March 2015 - Pharo-users - lists.pharo.org

Re: [Pharo-users] Get OS uptime

by Esteban Lorenzano

> On 19 Mar 2015, at 13:26, Esteban Lorenzano <estebanlm(a)gmail.com> wrote: > >> >> On 19 Mar 2015, at 13:08, Norbert Hartl <norbert(a)hartl.name <mailto:norbert@hartl.name>> wrote: >> >> >>> Am 19.03.2015 um 11:51 schrieb Esteban Lorenzano <estebanlm(a)gmail.com <mailto:estebanlm@gmail.com>>: >>> >>> >>>> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu <mailto:julien@tamere.eu>> wrote: >>>> >>>> >>>> On 19/03/15 11:10, Esteban Lorenzano wrote: >>>>> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. >>>>> >>>>> is better way. >>>>> >>>>> but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) >>>>> >>>>> you should use OSProcess instead (installable from Configurations Browser) >>>>> >>>>> (PipeableOSProcess command: 'uptime') upToEndOfFile. >>>>> >>>>> Esteban >>>> Oh, I didn't know '/proc' doesn't contains real files. I tought there >>>> were files in this directory since you do 'cat /proc/uptime' in a shell. >>> >>> thatâs the O.S. cheating you :) >>> >> Can you elaborate on that statement. What is a "real" file and why are the files in /proc not real? > > better: http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/proc.html <http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/proc.html> > > "proc is very special in that it is also a virtual filesystem. It's sometimes referred to as a process information pseudo-file system. It doesn't contain 'real' files but runtime system information (e.g. system memory, devices mounted, hardware configuration, etc). For this reason it can be regarded as a control and information centre for the kernel. In fact, quite a lot of system utilities are simply calls to files in this directory.â > > last part of that sentence is what made me think that *maybe* FilePlugin should thread them as regular filesâ¦ :) s/thread/treat > > Esteban > >> >> Norbert

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Esteban Lorenzano

> On 19 Mar 2015, at 13:08, Norbert Hartl <norbert(a)hartl.name> wrote: > > >> Am 19.03.2015 um 11:51 schrieb Esteban Lorenzano <estebanlm(a)gmail.com>: >> >> >>> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu> wrote: >>> >>> >>> On 19/03/15 11:10, Esteban Lorenzano wrote: >>>> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. >>>> >>>> is better way. >>>> >>>> but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) >>>> >>>> you should use OSProcess instead (installable from Configurations Browser) >>>> >>>> (PipeableOSProcess command: 'uptime') upToEndOfFile. >>>> >>>> Esteban >>> Oh, I didn't know '/proc' doesn't contains real files. I tought there >>> were files in this directory since you do 'cat /proc/uptime' in a shell. >> >> thatâs the O.S. cheating you :) >> > Can you elaborate on that statement. What is a "real" file and why are the files in /proc not real? better: http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/proc.html <http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/proc.html> "proc is very special in that it is also a virtual filesystem. It's sometimes referred to as a process information pseudo-file system. It doesn't contain 'real' files but runtime system information (e.g. system memory, devices mounted, hardware configuration, etc). For this reason it can be regarded as a control and information centre for the kernel. In fact, quite a lot of system utilities are simply calls to files in this directory.â last part of that sentence is what made me think that *maybe* FilePlugin should thread them as regular filesâ¦ :) Esteban > > Norbert > > >

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Damien Pollet

/proc are entries in the filesystem, as such I don't see why the file plugin would fail to access themâ¦ unless you cannot use block devices and such like any other file? In Unix, everything is a file, except those that have to be special-cased apart? On 19 March 2015 at 13:08, Norbert Hartl <norbert(a)hartl.name> wrote: > > > Am 19.03.2015 um 11:51 schrieb Esteban Lorenzano <estebanlm(a)gmail.com>: > > > > > >> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu> wrote: > >> > >> > >> On 19/03/15 11:10, Esteban Lorenzano wrote: > >>> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream > contents ]. > >>> > >>> is better way. > >>> > >>> but you will still get an empty string because actually â/procâ does > not contains real filesâ¦ so the file plugin does not applies there (and is > another debate if it shouldâ¦) > >>> > >>> you should use OSProcess instead (installable from Configurations > Browser) > >>> > >>> (PipeableOSProcess command: 'uptime') upToEndOfFile. > >>> > >>> Esteban > >> Oh, I didn't know '/proc' doesn't contains real files. I tought there > >> were files in this directory since you do 'cat /proc/uptime' in a shell. > > > > thatâs the O.S. cheating you :) > > > Can you elaborate on that statement. What is a "real" file and why are the > files in /proc not real? > > Norbert > > > >

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Norbert Hartl

> Am 19.03.2015 um 11:51 schrieb Esteban Lorenzano <estebanlm(a)gmail.com>: > > >> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu> wrote: >> >> >> On 19/03/15 11:10, Esteban Lorenzano wrote: >>> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. >>> >>> is better way. >>> >>> but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) >>> >>> you should use OSProcess instead (installable from Configurations Browser) >>> >>> (PipeableOSProcess command: 'uptime') upToEndOfFile. >>> >>> Esteban >> Oh, I didn't know '/proc' doesn't contains real files. I tought there >> were files in this directory since you do 'cat /proc/uptime' in a shell. > > thatâs the O.S. cheating you :) > Can you elaborate on that statement. What is a "real" file and why are the files in /proc not real? Norbert

March 19, 2015

Re: [Pharo-users] Fwd: Re: [ANN] BioSmalltalk

by stepharo

Hernan The pharo board could send a mail to the open bio informatic foundation. Are you member of their foundation? BTW I imagine that you will have to migrate https://code.google.com/p/biosmalltalk/ to github? Stef Le 19/3/15 07:39, HernÃ¡n Morales Durand a Ã©crit : > Hi Offray, > > For a biologist without interest in bioinformatics at all, it would be > hard to "sell" him any Bio* library. They could be better with > workflow systems like Galaxy, MyExperiment, or the Integrated Genome > Viewer, etc. biology is an extremely diversified field, but actually > Smalltalk is the perfect environment for biologists! > > To me, a demonstration of the power of BioSmalltalk is the realease of > PhyloclassTalk which I *know* couldn't be possible with Python, Java, > Perl, for a single developer in a short period of time. No matter how > many books and marketing they try to sell, the capability of exploring > and debugging objects in a live environment is unbeatable. > > But BioSmalltalk needs desperately other developers. I am open to > explain the internals and boring details to anyone. In the past I > tried to talk with pythonists but that was like talking to a wall, the > feeling I perceived was the environment was so different that they > seemed to be scared. Scared of everything they learnt was not worth > it. But the power is there for everyone, you can inspect a DNA > sequence, query for its properties in a new Inspector, send it to a > server and return its alignment, re-format and serialize, all like > using an exploratory data analysis with observational transformations. > > I also tried to BioSmalltalk gets accepted to the Open Bionformatics > Foundation (actually I only requested a page in their wiki for project > visibility & promotion), but **precisely** at the time of my request, > they occurred to implement a new whole policy of project acceptance > (but of course BioRuby, BioJava, BioPerl and BioPython were all in so > they were excluded) and I would have to pay international conference > calls to talk with them(?) about.... I don't know. > > So, the status is the same, but with more objects :). I have added > classes for parsing the Taxonomy Of Life, taxdb, EBI and file formats. > I hope to have the chance to work with the cools project people is > releasing in this community. > Cheers, > > HernÃ¡n > > 2015-03-18 23:06 GMT-03:00 Offray Vladimir Luna CÃ¡rdenas > <offray(a)riseup.net <mailto:offray@riseup.net>>: > > > > > -------- Mensaje reenviado -------- > Asunto: Re: [Pharo-users] [ANN] BioSmalltalk > Fecha: Wed, 18 Mar 2015 20:53:05 -0500 > De: Offray Vladimir Luna CÃ¡rdenas <offray(a)riseup.net > <mailto:offray@riseup.net>> > Para: pharo-users(a)lists.gforge.inria.fr > <mailto:pharo-users@lists.gforge.inria.fr> > > Hi, > > I just found this old mail. I know that BioSmalltalk is well and > advancing and I have a friend who works on biocomputing. I Saw the > Google Code page of the project, but as a not-programmer I found > difficult to understand what is the "selling point" of > Biosmalltalk for > a biologist... > > Anyway I'm just curious about which new experience brings Smalltalk to > old fields. In my own case, making my notebook for data narratives and > visualization has been very enriching and even if there are external > tools in other ecosystems to work on it (pandas, Jupyter, LaTeX), the > integration with them inside a moldable and modifiable tool is > hard to beat. > > Cheers, > > Offray > > El 15/03/12 a las 07:32, HernÃ¡n Morales Durand escribiÃ³: > > Dear all, > > It's been two years since I've started to work in > bioinformatics with > Smalltalk. It has been a difficult decision because the > quality and > amount of bioinformatics libraries is absolutely amazing, but I've > received a lot of support from the main researchers at the > Institute > of Genetics where I'm working in Argentina. > > Now the initial step for a BioSmalltalk release is done. I > hope the > FOSS community receive this pre-release as the basis for future > enhacements for bioinformatics with any Smalltalk flavor. > Although in > the short-term it is unlikely for a BioSmalltalk to reach the > users, > maturity and competitive level of major Bio* toolkits (BioPerl, > BioPython, BioRuby or BioJava), it could take too many years > more if I > continue this work alone. However, BioSmalltalk was not > conceived to > replace or defeat any other similar packages, but to provide > to the > bioinformatics community the features of a pure object system. > So feel > free to spread the word for all bioinformaticians, newcomers, > developers, or life scientists, for helping in any way and > discovering > why Smalltalk is such a special environment. > > This release was implemented in Pharo 1.3 custom Core, but cross > Smalltalk portability was a priority. I'm working now to release > versions for GemStone, Squeak and VisualWorks is there is enough > interest. Everybody is welcome to contribute. > > You may download a pre-compiled release from the project page: > http://code.google.com/p/biosmalltalk/ > > Best regards, > > HernÃ¡n > > > > > > >

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Julien Delplanque

On 19/03/15 11:51, Esteban Lorenzano wrote: >> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu> wrote: >> >> >> On 19/03/15 11:10, Esteban Lorenzano wrote: >>> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. >>> >>> is better way. >>> >>> but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) >>> >>> you should use OSProcess instead (installable from Configurations Browser) >>> >>> (PipeableOSProcess command: 'uptime') upToEndOfFile. >>> >>> Esteban >> Oh, I didn't know '/proc' doesn't contains real files. I tought there >> were files in this directory since you do 'cat /proc/uptime' in a shell. > thatâs the O.S. cheating you :) > > Esteban > Haha ok, nice to know :) Julien

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Esteban Lorenzano

> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu> wrote: > > > On 19/03/15 11:10, Esteban Lorenzano wrote: >> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. >> >> is better way. >> >> but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) >> >> you should use OSProcess instead (installable from Configurations Browser) >> >> (PipeableOSProcess command: 'uptime') upToEndOfFile. >> >> Esteban > Oh, I didn't know '/proc' doesn't contains real files. I tought there > were files in this directory since you do 'cat /proc/uptime' in a shell. thatâs the O.S. cheating you :) Esteban

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Julien Delplanque

On 19/03/15 11:10, Esteban Lorenzano wrote: > '/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. > > is better way. > > but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) > > you should use OSProcess instead (installable from Configurations Browser) > > (PipeableOSProcess command: 'uptime') upToEndOfFile. > > Esteban Oh, I didn't know '/proc' doesn't contains real files. I tought there were files in this directory since you do 'cat /proc/uptime' in a shell.

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Esteban Lorenzano

'/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. is better way. but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) you should use OSProcess instead (installable from Configurations Browser) (PipeableOSProcess command: 'uptime') upToEndOfFile. Esteban > On 19 Mar 2015, at 07:07, Julien Delplanque <julien(a)tamere.eu> wrote: > > Hi everyone, > > I can't find out how to get the uptime of the OS from pharo. > > I tried: > > (FileLocator root / 'proc' / 'uptime') readStream contents. > > and > > (FileSystem disk root / 'proc' / 'uptime') readStream contents. > > but all what I get is an empty string ''. > > I don't know if there are messages in some specific classes to do this > (in OSProcess for example?). > > Thanks in advance. > > Julien >

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Nicolai Hess

2015-03-19 10:27 GMT+01:00 Julien Delplanque <julien(a)tamere.eu>: > > > And, if there is a system library that provides this data, there is the > > NativeBoost way: > > For example( not linux but windows): > > > > new method: > > NBWin32Shell>>#getUptime > > > > <primitive: #primitiveNativeCall module: #NativeBoostPlugin error: > > errorCode > > > ^ self nbCall: #( ulonglong GetTickCount64() ) module: #Kernel32 > > > > and then you can call it like that: > > NBWin32Shell getUptime milliSeconds. > > > > Ok, nice to see there are different way to do it :) > > But I think I'll use Torsten's solution. > > Thank for the response anyway :) > Ah, I just saw, he already provides the same in OS-Windows. > > Julien >

March 19, 2015