 7.1 release. I accidentally made all of my build changes to the generated Makefile rather than the Makefile.static/Makefile.dynamic files that the Makefile is generated from. Thanks for the report.
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history_version7
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history_version7
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Bibutils
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The new version 7.0 should do this. Since the date field wants to be in ISO 8601, I implemented a check to ensure that the year/month/day information can be expressed properly in ISO 8601 (some of my test suite references have somewhat garbled dates like "c1989", etc.). If the year/month doesn't look right for ISO 8601, I'm defaulting to using the year/month tags.
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I just uploaded version 7.0 (I made a change to a structure that would break binary compatibility for people using bibutils as a library).
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My current version of nbib2xml parses both of these. This fix comes from merging all of the page management code from all of the importers, which I was doing more for code cleanliness reasons more than anything else. The "24-32,64-" is still something of an issue, though, as many bibliography formats either want a single page or a consecutive range and just can't express something like the above. I checked the last publically available version and found that nbib2xml did indeed crash on these inputs...
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I have no deep understanding of nbib formats, other than looking at examples and websites like you cited. But I think that you are running into the general problem that bibutils has always faced. That is that there are valid reference types (and data) that can be expressed in one format that simply don't exist in another format. Many people have asked that such "unexpressible" content be retained, but my response is always "show me what you would like it to look like". Some people have good ideas,...
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It's expected behavior with the current version of the program. I'd never seen an example of a nbib book before. But in looking at some documentation, the "BTI" tag is "Book Title", so clearly Book is ok. I've just added it to my local source and hope to upload it sometime soon (after I get done with some teaching).
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Conservation of essential genes in yeast species: POL12
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Conservation of essential genes in yeast species: POL12
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Conservation of essential genes in yeast species: NBL1
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Conservation of essential genes in yeast species: NBL1
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Conservation of essential genes in yeast species: NBL1
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Conservation of essential genes in yeast species: NBL1
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Conservation of essential genes in yeast species: POL12
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Conservation of essential genes in yeast species: POL12
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Conservation of essential genes in yeast species: POL12
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Conservation of essential genes: a quire analysis
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Conservation of essential genes: a quire analysis
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Conservation of essential genes: a quire analysis
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Conservation of essential genes: a quire analysis
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Essential genes and ohnologs: a quire analysis
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Essential genes and ohnologs: a quire analysis
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Essential genes and ohnologs: a quire analysis
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Essential genes and ohnologs: a quire analysis
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Essential genes and ohnologs: a quire analysis
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Essential genes and ohnologs: a quire analysis
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How many S. cerevisiae physical interactions in BioGRID are self-self interactions?
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Essential gene analysis in quire: An introduction
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How many S. cerevisiae physical interactions in BioGRID are self-self interactions?
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How many S. cerevisiae physical interactions in BioGRID are self-self interactions?
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This is a fine way to get patches to me. And your modifications look really good in general. So I've never seen a MODS file with a nonSort tag in the title. (I'd love to see an example.) Based on the way you've written this patch, you are maintaining nonSort titles as a separate entity and it looks like it's just a special form of a title prefix. If this is correct, I think the one change I'll make to your patch is to call the nonSort internally a "title prefix", which is the more general concept...
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Fixed in version 6.10. Thanks for the report.
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history_version6
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Bibutils
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history_version6
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Version 6.9 (just uploaded) fixes this in my testing. Turns out that the next latex parser wasn't needed for this particular bug, but the new parser does a better job, so I'm keeping it. Sorry for the delay; work has been a little complicated over the last month or so.
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Version 6.9 has an initial version of a xml2biblatex converter. Let me know if you find any problems with it.
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Yes, it's a bug. The only way I can think to solve it is to build a real parser for LaTeX. Until now I've been cheating by recognizing common LaTeX patterns, but that won't scale to all possible CJK names. The parser won't be that hard to write (I have a plan for it in my head) and in the end ought to simplify the way I've been handling LaTeX. I just need to find a little time to implement it.
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The simple answer is that no one has ever requested an xml2biblatex converter. In general, I don't want to write converters that aren't useful to people. So I tend to wait until someone seems interested. For example, I would have never guessed that an xml2isi converter would have been useful, but apparently it was. So is this a request for an xml2biblatex converter? It will probably take a couple of rounds to get one that's mostly "correct" as Biblatex is somewhat more complex than nbib or isi, for...
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There is no publically available git repository. But I'm very happy to take patches. And I'm sorry I haven't taken time to fix the xml2isi issue you've raised yet. My non-hobby programming time has gotten really complicated recently. If you don't have a fix yet, I'd suggest looking at lib/isiout.c and see if you can add an "output_simple()" call that catches the missing elements. Also running the programs with "--debug" gives lots of useful information for each step in the transformation to see what...
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Version 6.8 should properly handle the .isi output issues you found. Let me know if you have any other problems/suggestions. Thanks again.
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Sorry, I see the attachments now. I'll take a look. Thanks for being on top of this and sorry for the noise.
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Sorry, I see the attachments now. I'll take a look. Thanks for being on top of this and sorry for the noise.
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Can you post an .ris example that fails? I see where publisher info and isbn are falling through the cracks, but I would have thought that the url elements would have been preserved. Before I upload a "fixed" version, I'd like to make sure that it's really fixed.
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I've already included a modified version of your patch in version 6.7. Let me know if you find that 6.7 doesn't handle things correctly.
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These changes are now added to version 6.7. Note that I didn't comment out append_urls(), but rather removed DOI from that list of tags output by that function so that DOI's won't be repeated in the output.
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This is now updated in version 6.7
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history_version6
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history_version6
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It actually is fine, though apparently the cast should be ( long long ) under Windows, rather than ( long ), and the ( long long ) cast also works under Linux; long long is 64 bit under both architectures. This should silence the warning. fields_findv_each() will put pointers to str, pointers to char (C-style strings), or indicies of hits into the output void pointer list (vplist), depending on the mode that the user has chosen. In the case of storing indicies in the vplist, I'm abusing the cast...
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I just released version 6.6 that has a first stab at a xml2nbib converter. It seems to work pretty well for my testcases, but let me know if it should be behaving differently.
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history_version6
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Bibutils
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Sure. I can tackle it. I have a few upcoming deadlines, but I'll write it for the next release.
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history_version6
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history_version6
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I found the problem. Turns out that the defines SKIP and SIMPLE accidentally have the same value in lib/reftypes.h. For the mesh heading keywords ( tag "MH" ), the tag needs to be defined in nbibtypes.c The fix will be in the version 6.5 release.
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Oops. That's embarrassing. I've just uploaded version 6.4 that contains this (and the missing return) patch.
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Yes. It'll be in the next version. It turns out that the return isn't absolutely necessary (except for efficiency) as the rest of the function can gracefully handle an illegal value for n.
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Bibutils
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bibdiff
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Bibutils
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history_version6
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history_version6
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history_version6
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Bibutils
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I don't serve a git repository on sourceforge. You can use the "Files" tab to download the .tar.gz file https://sourceforge.net/projects/bibutils/files/?source=navbar
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I happily take patches. C.
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FYI, I had nothing to do this 'existing' repository, and I have no idea what is in it.
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Thanks for catching these. I have one important question, though. While I've added reporting the unknown error code in bibl_reporterr(), I don't think that that function should ever see an unknown error code. Do you remember what value for the unknown error code made its way into bibl_reporterr()? I'm worried that something internal leaked its way out to the general user. Thanks again.
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These are all good catches and will be fixed in the next release. And thanks for pointing me to cppcheck. I'm having fun generating library rules to check the calls for my core code.
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Thanks for catching this. This will be fixed in the next release.
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I don't currently have any way to make Windows binary...
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I've been writing cppcheck library rules for some of my core C libraries. One thing that I'd love to check for is a case where a constructor is called, but isn't balanced by a call to a destructor (sort of analogous to the resource tag for allocators/deallocators). A typical (correct) function would look like: void f( void ) { str s; str_init( &s ); /* do something */ str_free( &s ); } I'd love to catch when the str_free() has been forgotten (or even if str_init() is forgotten in a path containing...
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Actually, not outputing a URL for the DOI for bibtex, ris, and some other formats was the expected behavior, as these formats have other ways to output DOI information. (I had a rationale for this behavior at least.) The reason that the older versions output the url was that bibutils wasn't recognizing the new format of DOI urls. But since you want the redundant information, I've added the url output of DOIs to these formats in the current version that I've just uploaded as bibutils version 6.2....
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Version 6.1 now handles the new and old URLs for DOIs. I had to make additional changes to make sure that everything was handled properly. Thanks for the report.
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Version 6.1 should handle these non-compliant RIS files. (Also note that they use "and" to separate authors in the A1 tag, which I haven't seen before in my other RIS sources. I've added support for this as well.)
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I'll fix ris2xml to recognize this mangled RIS format. But someone should pester them that they're generating non-compliant RIS files. Thanks for the heads up.
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I've added the support for arXiv references into version 6.0. I still don't export the eprintClass/primaryClass information into references formats other than bibtex. I'm not sure what those format might want. Thanks for the report.
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The fix is now available in bibutils version 6.0.
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The patch is correct. As you identified, the problem is that ris2xml wasn't recognizing...
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history_version5
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Bibutils
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history_version5
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Sorry for the delay in replying. In this case it wasn't my (just) my schedule, but...
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It's unexpected behavior, so it's a bug. The fix is a little tricky due to the recursive...
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Sorry you feel that way as there is no Sourceforge Git repository. But I'm quite...
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Version 5.8 should handle this much better. (Though I've only had time to test it...
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This is now updated in the fixed version 5.8.
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This is correct. Clearly I was getting confused between chapter/title for @inbook....
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