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Issue collector

A collection of issues and problems.
UnicodeError uploading to VL
I am just trying to upload an article: vonAndrian2002.pdf on my desktop here at I am not sure what the problem is. Whatever I try, zope comes back with an error: Zope Error Zope has encountered an error while publishing this resource. Error Type: UnicodeError Error Value: ASCII encoding error: ordinal not in range(128) I would be grateful if you could look into it (maybe you are currently trying things out and this might help you...)
Wrong link to PDF
On clicking on the pdf sign to view the articles this evening there is an error message: could not connect to remote server When I replace the with I get the article (works, but not ideal).
Searching for numbers
Numbers seem to get ignored: 1234567 retrieves a large number of articles... numbers should be used like normal text, for example it would be nice to search for "Author Year" to find an article by an author in a given year...
Automatic year update
I have just added a new article (Tewari2004) and added the 2004 to creation date and subject topic areas. 2004 did not appear in the years folder. The best would be if it would appear automatically. But for now it is probably OK to just add it manually.
Sort by author name
In year view: sort articles by author name
Use e-tools when submitting
When I upload an article, it would be nice if I could enter some keywords (author, year, word from title and then use the e-tools directly).
InBook shows as Unknown Journal
If a file (manual entry) is not an article (for example InBook), in the table view it should not say "Unkown Journal" but give the type of publication.
first author search & algorithm
I would like to be able to search for an article by the first author (rather than any of the authors or any name quoted in the article) (advanced search). I would also like to be able to match articles with pubmed using just the first author and a year (& select the article myself if there are more than 1)
etools algorithm
could you run the e-tools on the articles which haven't got the medline/Pubmed number yet using: Title: the 2 longest words in the title author: (search as first author) Year (as before) This should give quite a few more from what I have tried out so that I don't have to do too much by hand...
Crash when updating heydtmann2003
I tried to change metadata for Heydtmann2003 (an abstract from a conference this year): Type: Conference Title: Dynamics of adhesion of lymphocytes activated with the novel chemokine CXCL16 to VCAM-1 Journal: Journal of Hepatology Description: EASL 2003 abstract Zope crashes.
Crash when updating Mellado2001
In the article Mellado2001 I tried to enter: "chemokine receptor heterodimerization" as title and try to save so that I can use the e-tools. Zope crashes. I am not too sure why?
lost article
Only kidding! I uploaded an article from 1988 (!), the oldest one in the VL. Unfortunately, the year 1988 doesn't show up (same problem as the 2004 one) despite putting all the info in... Would be nice if it created the year automatically. The article can be found by searching for Akbar as first author.
Save directly from etools match
After using e-tools to manually select an article: On clicking on the article I choose (use article), could it fetch the metadata and directly save?
etools matching is cumbersome
Going through all the 352 "unmatched" documents is a bit cumbersome because I have to save the metadata and run the medline fetcher a couple of times. Would it be possible to have the medline fetcher save the data first and then run?
Matched document in unmatched list
Fiorentini2001 (about 10 docs down on the unmatched Documents) is now "matched" (found medline equivalent) but still shows up on the unmatched page. If you look at Edit: the info is there. There is a + in the title. Do you think this might be related?
search ebv fails
Simple search for "ebv" gives UnicodeError.
etools volume and pages
When it fetches the metadata, the volume, & pages don't get filled in (also I would find it usefull to also have the number as metadata)
Icons for each document in the virtual library have a different URL. There should only be a different URL for each document type.
dnrd died
Bigsister informed me that dnrd again died this morning and wasn't resurrected. I've manually brought it up by running /etc/ppp/ip-up.local, but need to figure out why it's dying and how to keep it alive.
delete article
I have tried to remove the second paper on the "Unmatched list". (JVI paper A2.pdf (file corrupt)) I clicked on Reject - not too sure how this changed things. When I refreshed, the button changed to Delete. Clicking on that causes a zope error. Hm... The file still shows up.
Creation Date trap
(almost critical). I have spent another 1/4 hour because I forgot to put the right format in for the date. Solution 1: errors show up in red (I didn't see the line under "creation date") Solution 2: Instead of "creation date" Creation year gets displayd.
metadata search before file upload
To ease the upload I want to: 1) Have an upload (supply document) button on the frontpage (header / footer) even when not logged in. 2) When I click on the supply document button I want to get the form that I can fill out partially by hand and then fetch the rest using E-tools. When I have the metadata in the form, I want to press a single button to upload (preferably in the background so that I can get on with things...)
double article prevention
I have recenly found myself uploading the same document twice (impatient double clicking). It would be nice, if the system would check the same article isn't in the library already (checksum / check of medline ID). Output could be a warning: a similar article (Author / Year / Journal / Title) already exists. Are you sure you want to upload?
metadata in review
When medline metadata is in review (usually incomplete / abstract missing, ...) I want this to be FF(internally) tagged in the VL. The VL should then (automatically, from time to time / in the background) check and update when review is complete (see STAT tag in files attached (MEDLINE format)
unmatched vs unreviewed
I have noticed that when I edit the metadata of an article by hand (Faint2004, see top of the list), and click on Accept, it still shows up on the list of unmatched documents. I would be grateful if you could change that (Maybe it should be called different - unreviewed documents?)
can't delete document
log in -> unmatched documents -> next page I tried to delete Shashkin 2003 (no title, the second one). No delete button on editing (? was there in other forms?), so I rejected the article. Now instead of the reject button there is a delete button which leads to a zope error. (what I would really want to do is delete the file completely to save space)
WikiLiver bugs after upgrade
- loss of edit button. Clicking on a link on the mainpage lets the edit button disappear (everybody should be able to edit - not only the frontpage). - loss of hierarchy even when full & the appropriate preference is set...
programs on zeck
Since I now use VNC on zeck more, I would like some more programs set up on zeck: - some mail client (Kmail) - cerevisia - gnucash
putty setup minor problems
When I use putty & VNC viewer to work on Zeck, the alt key doesn't work. I have to use the esc key instead. Is there a way of setting this so that it works?
Broken links
The navigator lets the user click on nodes which don't yet have a corresponding wiki page. That is, if a WikiLink appears in a page, but the linked page hasn't been created yet, then the WikiLink will appear as a node in the navigator which can be clicked on. Unfortunately, clicking on the node raises an error, which is confusing.
netscape applet viewer bug
Error: uncaught exception: Permission denied to get property Window.navigatorFrame
Navigator tracking
Clicking on a node in the navigator should cause the displayed wiki page to jump straight away, however it seems as if the graph is first shuffled before the page is loaded. We need to find out if it is just the case that each page takes a few seconds to render, or if there is genuinely a problem with the logic (I could avoid zooming to the next node, and wait till the page load forces the re-centering). In any case, the pages seem to take a long while to render.
Wiki zoom
It would be nice to be able to zoom in and out in the wiki navigator and have the scale changed accordingly, so that nodes which are offscreen come in, or nodes which are bundled together move out.
login for edit
at present I have to log in to create a new page!
Duplicate FrontPage in WikiLiver
There are two front pages in the WikiLiver: FrontPage and TheWikiLiverFrontPage. This is probably the reason for confusion when editing and thinking that the changes aren't working. We need to figure out the differences between the two pages and remove one of them.
Title on edit page
When I create a page (on edit form), the name of the WikiPage does not get displayed at the top. This is a bit annoying because I have to remember it.
addresses for birth announcement database problem
not really critical, but: We want to send birth announcements and want to create a database of friends & relatives to be used to print labels. There are a couple of considerations: 1) Label format should be preferably be in the latex file I created a while ago (see attached) because it positiones the text nicely independent of the line length. I don't mind changing the multiput commands to the (3 x 8) put commands to have different addresses on one page of labls. But maybe you have something similar previously. 2) Database: The simplest way is probably to type the addresses directly into the fields, but is there a different database you would use? (this is really why I write to you i.e. the semantic Web side of things...) Would it even be possible to tap onto the tkcAddressbook? Probably not - maybe I should change to something more generic? 3) Printer: I am still not too sure how to configure this. The printer works from the laptops, but currently I e-mail myself pdfs from ellen to print something out. If I open file:/home/mathis/texts/LabelTemplates/test.pdf in Konqueror for example and click on print, I can choose the printer and print, but nothing happens (no complaints). Nothing shows up in the printer queue (Jobs of Configure Print Manager) and no lights flash up on WolfGang (print server box). Printing Pdfs via the laptop are too difficult to get acurate for the labels (offset problems...)
Wiki crashed !!!!!
Alex, Wiki has crashed while I was working on my talk!! Help!!! I can't get into it at all!!
PDF resolution loss
Somewhere along the lines there is a decrease in resolution. If you look at the figure: ref{fig:CXCR6HistogramsNormalAndHCV} The resolution is lower than in the original OO file. In the .pdf file there is "dirt" around the lines. I suppose that is due to compression. Any way of getting that nicer?
figures: insert tif files (results L31), arrows
see \AlexTodo - best way to insert tiff files? - what is the best way to put arrows onto a figure? Within the figure with a graphics program?
IBR108 printer fonts
The output from the printer connected to IBR108 is sometimes unreadable due to what looks like bad font substitution.
Zope Errors
The current Zope errors as given by the default "standard_error_message" template are ugly and uniformative. At least for WikiLiver they should look nice and give some indication of what to do.
zora connection problem
Not too sure what happens. I frequently have problems connecting husky (zora) to the wireless net here. Today in the labs I connected husky to the laptop via the laptop-USB--Zora cable. I had connection pretty much immediately. When I tried to connect to the wireless network at home, I had to initialize at least 4 times, but succeded (I was connecetd while you were on the phone). After dinner I came back and husky was disconnected (I think the icons were all still there but it said something about DNS nameserver not found). I tried reconnecting and since then I can't re connect at all. I tried a reboot even and once the device crashed on attempt to reconnect. Do you think there could be a problem with the card again? Sorry, at the moment I don't think you can log into husky. Did you have any problems yesterday when you worked on the X10 java stuff?
Wiki crashed 2
Wiki crashed again. What I did was: I created a page: N-acetylcysteine (links didn't show up) I then decided to rename it to Acetylcysteine which caused the crash... Also, I can't reparent at the moment. Does this need login? Mathis
uncentre "figure 12.1:"
The text "figure 12.1" generated by pdflatex (probably true in all figures?) is put on its own in a line under the figure. I would want it with the text that follows (in the same line as the bold stuff). The blurbcaption (see table 12.1) seems to do that... as does Nancys thesis and I tried to do the same here... See recent commit of PhD
fedora installation
Fedora installation proves a bit more difficult than I thought: I ignored the error message: "unable to align partition properly..., may cause (fixable) problems with some bootloaders" 2 options: upgrade or re-install. - re-install: It looked like it found some partitions and wanted to overwrite them (I thought automatic partitioning is probably not save). I wasn't too sure about the mount points and I therefore left it at that. - upgrade: (/root/upgrade.log) caused "install exited abnormaly" ... "you may savely reboot" I am not too sure about that, but do you think this could be due to hardware selection? I couldn't find the exact monitor and I couldn't find the exact mouse?
Topic is ellen actually... I installed kspread onto ellen because I wanted to read something I wrote a while ago... I used apt-get in a shell as su. It seemed to install something. Tried to run it as root and as mathis (from a console). Both failed although root gave more information.
Remote Desktop Connection
When I try to use Remote Desktop Connection to connect into zeck from ellen, I get the error message: Connection failed. No server running at the given address.
OO on ellen crash
The openoffice still crashes when I try to run it on ellen. I think you looked at it before and there was a permission problem? Mathis
Fetch using this ID broken
I wanted to fetch metadata on one of the articles in the library (Wilbanks 2001) to get the journal name, ... for bibtex. Clicking the button however, leads to an error message. This behaviour could be reproduced with different browsers (opera, netscape, Konqeror) and different files which are marked as "(unknown Journal)". While you are there, maybe you could look at the following problem as well: When I am not logged in but want to open a file (pdf article) that requires authentication an error message along the lines "document doesn't exist" appears. It would be nice if it would ask to log in instead...
on Ellen (& Zeck?) Cerevisia doesn't seem to work which I would need for my thesis...
Openoffice doesn't work on ellen or zeck
after the upgrade OO neither works on ellen nor on zeck. The windows version is playing up so I would like to try and sort things out using linux...
flip diagonally problem
I have two figures in the file ../figures/TetramersOnNormalLIL.sxd (see repository). I want to flip the figures diagonally so that the X and Y axes are exchanged. I failed to do so with the flip function of OO and with the mirror function of OO (which for some reason is a rotate really - my OO issue # 31678). Have you got any quick fix? Alternatively, I can leave it as it is or redo the FACS analysis...
Konqueror print problem & printer setup problem
I am not too sure whether you can reproduce this. I can not print under Konqueror (on Okipage16n). However, if I use OO, printing is fine (although under OO I can't look at the printer settings) and the testpage is fine. This might be of help: OO sais it uses the okipage printer type CUPS, but I can't get into the printer settings and can't get into the printer setup. Also, I I tried to install the other printer (epson stylus color 640) - I am not too sure whether I got it right (remote lpd queue, on WolfGang, port lpd1) but it said something like you don't have permission to create the foomatic driver or the driver needed is not present. Do you remember what the settings for the okipage were? Mathis
nice tables
A couple of tables I have created don't look terribly nice: in results.tex: \label{tab:CXCR6inLIL} and \label{tab:CXCR6subtypesInLIL} I would like the "%" and "SEM" as well as the numbers roughly centered in the columns. I did a lot of trial and error and this is about as good as it gets. I don't like the gaps in the corners where the double lines meet. Is there a nicer way? If it is too complicated I will use only horizontal lines (in which case the centering problem as above will be more important.
X10 baby room
Background: We want to have macro settings for Diana getting up at night breastfeeding without switching the lights on to full ... I have wasted some time trying to get my X10 computer software to work, but failed because the software settings didn't allow me to use com1 to which the transceiver module is attached. Therfore it would be nice to attach the transceiver to zeck and run things under linux (which would also enable me to use the zaurus to control things). There are some links: Do you mind looking into whether this is setup would consume tremendous amount of time?
Myfanwys Webpage
We want Myfanwy to have her own webpage with photos: I have created a folder on zeck: file:/home/mathis/MyfanwysFirstTwoWeeks which contains a picture gallery for people to see on the web. I have created a folder in plone under root: /myfanwy People should get to the picture gallery via (link from for example (probably needs Carl to set up?) The site should be protected (user: friend, pw: myfanwy - that will teach people the spelling) and I think I have set that up. I am not too sure about the security settings though. Is it possible to do it via a link so that photos can be added without changing / uploading things too much?
hardware use over the intranet
I would like to use certain devices over the intranet to avoid crawling behind my desk too much plugging things in and out again... - printer (Epson Stylus Color 640) - highest priority - CD ROM on Ellen (My CD ROM on the laptop is broken and it would be nice to just read from the CD ROM on ellen over the intranet) - CD writer: I have a HP CD-Writer Plus 8200e or 8210e (I'm not at home at present, but can look up which one) which would be nice Diana and I could share via Ellen. lowest priority: - DVD (same drive as CD ROM on ellen) - I never saw a DVD working on it, but maybe we will get a DVD player (until we have a tablet PC and want to watch DVDs in bed... with the lights going on and off synchronous to the film of course)
PDF viewing issue
At present I can only view the pdf files I create with pdflatex under linux (but there without any problems (with Konqueror, acrobat reader 5.0.8, xpdf and kpdf)). If I try to open it under windows2000 on my laptop (transfered as binary using winscp) I can't open it anymore (file attached). On opening with Adobe reader 6.0.2 (18/5/04) or adobe acrobat 5.0.5 (26/10/01) I get the message (for 6.0.2): The file is damaged but is being repaired... Then: There was an error opening this document. The file is damaged and could not be repaired. If I leave out the results chapter it works. If I only put the results chapter in it doesn't work. So the problem must be in the results chapter. Interestingly, the problem in windows is (or rather might be) correlated with konqueror complaining if the pdf file is open _while_ it gets redone (error message: couldn't open file) but I haven't tested that extensively. Maybe it is the error messages which somehow get into the pdf file? If there is no obvious problem in the file I think I / we should send the file to the adobe tech service (and see what they think)
Spring Clean!!! Disk now full
(super critical!) I suppose that at least some of the problems I had with the pdf viewing are due to the fact that my disk is full. (I just tried to do some work on Myfanwys Picture Gallery and couldn't create a folder). I think we should sit down together when you are back to sort things out - otherwise things will just get worse... Mathis
VL bibtex error
I tried clicking on bibtex for the article De Rosa 2001 and got an error. So I had a look round: De Bari 2001 and Hassan-something 2001 too. So I suppose it is white space and funny symbols in first names which causes it to crash...
pdf graphics
I have graphics as a pdf which I want to include into the thesis. See for example: NLVpeCy7OnPatient.pdf and: GLCpeOnCellLine.pdf (see repository) and a couple of others which only exist as pdf (more to come) there are 2 problems: 1) I want to include 4 or so as one figure but can not import them into openoffice draw. 2) I need to do some minor editing: a) The texline with the proimmune needs to disappear b) when I look at the graphics with Konquerer the "page" size is too big & needs cropping.
OO on ellen doesn't work
OO still crashes on Ellen. Somehow I have not got the possibility of running it from zeck anymore.
k3b does not find suitable writer
I tried to burn a CD after I used the writer in the labs & plugged it into ellen again. I am not too sure, but it doesn't seem to hotplug. k3b gives an error message that it doesn't find a suitable writer and only simulates. At startup it also suggested to change it to run under root, but I think we left it as it is for safety reasons.
invalid action object
In IE (but not Konqueror): On opening some (but not all) pdf files I only get the first page displayd, for the rest there are small boxes instead of pagenumbers. Example: Lauer 2004. On opening there is an error message which usually reads something like:"There was an error opening this document. Invalid action object" Viewing with Konqueror is fine This might be related to the fact that these .pdf files were saved from the browser (opened with pdfstart)? Attached the original pdf as uploaded
Mailserver on Zeck
1) Diana has problems with her in that she can't get large files (on hotmail). 2) My dad complained for some while about spam he can't get rid of 3) The univeristy e-mail is pretty unreliable Therefore the E-mail server on Zeck has gone up in priority (Zeck is pretty reliable now). How long do you think setup would take?
fetch with ID script
if it doesn't take too much time: I find myself spending quite some time updating the references by clicking on "fetch using this ID" and waiting for that to happen. It would be nice if one could run a simple script "Update using all known IDs" type thing. If it takes too long I'll do it manually - if it doesnt' take too long but you are busy - I'll just wait before putting the references into the thesis until the magic button appears...
invalid action object
In IE (but not Konqueror): On opening some (but not all) pdf files I only get the first page displayd, for the rest there are small boxes instead of pagenumbers. Example: Lauer 2004. On opening there is an error message which usually reads something like:"There was an error opening this document. Invalid action object" Viewing with Konqueror is fine This might be related to the fact that these .pdf files were saved from the browser (opened with pdfstart)? Attached the original pdf as uploaded
VL submit without PubMed ID
Having added a PubMed ID field in the document submission form, which automagically fills out the rest of the document attributes when a document is submitted, submitting a document without a PubMed ID no longer works :(
VL search improvements
Is it possible to combine the advanced and simple search page? I want to be able to search for an article by author X with word Y anywhere in text? search restriction: "" causes confusion (which happened when you were there & searched for 2005 but were in a subfolder (default: search whole library) default: if "A B" put into field: search for "A AND B" not "A OR B". if I search for "A AND B" or more complicated? (A AND (B OR C)) I would like to see something like: A: 111 results B: 22 results A & B: 11 results Search in previous results button? Sort search results options: by date, name, frequency of keyword?
VL article informativeURL
The URL displayed for an article is currently not informative. Having several articles open at a time it would be useful to have the author, year and journal for example as the URL (or HTML title?) so that it gets displayed somewhere on the window when the article is viewed.
Alex Plone secutity issue
I think I have more access to your plone site than you are aware (probably more than I should have). I clicked on Invoices expecting to see how much time you have spent on work for me but the invoices must have been for somebody else... Not sure what else I could see or who else could see the invoices...
Alex Plone secutity issue
I think I have more access to your plone site than you are aware (probably more than I should have). I clicked on Invoices expecting to see how much time you have spent on work for me but the invoices must have been for somebody else... Not sure what else I could see or who else could see the invoices... (understadably, I haven't tried to find out nor have I tried to edit the stuff ;)
VL to use better search facilities
It would be nice to have better serach facilities for the VL. Near search? I will play around with desktop google Maybe there is something out there that can be plugged in...
2005 folder
No 2005 folder exists. Would it be possible to get it created automatically?
VL search result number per page and display by option
VL search results are only displayed in pages of 20. Would be nice to have the option of 20 / 50 / 100 / unlimited. Would be also nice to have displayed something like: 44 of 700 articles in the whole library (or in the 2004 folder) matched your criteria (or with the display as suggested in a previous issue: total library: 700 articles A: 22 articles B: 100 articles A & B: 11 articles matched your criteria Options to display the search results by year, author, ... (same as "folder" content).
submit document button more prominent
The submit button should be more prominent & visible also when not logged in. It should be on every page including the frontpage. Also the number of articles in the VL should be on all pages. The search buttons & submit buttons should be on top & bottom of the pages.
VL Section recognition
It would be nice if the VL could recognize sections of an article such as abstract (same text as from medline), Materials & methods, results, discussion, reference list (lots of names) and maybe paragraphs. This would be used for advanced search functions: X in materials Y in text (rather than in the title of an article quoted) A AND B in same paragraph ...

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