Hi Gauthier,
I really didn't like the previous design of batch mode, for several reasons:
1) Some modules are simply not supposed to take the previous module's output as
their input. A typical example is the alignment module, which may require a
combined output of several previous steps.
2) In the previous design it was absolutely impossible to process 2 groups of
files simultaneously with slightly different methods or parameters. For
example, in our lab we often acquire data in positive and negative ionization
modes, and I want to be able to process all this data using a single batch.
3) The requirement that modules must report newly generated objects is a burden
for module developers. Based on previous experience, I want to make module
development as simple as possible.
However, you have a good point that the user should be able to run the same
batch on different files in the GUI mode. I propose the following solution: the
RawDataFileParameter and PeakListParameter can have a special checkbox "Use
currently selected files", which, if selected, will run the methods on the
files that are selected in the tree (just like in the previous implementation).
In the subsequent batch steps, the input data files or peak lists can be
defined using wildcards (e.g. "*filtered") - that is already possible now.
What do you think?
Tomas
On Dec 17, 2014, at 16:04, Gauthier Boaglio
<gauthier.boag...@gmail.com<mailto:gauthier.boag...@gmail.com>> wrote:
Hi Tomas,
I understand that this is important to have it work this way for better
compatibility in Headless Mode, but wouldn't it be more practical to have the
choice of using pattern or using the result of the previous step (as it used to
be), at least in GUI mode? That was very handy that way, because we were able
to run several times a batch in the same session/project on different input
files (string pattern - regex - doesn't allow to make the distinction between 2
different runs of a given batch). A simple suggestion: couldn't we restore that
possibility and in some way (for example, adding some sort of predefined tags
to the RawDataFilesComponent/PeakListsComponent), such that we can, for example
say: "${previous.step}" as a valid/recognized "pattern"/entry. Or, another way
could be to give the possibility to prepend a user define prefix to the
resulting file/list of the result of the first step (which would be used
recursiveley throug the steps, such that we don't have to update every
RawDataFilesParameter/PeakListsParameter, for every single step, each time we
run the batch one more time in the same project). As a simple user, I would
prefer to have "${previous.step}" recognized as a valid pattern entry. As a
developer, I understand that this can make the code a bit more complicated/less
flexible (since we would have to restore the ability of a Task to remember what
objects it actually generated).
What do you say?
Best
Gaut
On 12/16/2014 01:40 AM, Tomas Pluskal wrote:
- I updated the RawDataFileParameter and PeakListParameter (selection of inputs
of individual modules) to be real, visible parameters with their own selection
components. In these components, users can set wildcards (*) to apply methods
to certain groups of data files or peak lists. This also changes the philosophy
of the batch mode. In previous versions, the batch mode steps were always
applied to the output of the previous step. Now, the user can setup what each
batch mode step is actually applied to. This change is still a work in
progress, as some modules will have to be updated to reflect the new philosophy
(e.g., the spectra visualizer now complains when multiple raw data files are
selected - but these are cosmetic issues).
--
Gauthier BOAGLIO
CEFE - UMR 5175
1919 route de Mende
F-34293 Montpellier cedex 5
Tel: +33/0 4 67 61 32 15
Fax: +33/0 4 67 61 33 36
email: gauthier.boag...@cefe.cnrs.fr<mailto:gauthier.boag...@cefe.cnrs.fr>
www:
http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio
http://www.evolepid.org/people.php?name=boaglio
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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