| Time |
S |
Nick |
Message |
| 01:04 |
|
|
zarah joined #bioclipse |
| 06:53 |
|
|
egonw joined #bioclipse |
| 07:03 |
|
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Gpox joined #bioclipse |
| 07:10 |
|
egonw |
hi Gpox |
| 07:10 |
|
zarah |
egonw: You have new messages. Write '/msg zarah @messages' to read them. |
| 07:10 |
|
egonw |
@msg |
| 07:10 |
|
zarah |
egonw: 1 d 16 h 38 m 20 s ago, sneumann said your links in the blog cdk#2 post are https: which require authentication. |
| 07:13 |
|
|
olass joined #bioclipse |
| 07:13 |
|
olass |
moin |
| 07:13 |
|
zarah |
hello olass, you fantastic person you |
| 07:13 |
|
zarah |
olass: You have new messages. Write '/msg zarah @messages' to read them. |
| 07:13 |
|
egonw |
hi olass |
| 07:13 |
|
olass |
@msg |
| 07:13 |
|
zarah |
olass: 16 h 4 m 46 s ago, jonalv said have a look at bug 899 |
| 07:13 |
|
olass |
@bug 899 |
| 07:13 |
|
zarah |
http://pele.farmbio.uu.se/cgi-[…]ow_bug.cgi?id=899 |
| 07:14 |
|
olass |
@tell jonalv: I have looked at bug 899. It is closed. Do you want me to reopen it? |
| 07:14 |
|
zarah |
Consider it noted. |
| 07:15 |
|
|
rojasm joined #bioclipse |
| 08:10 |
|
|
shk3 joined #bioclipse |
| 08:18 |
|
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jonalv joined #bioclipse |
| 08:24 |
|
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masak joined #bioclipse |
| 08:31 |
|
shk3 |
hi uppsala |
| 08:31 |
|
egonw |
hi shk3 |
| 08:31 |
|
* masak |
waves from Uppsala |
| 08:31 |
|
shk3 |
how is bioclipse doing? |
| 08:31 |
|
shk3 |
anything I can help with? |
| 08:31 |
|
masak |
documentation. |
| 08:32 |
|
shk3 |
hm |
| 08:32 |
|
egonw |
rojasm: http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1725 |
| 08:32 |
|
zarah |
egonw's link is also http://tinyurl.com/cfpk56 |
| 08:32 |
|
egonw |
quote: |
| 08:32 |
|
shk3 |
it's hard to write help for the plugins I didn't do |
| 08:32 |
|
shk3 |
but I will have a look what I could do |
| 08:32 |
|
egonw |
"The WebBook is Open Data which is where the spectra would go first/initially." |
| 08:32 |
|
egonw |
talking about MS spectra |
| 08:32 |
|
masak |
shk3: better to start with things you are familiar with, I think. |
| 08:38 |
|
rojasm |
egonw looks great. But in this case it will be only EI MS spectra, isn't it |
| 08:39 |
|
egonw |
dunno |
| 08:39 |
|
egonw |
I'm right now writing up email to Steve |
| 08:39 |
|
rojasm |
which make sense because it is more reproducible |
| 08:39 |
|
jonalv |
shk3: I am pretty sure that we could use someone testing and hunting/reporting bugs |
| 08:39 |
|
egonw |
rojasm: the ionization potentials you got from NIST WebBook too, right? |
| 08:41 |
|
rojasm |
yes it was |
| 08:41 |
|
shk3 |
how are the job things going? |
| 08:43 |
|
jonalv |
shk3: I am just about to start it. There has however already turned up yet another feature request about them. olass want to be bale to get a callback on partial results for example to show found substructure during the search |
| 08:43 |
|
jonalv |
shk3: so things are still sort of a moving target I would say... |
| 08:43 |
|
jonalv |
they get better and better though :) |
| 08:43 |
|
olass |
jonalv: we could push that to 2.1 |
| 08:43 |
|
olass |
if too hard |
| 08:43 |
|
jonalv |
olass: no |
| 08:43 |
|
olass |
ok :) |
| 08:43 |
|
* olass |
is happy if this makes 2.0 |
| 08:43 |
|
olass |
that means less changes later |
| 08:44 |
|
jonalv |
olass: I think it's time to do both that and the interface manager seperation now |
| 08:44 |
|
olass |
jonalv++ |
| 08:44 |
|
jonalv |
I can imagine not all managers using this in the 2.0 release though... |
| 08:44 |
|
olass |
yup |
| 08:44 |
|
olass |
shk3: we'll have to live with changes now |
| 08:44 |
|
olass |
there is no alternative |
| 08:44 |
|
olass |
do not be upset about this |
| 08:44 |
|
olass |
it is for the benefit of us all |
| 08:45 |
|
egonw |
jonalv: can you give me an update? did you finishd transition of some managers? |
| 08:45 |
|
shk3 |
don't worry |
| 08:45 |
|
jonalv |
egonw: I am working on the gist manager |
| 08:45 |
|
olass |
egonw: let's take this on tues next week |
| 08:45 |
|
shk3 |
I just wait for you to come up with something |
| 08:45 |
|
jonalv |
egonw: see my branch at pele |
| 08:45 |
|
olass |
in a meting |
| 08:45 |
|
egonw |
jonalv: URL? |
| 08:45 |
|
egonw |
jonalv: nvm |
| 08:45 |
|
egonw |
will find it |
| 08:45 |
|
olass |
jonalv, egonw: meeting tuesday is fine with you two? |
| 08:45 |
|
olass |
in the morning? |
| 08:45 |
|
egonw |
olass: yes |
| 08:45 |
|
jonalv |
pele:/var/www/gist/jonalv.gist or something like that |
| 08:45 |
|
egonw |
olass: what about Thu |
| 08:45 |
|
egonw |
ir that a holiday? |
| 08:46 |
|
olass |
? |
| 08:46 |
|
egonw |
30 Apr |
| 08:46 |
|
olass |
ah |
| 08:46 |
|
egonw |
burning things |
| 08:46 |
|
olass |
no, don't think thur is holiday |
| 08:46 |
|
olass |
fri is |
| 08:46 |
|
egonw |
oh... |
| 08:46 |
|
olass |
I have not yet decided if I should take thurs off but probably |
| 08:47 |
|
jonalv |
egonw: well put it this way, I won't get much done that day... |
| 08:48 |
|
* egonw |
is invited for burning stuff ... so won't do much either |
| 08:48 |
|
egonw |
other than putting fire to things |
| 08:48 |
|
egonw |
(not sure what those things are) |
| 08:48 |
|
egonw |
because our x-mas tree is long time gone :) |
| 08:48 |
|
egonw |
but don't care either |
| 08:48 |
|
jonalv |
hehe but isn't that at the evening? |
| 08:48 |
|
egonw |
putting fire to things is alwyas fun |
| 08:49 |
|
egonw |
jonalv: no clue :) |
| 08:49 |
|
egonw |
I'm new here |
| 08:49 |
|
jonalv |
I thought it would be... |
| 08:52 |
|
sneumann |
Hi |
| 08:52 |
|
zarah |
hi sneumann |
| 08:52 |
|
sneumann |
[10:43] <olass> jonalv: we could push that to 2.1 |
| 08:52 |
|
sneumann |
[10:43] <jonalv> olass: no |
| 08:53 |
|
sneumann |
I remeber a few articles e.g. on lwn.net |
| 08:53 |
|
sneumann |
on development strategies and releases et al |
| 08:53 |
|
jonalv |
sneumann: hi |
| 08:53 |
|
sneumann |
with a few examples: |
| 08:53 |
|
jonalv |
sneumann: okey |
| 08:53 |
|
jonalv |
:) |
| 08:53 |
|
sneumann |
KDE4 broken -> 4.2 usable |
| 08:53 |
|
sneumann |
Python 3.0 broken |
| 08:54 |
|
jonalv |
oh I see... |
| 08:54 |
|
sneumann |
and 3.1 to be release before regular schedule |
| 08:54 |
|
sneumann |
such that 3.1 becomes usable |
| 08:54 |
|
sneumann |
but at least you get 3.0 out of the door |
| 08:54 |
|
sneumann |
and currently the discussion how gnome 3 will do that |
| 08:54 |
|
sneumann |
so my interpretation is: |
| 08:54 |
|
sneumann |
bc2 will be a major change in the architecture |
| 08:55 |
|
sneumann |
so my 2c: get that out of the door rather sooner than later |
| 08:55 |
|
sneumann |
and push these "nice to have" features |
| 08:55 |
|
sneumann |
into 2.1 |
| 08:56 |
|
sneumann |
otherwise you'll end up with bc2 beta19 |
| 08:56 |
|
jonalv |
okey put it like this then: I am doing this now for the gist manager and the inchi manager in a branch. If they work we merge it into master for the 2.0 release and perhaps redo the cdk manager according to this scheme. If not we put it in 2.1... |
| 08:56 |
|
sneumann |
I have no clue what your're talking about, |
| 08:56 |
|
sneumann |
because Im watching you from very far away |
| 08:57 |
|
sneumann |
which also means that I am not in the position to tell what's right to do |
| 08:57 |
|
sneumann |
but just giving points to think about. |
| 08:57 |
|
sneumann |
to quote some blog I read recently |
| 08:57 |
|
sneumann |
whatever happens at a given time was the right thing(tm) |
| 08:57 |
|
sneumann |
or something like that ... |
| 08:57 |
|
jonalv |
sneumann: No I am probbaly the only one with enough insight in what I am doing. But your point is good and I will try to make sure it's well tested before I merge my branch into master |
| 08:58 |
|
sneumann |
because Im watching you from very far away |
| 08:58 |
|
egonw |
:) |
| 08:58 |
|
jonalv |
anyway I am going to work on this now. |
| 08:58 |
|
sneumann |
where you== whole BC development team |
| 08:58 |
|
egonw |
2 hours by RyanAir |
| 08:58 |
|
jonalv |
sneumann: so where are you? :) |
| 08:58 |
|
sneumann |
home == www.ipb-halle.de |
| 08:59 |
|
sneumann |
and not BC developer and not even regular BC user |
| 08:59 |
|
olass |
sneumann: thanks for your input |
| 08:59 |
|
sneumann |
but friend of shk3 and egonw and talking about things every now and then |
| 08:59 |
|
olass |
it's valuable |
| 08:59 |
|
olass |
and I completely agree with you |
| 08:59 |
|
egonw |
"and not even regular BC user" *yet* |
| 09:00 |
|
egonw |
I think I'll get sneumann beta testing when I finally get around makin that Metabolomics feature |
| 09:00 |
|
sneumann |
Yes, we were talking about getting features for LC/MS into BC2 (or BC2.1 for that matter ;-) |
| 09:01 |
|
sneumann |
BTW: we're among the people who do XCMS for MS processing |
| 09:01 |
|
sneumann |
which is an R / Bioconductor package |
| 09:01 |
|
egonw |
sneumann: regarding that... |
| 09:01 |
|
egonw |
have you tried running XCMS inside BC2 yet? |
| 09:01 |
|
egonw |
masak: do we have a demo script that takes data from the JS to the R console and back? |
| 09:02 |
|
egonw |
use case is fairly simple: |
| 09:02 |
|
masak |
egonw: no. sounds worthwhile, though. |
| 09:02 |
|
egonw |
1. store RAW data in a Bioclipse project |
| 09:02 |
|
egonw |
2. process those files with R console using the XCMS package |
| 09:02 |
|
egonw |
3. move the extracted MF info to the JS console |
| 09:03 |
|
egonw |
4. use PubChem/ChemSpider/CDK code to work with the MF info from the JS console |
| 09:03 |
|
olass |
egonw: R connsole is unfortunately broken in release |
| 09:03 |
|
masak |
:( |
| 09:03 |
|
jonalv |
olass: broken how? |
| 09:03 |
|
masak |
I didn't know that. |
| 09:03 |
|
egonw |
masak-- |
| 09:03 |
|
olass |
well |
| 09:03 |
|
olass |
I haven't reported it |
| 09:03 |
|
egonw |
ok, ok |
| 09:03 |
|
egonw |
masak++ |
| 09:03 |
|
olass |
but please try |
| 09:03 |
|
masak |
:/ |
| 09:04 |
|
olass |
I could not say why |
| 09:04 |
|
olass |
masak: have you expoerted bioclipse any time? |
| 09:04 |
|
masak |
olass: no. |
| 09:04 |
|
olass |
if not, I'll take that bug |
| 09:04 |
|
olass |
which I report now |
| 09:05 |
|
masak |
excellent. |
| 09:05 |
|
olass |
(please try in the release and correct me if I'm wrong) |
| 09:05 |
|
olass |
debugging things that fail in release is a pain... |
| 09:05 |
|
olass |
you need to add sysout and export betwen fixing things |
| 09:05 |
|
olass |
no debugging :( |
| 09:05 |
|
masak |
I read this blog post yesterday. http://www.modernperlbooks.com[…]ndidate-trap.html |
| 09:05 |
|
zarah |
masak's link is also http://tinyurl.com/ckedvp |
| 09:06 |
|
masak |
lots of things relevant for us. |
| 09:06 |
|
masak |
some traps we don't fall into, such as the QA trap. |
| 09:06 |
|
masak |
but that's mainly because we're small and not a company. :) |
| 09:06 |
|
egonw |
hahaha... |
| 09:06 |
|
egonw |
like companies do much better |
| 09:06 |
|
egonw |
Vista :) |
| 09:06 |
|
masak |
that's what I'm saying. |
| 09:07 |
|
masak |
we're avoiding that mistake by not being a company. |
| 09:07 |
|
egonw |
ah, in that way |
| 09:07 |
|
egonw |
we're just delaying ad infinity |
| 09:07 |
|
* egonw |
enjoying messing up yet another language |
| 09:07 |
|
masak |
I'd describe us as "release-averse". |
| 09:30 |
|
CIA-73 |
bioclipse: shk3 * r9917 /bioclipse2/trunk/plugins/net.bioclipse.nmrshiftdb/src/net/bioclipse/nmrshiftdb/ (2 files in 2 dirs): changed server, corrected typo |
| 09:38 |
|
CIA-73 |
bioclipse: shk3 * r9918 /bioclipse2/trunk/plugins/net.bioclipse.chemoinformatics/cheatsheets/GeneralChemoinformaticsCheatSheet.xml: some typos etc. in the cheat sheet. |
| 09:42 |
|
shk3 |
two questions with respect to jcp: |
| 09:42 |
|
shk3 |
1. There are stil two definitions of the jcp editor in the plugin.xml, one unused, it seems. |
| 09:42 |
|
shk3 |
Shouldn't we just remove the unused one? |
| 09:43 |
|
shk3 |
2. Shouldn't jcp be registered with net.bioclipse.cdk.ui.moleculeType in addition to the types it handles? |
| 09:43 |
|
shk3 |
ok, I go to the look and look for answers when coming back... |
| 09:48 |
|
shk3 |
hm, no answers? |
| 09:50 |
|
egonw |
shk3: about 1, file a bug report for Gpox |
| 09:50 |
|
egonw |
2: no, don't think so |
| 09:50 |
|
egonw |
because there still is IO involved which the editor must support |
| 09:51 |
|
shk3 |
right |
| 09:51 |
|
shk3 |
but we are not handling quite a few formats which cdk/jcp could handle |
| 09:51 |
|
shk3 |
ok, looking at the formats, I see some problems |
| 09:51 |
|
shk3 |
rxn is in |
| 09:51 |
|
shk3 |
but jcp in bc does not do reactions right now |
| 09:52 |
|
egonw |
rxn should indeed not be there yet |
| 09:52 |
|
egonw |
file a bug report for that |
| 09:59 |
|
shk3 |
ok |
| 09:59 |
|
Gpox |
shk3: about 1. where did you find the second definition? |
| 10:00 |
|
shk3 |
in the plugin.xml |
| 10:00 |
|
shk3 |
line 28 |
| 10:01 |
|
shk3 |
just files bug #968 |
| 10:01 |
|
shk3 |
files=filed |
| 10:01 |
|
shk3 |
I would love to do the save as dialog |
| 10:01 |
|
|
edrin joined #bioclipse |
| 10:01 |
|
shk3 |
since I think this is really important |
| 10:01 |
|
edrin |
hi |
| 10:01 |
|
zarah |
saluton edrin |
| 10:01 |
|
shk3 |
does anybody have an idea how that can be done? |
| 10:02 |
|
shk3 |
do we need a new dialog |
| 10:02 |
|
egonw |
you'll have to look at the Eclipse dialog sources |
| 10:02 |
|
shk3 |
or can the existing one be changed? |
| 10:02 |
|
egonw |
and start from there |
| 10:02 |
|
Gpox |
there are 5 definitions for JCP-editor, they do nothing yet |
| 10:02 |
|
shk3 |
you mean modifying their source? |
| 10:03 |
|
shk3 |
right, and the first has no content-type associated |
| 10:03 |
|
shk3 |
that was for Gpox |
| 10:03 |
|
egonw |
shk3: metadata tabs specific for a particular format are planned |
| 10:03 |
|
shk3 |
and the four other editor definitions could become one, I think |
| 10:04 |
|
shk3 |
metadata tabs? |
| 10:04 |
|
egonw |
Title: |
| 10:05 |
|
egonw |
Created With: |
| 10:05 |
|
egonw |
Author: |
| 10:05 |
|
egonw |
like the first three lines in MDL molfiles, e.g. |
| 10:06 |
|
shk3 |
in the jcp editor, you mean? |
| 10:06 |
|
shk3 |
ok |
| 10:06 |
|
shk3 |
obviously, you can keep the different editors |
| 10:06 |
|
shk3 |
was just something which came to my mind when looking at it. |
| 10:08 |
|
egonw |
well, there is some controversy here on having multiple editors too... |
| 10:08 |
|
egonw |
so, no worries there... |
| 10:15 |
|
CIA-73 |
bioclipse: shk3 * r9919 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/src/net/bioclipse/spectrum/wizards/NewSpectrumWizard.java: explicit instanceof avoids classcastexception |
| 10:18 |
|
|
rednael joined #bioclipse |
| 10:22 |
|
rednael |
[Leander Git] Added a very basic command line wrapper for starting rednael http://github.com/egonw/rednae[…]e3d20137384e7ec88 |
| 10:22 |
|
rednael |
[Leander Git] Ignore autogenerated .class files http://github.com/egonw/rednae[…]24946203e4121a55a |
| 10:22 |
|
zarah |
rednael's link is also http://tinyurl.com/c9ekm6 |
| 10:22 |
|
zarah |
rednael's link is also http://tinyurl.com/def9gg |
| 12:18 |
|
CIA-73 |
bioclipse: carl_masak * r9920 /bioclipse2/trunk/plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/views/JsConsoleView.java: |
| 12:18 |
|
CIA-73 |
bioclipse: [JsConsoleView] double \n between method candidates |
| 12:18 |
|
CIA-73 |
bioclipse: Fixes bug #907. |
| 12:18 |
|
zarah |
bug #907 | http://tinyurl.com/cfe2zm |
| 12:18 |
|
masak |
@pz ignores |
| 12:19 |
|
zarah |
[841] Pasting commands in JsConsole t... http://tinyurl.com/c7z6ua |
| 12:19 |
|
zarah |
[795] Balloon ignores value given for... http://tinyurl.com/cgcwnk |
| 12:19 |
|
zarah |
Entire list at http://tinyurl.com/c8ecqb |
| 12:19 |
|
masak |
@pz // |
| 12:19 |
|
zarah |
[898] Adapt scripts on http://wiki.bi... http://tinyurl.com/cugxk5 |
| 12:19 |
|
zarah |
[949] Home link broken http://tinyurl.com/d8355h |
| 12:19 |
|
zarah |
[800] Refactor ValidateCMLManager int... http://tinyurl.com/c6u9hj |
| 12:19 |
|
zarah |
[804] Refactor SpectrumManager into t... http://tinyurl.com/d99dnq |
| 12:19 |
|
zarah |
[805] Refactor SpecmolManager into th... http://tinyurl.com/c4yf5o |
| 12:19 |
|
zarah |
Entire list (54) at http://tinyurl.com/cqgnlh |
| 12:40 |
|
|
jonalv joined #bioclipse |
| 12:41 |
|
* jonalv |
hates his computer. Been with the nice admin for an eternity. Now he gave up for today... |
| 12:41 |
|
jonalv |
mac-- |
| 12:54 |
|
sneumann |
Hi again, |
| 12:54 |
|
sneumann |
just as further reading here the article I mentioned this morning |
| 12:54 |
|
sneumann |
http://lwn.net/Articles/317900/ |
| 12:54 |
|
zarah |
sneumann's link is also http://tinyurl.com/cdr4rx |
| 12:54 |
|
sneumann |
quoting: |
| 12:54 |
|
sneumann |
There are others who argue that the 3.0 series should be abandoned entirely in the near term. Rather than have a 3.0.1 with substantial changes from |
| 12:55 |
|
sneumann |
3.0—including the incompatible removal of cmp()—3.1 should be released quickly so that it is the release targeted by developers. |
| 12:55 |
|
sneumann |
where "developers" here means "users". |
| 12:55 |
|
sneumann |
So long, |
| 12:55 |
|
sneumann |
Steffen |
| 13:04 |
|
egonw |
:) |
| 13:04 |
|
egonw |
CDK has the concept of developer versions... |
| 13:04 |
|
egonw |
so does Linux |
| 13:04 |
|
egonw |
where 2.odd is developers oriented |
| 13:05 |
|
egonw |
and 2.even is for users |
| 13:05 |
|
egonw |
CDK, likewise, has had 1.0 and 1.2 for users, and 1.1 for developers |
| 13:08 |
|
CIA-73 |
bioclipse: shk3 * r9921 /bioclipse2/trunk/plugins/net.bioclipse.data.seneca/data/ (4 files in 4 dirs): changed the examples to actually run |
| 14:02 |
|
CIA-73 |
bioclipse: shk3 * r9922 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/ (2 files in 2 dirs): the randomstructuregenerator based jobs now actually run. code still ugly |
| 14:18 |
|
jonalv |
bah I am trying to write tests for aop stuff. Not easy... :( |
| 15:16 |
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edrin left #bioclipse |
| 15:27 |
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rojasm left #bioclipse |
| 16:46 |
|
* jonalv |
gives up for today now |
| 16:46 |
|
jonalv |
cya |
