Help:Wiki questions

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This is a question and answer forum for wiki-related help. Please ask editing-related questions here.

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Renaming iGEM lab notebook name

We are trying to edit our lab notebook name, but we can't find out how. We want to change the '2009' into '2013'

http://openwetware.org/wiki/IGEM:University_of_East_Anglia_%28UEA%29%2C_Norwich%2C_UK/2009/Notebook/NRP-UEA-Norwich_iGEM

Can you help us out? Thanks

External Links

Question

Is there anyway to add external links to open in a new window (equivalent to target="_blank" function)? Thanks. *Sung-Hye Grieco 15:23, 1 February 2011 (EST)

Question

I'm trying to set up a menu in a lab template, with little boxes for each major section of the site. I'd like to have it so that when you click on, say, the "research" box, when you're on the "research" page (and lower-level pages), the "research" box appears in a different color. Is there a way to do this with the template system? Thanks very much-- *Kunal Mehta 05:24, 30 July 2010 (EDT):

Biblio & Show / Hide

Question

Hi, I would like to know if it is possible to do the following. I think it's a really useful way of displaying a bibliography:

<showhide>2002-2007 Publications__HIDER__ 
<hide>
<biblio>
#[[Streptomyces:PublicationsKelemen]]
</biblio>
</hide>
</showhide>


I can get the biblio tags to work fine & display the list on Streptomyces:PublicationsKelemen page, just not in a useful show/hide display. I thought this would be good to show publications in 5 year groups that a reader could show/hide rather than one great long list. If someone knows a way around this, i would be grateful for some help. Thanks, Jim @ Streptomyces 11:59, 13 March 2007 (GMT)

Answer

  • Reshma 09:11, 13 March 2007 (EDT): Just tried playing around with this at the Sandbox and couldn't make it work either. I think the extension itself might have to be changed to accommodate what you want to do. You could try leaving a note on Martin Jambon's talk page. He might be able to help since he wrote the Biblio extension. (Though the problem could be with the show/hide extension.)

Thanks

Thanks for your suggestion Reshma, I left a message on Martin Jambon's talk page. He's not sure about it, but said he'll contact someone about the show/hide code. Jim @ Streptomyces 06:36, 16 March 2007 (EDT)

  • Austin Che 14:38, 18 March 2007 (EDT): I'm deprecating the showhide extension so don't use it any more. There are much too many problems with it and it's unnecessary. I've rewritten something that is completely editable via the wiki and is much better in every way. See OpenWetWare:Toggle for more details. Your example code above can be changed to:
2002-2007 Publications

{{hide|
<biblio>
#[[Streptomyces:PublicationsKelemenList]]
</biblio>
}}

Streptomyces 07:07, 20 March 2007 (EDT) Great / brilliant. Thanks :-)

Openness of openwetware

Question

  • Thanks for help with my last question. I am now curious about where I can go to download the openwetware software or the database dumps. Is this currently possible? PaulGrayson 02:16, 30 January 2007 (EST)

Answer

OWW is running the stock Mediawiki software with several extensions. We have recently started making the daily dumps of all revisions of all OWW pages available in XML format here. --Ilya 03:43, 30 January 2007 (EST)

Thanks

Thanks for the link. I'm thinking that any lab seriously using openwetware will want to maintain a complete local backup of their contributions, so how about a way to download all of the uploaded files as well? Eventually it might be important for you to make it possible for a lab to get a complete backup of its files with a single click. PaulGrayson 16:25, 6 February 2007 (EST)

Question

I'm in the process of setting up a lab site. My lab currently maintains its own wiki, and I hope to move most or all of it to OWW. Parts of it need to stay private, especially as we use it for writing papers with collaborators who don't want to make paper drafts public. From poking around on OWW, I see that there are private wikis. What's involved in setting one of these up -- I haven't been able to find documentation. Gordon Fox 23:23, 27 February 2009 (EST)

Very small edit window

Question

  • Hello, I just joined the site and edited my first page. But the edit form is so small! It's only 3 lines high. By contrast, Wikipedia gives me a 30-line high form. Was this a conscious decision, or is the problem unique to my computer? I don't think it is because of a small window - there is a ton of white space (actually, blue space) below the form. PaulGrayson 00:50, 30 January 2007 (EST)

Answer

  • You can change it by going to 'my preferences' in the top right of the screen. Select 'Editing', then change the number of rows.-Jkm
  • That said, I'm not sure why that happens, but it depends on who created your account (or, more likely, on how they did it). When I create an account at Special:Userlogin&type=signup, it gives 25 rows. A number of people (BioControl folks) have had the same problem - but I'm not sure who created their accounts (not me).-Jkm
  • Thanks Josh for noticing this. There was a bug in the user system that I've patched so new accounts should not have this problem. I've also updated most existing accounts that may have been affected by this with a more reasonable window size. --Austin Che 14:32, 7 February 2007 (EST)

Wiki mystery #1

Question from skoch3

I noticed that when I created a lab notebook per the instructions, I have convenient links automatically at the top of the page (to go back to main notebook). I suspect this may be do to the "calendar" extensions, but it's sort of magic to me. Is there some way to do this for otherpages with the forward slash heirarchy?--Skoch3 01:36, 20 January 2007 (EST)

Answer


Follow-on

  • Skoch3 22:03, 20 January 2007 (EST): Thanks for the help, Reshma -- I had thought this may be true. My specific page I am thinking of is: PHYC500/2007:Discussions/Steve_Koch_talk. I do see the backlinks on your page, but not on this one. I wonder if it's because of (a) the 2007:Discussions part of the link or (b) the template I am using (the normal course template)? Thanks if you have more hints!

Answer

  • Reshma 11:25, 21 January 2007 (EST): Hey, Steve. OK with a little bit of playing around, I figured it out. It was because the page PHYC500 did not exist that you weren't getting any backlinks. I've created PHYC500 and made it a redirect to PHYC500/2007 and so it looks like the backlinks are all showing up now. Sorry about the trouble.

Thank you!

  • Skoch3 16:14, 21 January 2007 (EST): Thanks for fixing that! It would have taken me quite a while to figure that out, but hopefully I'll remember for the next time. Thanks for doing the research! I'll see if I can find a place to add a tip under the "courses" instructions.

Wiki mystery #2

Question from skoch3

Some pages I use (such as the user talk pages) have a "+" button that is convenient. For example, I would like to use that button in my lab notebook. Is there some way of adding that button to other pages? This again is a mystery to me. Thanks!--Skoch3 01:36, 20 January 2007 (EST) PS: Am I supposed to delete questions when I they've been answered or leave them for others to learn???

Etiquette for disk usage?

Question by skoch3

I'm new to OWW and to wikis in general. I'm curious whether there are limits on individual file sizes or total disk usage by a user / group? My current question is related to seminar slides and movies for the course I am adding to OWW. Not sure how soon I will hear back (and am wary of bugging you all too much on email!) so I will go ahead and try it now at a cost of about 40 MB. But definitely would like to know the etiquette for the future!--Skoch3 00:21, 19 January 2007 (EST)

Answer

There's no official policy on large file uploads although we have tried to not have limits on file sizes. However, OWW shouldn't be treated as a file storage area. For large movies, putting them on another service like Google Video and embedding it or linking from OWW works fine (kind of like the video on the front page of OWW). --Austin Che 10:09, 19 January 2007 (EST)

Thanks!

--Skoch3 13:15, 19 January 2007 (EST)

dewikifying problem

Question by halayc

I am trying to dewikify this page:http://www.openwetware.org/wiki/Richard_Lab . I followed the subfiles naming convention, and created the page Dewikify:Richard_Lab , and added " !BODY! in the content. The problem is that I still don't automatically get the dewikified version when I go to http://www.Richard_Lab.openwetware.org. Any suggestions? Please email me back at halayc @ gmail.com .

Answer

http://richardlab.openwetware.org

--Sri Kosuri (talk) 21:17, 22 October 2006 (CDT)

Case issue with dewikify

I am having the same problem. The wikified page is located at http://www.openwetware.org/wiki/BDRD, and I created a Dewikify:BDRD page (not sure if that step is necessary if I just want to use the default). http://bdrd.openwetware.org does not send me to an automatically dewikified version of BDRD. Instead it sends me to the openwetware homepage. --Stewarta 16:53, 18 December 2006 (EST)

Answer

  • Reshma 17:20, 18 December 2006 (EST): I think the problem with BDRD is a case problem. The dewikify extension is looking for a page named Bdrd rather than BDRD. I believe that this can be fixed manually on the OpenWetWare server side, but I don't have access. Either Austin Che or Ilya Sytchev will be able to fix this for you. If you give it a day, I think they will get to it. Sorry for the trouble!
  • Jasonk 18:25, 18 December 2006 (EST): OK, I added a redirect from Bdrd to BDRD and that looks to have fixed it: http://bdrd.openwetware.org. (not sure if this is the best long term solution (have to see what austin/ilya say), but should work for now.
  • Andrew Stewart 09:42, 19 December 2006 (EST): Ya know, it had occurred to me that that might be the problem. Redirect should work just fine, I would think. Thanks.
    • Andrew Stewart 10:01, 19 December 2006 (EST): Perhaps I spoke too soon. I've changed the content of BDRD since the redirect from Bdrd to BDRD was created, however the page generated from http://bdrd.openwetware.org still shows the same content that existed on that page at the time the redirect was created. I wonder if the redirect is somehow preventing the dewikify script from updating its knowledge of the contents on BDRD?
    • Jasonk 15:28, 19 December 2006 (EST): OK, should be updated now. The problem is that the dewikify script updates the dewikfied page once a day, currently. You can read about it here: Dewikify#Cache - but you can force it to update immediately by visiting the link http://bdrd.openwetware.org/x. If you think it would be better to have it update after every change rather than once a day contact Austin Che - looks like he was soliciting feedback about this based on the Dewikify page.

Similar dewikify question

I am having a similar dewikifying problem as the above user. I am trying to dewikify this page:http://www.openwetware.org/wiki/Wei_He. I followed the subfiles naming convention, and created the page Dewikify:Wei_He , and added " !BODY! in the content. The problem is that I still don't automatically get the dewikified version. Could anyone help? Thanks a lot! (Wei 10/4/2007)

Thanks a lot for your help! It was an accident that we edited the openwetware:getting started paper. I'm still trying to learn how to use wiki. Again, I truly appreciated your help!


dewikify question

similar problem: I dont get dewikified version of http://openwetware.org/wiki/Li_Lab.

dewikify question again

Thanks Austin, can I dewikify http://openwetware.org/wiki/Li_Lab to http://lilab.openwetware.org/ or http://li_lab.openwetware.org/, thanks a million. -Wei


Calendar

Question

Does anyone know how to cycle repetitive codes without the use for copying and pasting for every day of the calendar? please email me back rjs397@psu.edu

Answer

LaTex to Wiki

Question

Diacritical marks and special symbols/characters: how is a hacek/caron symbol created? In LaTex, such a symbol over a lowercase "s" would be Bene\v{s}.

Answer

Sri Kosuri 17:01, 4 April 2006 (EDT): Here are two resources you can look at

  1. Mediawiki markup - You can directly encode characters using mediawiki's markup language.
  2. If you need to do math equations, you can directly use LaTex format using the math markup. For example, see this page

Hope this helps... if it didn't, update it here, and I'm sure there will be other ways to solve the problem.

  • One option is to cut and paste from a caron/hacek Wiki page. However, the result depends upon the character size in a browser: Beneš

Password protection

Question

  • Pdextras 13:05, 24 March 2006 (EST): Does anyone know if it's possible to restrict access to a document to specific users?

Answer

  • RS 14:12, 24 March 2006 (EST): Sorry but we don't have a way of doing this on OpenWetWare. You can put the document in your own public directory and restrict access to it using htaccess and just link to it from OpenWetWare if you like. You can read more about the debate over whether to permit restricting access to certain pages on OWW at the ideas archive.

Uploading pdfs

Question

  • RS 13:10, 19 March 2006 (EST): I tried several times to upload this pdf to OpenWetWare but every time it gave me the following error message "The file you uploaded seems to be empty. This might be due to a typo in the file name. Please check whether you really want to upload this file." I've tried resaving the file using Adobe Acrobat and Preview as well as remaking the file by printing to pdf from Microsoft Powerpoint but nothing works. I was able to successfully upload another pdf file just fine. A quick google search reveals that you can get this message if you are approaching the maximum file size or the maximum http request size (see Mediawiki on uploading file). (My file size is 2 MB.) Anyone have a good solution to this?
    • Jasonk 16:38, 25 March 2006 (EST):Getting the same problem with a 3MB powerpoint file.
    • BC 14:10, 25 April 2006 (EDT):Same problem, 2MB image.

Answer

  • Sri Kosuri 17:05, 19 March 2006 (EST): I believe we set the upload limit to 10MB. For example, see this PDF. I don't know about the maximum http request size. Maybe something broke on one of our upgrades? Anyone else have a clue?
  • Ilya 13:28, 28 April 2006 (EDT): This was caused by a change of server configuration after upgrade to PHP5. I'm working with Biosupport to resolve this.
  • Ilya 14:51, 1 May 2006 (EDT): I have implemented a workaround to increase the file size limit. It is now set to 20MB but you'll receive a warning if you upload something larger than 10MB.

Image links

Question 2

  • Burak YILMAZ 17.28, 02 may 2009 (EST): I wanna ask How can I put a picture as a backround in my site.And how can put button on my banner .
    • Steve Koch 15:10, 2 May 2009 (EDT): Hi Burak, I don't think I'm going to be able to answer your question, but hopefully someone else can. Just to clarify, though: Do you want to change from the regular white background to an image background? I don't know if that's possible. Also, you want an actual button (clickable image) versus just a link on your banner?

Question 1

  • Nikolai.windbichler 05:05, 10 March 2006 (EST): I have this small problem: On this site I want the image to link to the .doc file which can be found when clicking on the link above the image. How would I do that? I searched a little bit through oww and wiki help sites but couldn't get ot done. If you have any ideas please let me know.


Answer

  • RS 09:22, 10 March 2006 (EST): Have you tried looking at the code for the Main Page? The icons under the OWW logo do something similar. It looks something like this {{Click || image=MainPage LookChange.jpg | link=Highlights:Considering_a_new_look | width=50px | height=50px }}. By replacing the link= field with your link, I assume you would get what you want. Hope this helps.
    • Nikolai.windbichler 17:25, 10 March 2006 (EST): Thank you. It is very close to what I want but now not the whole area of the image links to the file but only the left half of it. I'm not sure why that is tough. Well 50% is not bad when you start at 0. ;)
    • BC 19:48, 3 April 2006 (EDT):Sorry this is so late, but you should be able to fix this by reading the discussion on this page - Template talk:Click. If you have any problems getting this fix to work, let me know.

Printable Subsections

  • smd 12:58, 26 April 2006 (EDT):

Question

  • Anyone know of an extension/patch that has been written to display a printable version of a subsection of a wiki page? It would be great for printing protocols or other partial documents if (for example) next to the [edit] link there was a [printable] link, which took you to a URL that looked something like:
http://openwetware.org/index.php?Help:Wiki_questions&printable=yes&section=5                                 

If anyone has interest in this, I could possibly just write it myself, but I'm a little busy these days. I thought I'd check here first. Thanks.

Deleting pages

Question

  • <font=red>If I want to delete a website, how can I do that?

Thanks!

Answer

  • Austin Che 07:34, 27 April 2007 (EDT): Include {{deleteme}} on the page and an admin will delete the page eventually.

Loss of session data

Question

  • I receive the following message upon trying to edit any page (including this one): "Sorry! We could not process your edit due to a loss of session data. Because this wiki has raw HTML enabled, the preview is hidden as a precaution against JavaScript attacks.If this is a legitimate edit attempt, please try again. If it still doesn't work, try logging out and logging back in."

Logging out and logging back in doesn't help. On my publications page, the error actually prevents me from editing at all. Help! Thanks --Drummond 12:12, 19 June 2007 (EDT)

Answer

  • Austin Che 13:51, 19 June 2007 (EDT): The warning message is harmless. That's a side effect of it trying to preview for you. Go into your preferences->editing and uncheck "Show preview on first edit". That should get rid of the warning message. I'm not sure why you can't edit your publications page. It seems to work for me.
  • Reshma 14:00, 19 June 2007 (EDT): Also, if you just click the button again, it should work.
  • Ilya 14:03, 19 June 2007 (EDT): I sometimes receive this error message when my session times out while I edit a page in one Firefox tab, then open a new tab, log back in from there and try to save the page in the first tab. If logging out and back in doesn't help, simply refresh your browser session. In Firefox 2 you can go to Tools -> Clear Private Data, select Cookies and Authenticated Sessions, then click Clear Private Data Now. Then after you log in again, everything should be back to normal.

Drummond 14:53, 19 June 2007 (EDT): Thanks. The first suggestion seemed to do it; the last suggestion didn't seem to affect the problem. I'm now happily editing, error-free.

Biblio comment disruption

Question

I learned how to add comments to a biblio entry (see here). On one of my pages, adding a comment disrupts the rest of the biblio entries. Are we running the latest biblio?

Answer

  • Reshma 10:21, 5 October 2007 (EDT): It appears that we're not running the latest version of Biblio ... we're running 0.7 and the latest is 0.8. I am not sure if this is why your comment is not working. Sorry about that. I'll mention is to Bill. And sorry that it took so long to get a response.

Setting up lab page: how to link to template?

Question

I followed the instructions for setting up a new lab page Help:Starting_a_lab_wiki and got to the point where the actual lab page is supposed to be linked to the new template:

Quote:

  1. First, go to the generic lab wiki page (open it in a new browser window if you want to keep reading this text).
  2. Click Image:EditButton.jpg and copy all the wiki markup on that page.

However, this step brings me back to the generic TEMPLATE template, not the lab template. So there is no working description how to use the Template for a lab page. PS: the template is Templates:PrbbBB


Repeat of problem

I am currently experiencing the same problem ... the lab template is linking to the generic Template template.

I also noticed that when following the instructions for setting up the new template. The instructions direct you to replace Image:Placeholder.png in Template:LabNamewith the appropriate link for your own image. However Template:LabName doesn't contain any image references.

Answer

  • DAD 22:52, 4 July 2008 (UTC): This may have occurred because a user had moved the Template:LabName page (presumably without knowing what they were doing). I've restored the page; try again and see if things work this time.

Math rendering problem

Question

I'm getting errors trying to render even very simple math equations: "Failed to parse (Missing texvc executable; please see math/README to configure.): n_i(t)" Should replicate here: [math]n_i(t)[/math]
I can correctly render anything that has previously been rendered on the site, such as [math]n_i[/math], suggesting that caching is at work; novel math expressions fail to parse and render. See, e.g., Drummond:PopGen. Help! Thanks -- DAD 21:25, 4 July 2008 (UTC):

Answer

  • Austin Che 14:13, 6 July 2008 (UTC): Thanks. We forget to install some programs on a server move. Should work now.
  • DAD 14:37, 6 July 2008 (UTC): It does indeed! Thank you.

Superscript/Subscript line spacing adjustment

Question

When I use superscripts or subscripts in a line of wiki text, the affected characters slightly disrupt the regular line spacing in the document because they are respectively higher or lower than the standard line of text. Is there a way to adjust the line spacing or super- sub- script formatting to compensate for this effect?

Thanks,

Tyler (July 30, 2008)

  • Reshma 13:59, 30 July 2008 (UTC): Hey Tyler. In searching quickly, it seems that there is some discussion of fixes (see [1]). But they involve modifying the .css file. (So there is no quick fix that you can do in the page itself. You have to change how browsers format the text.) Are you interested in fixing the spacing issue just for yourself or anyone who views the page? If you want to fix it for everyone, I'd suggest contacting Bill Flanagan, the technical developer at bill AT openwetare.org. But from a brief reading at the link above, it seems like it might be pretty hard to get sub- and superscript looking nice across all browsers.

RSS feeds: complicated Boolean filtering

Question

  • Alex O. Holcombe 18:02, 3 September 2008 (EDT):Having RSS feeds is great, and of course being able to filter by lab is essential

For example, here is the feed for the Endy lab: http://openwetware.org/index.php?filter=Endy&feed=rss&title=Special:Recentchanges But I need one more level of filtering, to exclude changes made by myself! Otherwise my RSS feed gets totally crowded by all the changes I already know about, because I myself made them. Is there any way to do this?

Automatic reference list generation

Is there some way to include an automatic list of references from PubMed? In HTML, this code works:


href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=PureSearch&db=PubMed&details_term=Beauchamp MS[Author]"

But the spaces and square brackets seem to mess up mediawiki. Thanks! Mike

Follow-up

I can't seem to use the normal references tags: I would like to use footnotes so that the full reference is visible, like this<ref>Muratore, KE. (2011) ''A Journal.'' '''1''' 1:1-10.[[doi:12.3456/abcdefg]]</ref>.

==References==

{{Reflist}}

Kathryn Muratore 12:25, 24 May 2011 (EDT)

Automatic reference list Errors with PubMed

There seems to be errors when linking to PubMed using the method that's been working for 2 years.

Please advise about the new method. Thanks, Andor

Yes, please fix biblio!

Please let us know what the plan is! This makes my publications page unreadable -- right in the middle of a job search. (For others looking on, this issue is known: see here, although the fix is not.) Thanks! DAD

Specifying list starting value

  • Kathryn Muratore 16:46, 29 June 2011 (EDT):Wikipedia's help says that you can specify a list's starting value by inserting <li value="x"> (where x is the number you want to start at) after the # in a list. I tried to do this here on OWW and I get a "1." first with nothing after it, and then the next line starts with the number I specify. (See here. If you change the value of x to "9" or something, you'll see what I mean more clearly - the extra 1 doesn't go away.) At the same time, I confirmed that this is the correct code over at Wikipedia. Anyone know why this isn't working and if there's a way around it without completely switching over to html lists?


Unsolicited page redirect

Question

Delete account

Question

  • I accidentally made 2 accounts. How do I delete one? Thanks.

Delete uploaded file

Question

  • How do you delete a file that was uploaded. I uploaded an incorrect file and I want to delete it, but I can't figure out how. Thanks!
  • Me too - how do you delete uploaded files ??
  • I have the same issue. How can I delete a file?

Can't upload .pptx file

Question

  • I'm getting an error saying that the file I'm uploading is "empty". This appears to be the same problem some people were having back in 2006. I'm trying to upload a 3.7MB .pptx file. Is there another server update that is causing this? Thanks.

--Shelly Peyton 12:27, 19 January 2014 (EST)

  • Me too. Was working fine a few days ago, but am now having trouble uploading a 350K .png image.

Matthew Todd 20:02, 20 January 2014 (EST):

  • Also getting this same "empty" file error message with all file types tried. Glad to see I am not crazy. Thanks for the support.
    Meg Bentley 15:47, 21 January 2014 (EST)

Answer

  • Hi from the sysadmin -- I apologize for the difficulty. I'm tracking down why this happened and how to fix it.
    --Jeff Brock 21:13, 22 January 2014 (EST)
  • This is now fixed. Thanks for your patience.
    --Jeff Brock 17:57, 30 January 2014 (EST):

MySQL returned error 126?

When trying to update a couple of pages recently (just now this one) I've received an error page containing all text on the page, unformatted, along with a message at the bottom reading "from within function "SearchMySQL::update". MySQL returned error "126: Incorrect key file for table './owwdb/searchindex.MYI'; try to repair it (localhost)"." Not sure what this means. When I return to the page I was editing the edit has gotten through, so it's not clear what the error was.

Line spacing

Question

When trying to update a couple of pages recently (just now this one) I'm having a problem adjusting the top text box line spacing for a subset of the text box to be single-spaced lines. I can change font attributes but not line spacing. Any suggestions? Thanks!!
https://openwetware.org/wiki/OpenWetWare:Wiki_questions
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