Validate spectra - adjust paths

Analysis Version 3
#1

Hi,

One of the nice features in v2 was the ability to move all the paths of files when you open the project from a different location, or after moving data around. I found the `Validate spectra` feature, but I am not sure that I fully understand the employed nomenclature. Is there an explainer anywhere about how that dialog works and what things like `$INSIDE` and `$ALONGSIDE` are supposed to mean/do?



Best wishes,
Patrick

#2

Hi here is my understanding for people to shoot done modify and comment on!

So VP (validate spectra or validate paths) shows you the key data paths and shortcuts for them

$DATA is the users homie directory
$INSIDE is the directory that holds the projects contents
$ALONGSIDE is the directory that contains the project directory and you can puts spectra on a relative path to it to ake moving the project around easy

So for example say my home is

/Users/garyt

and I have a project stored in

/Users/garyt/projects/abc.ccpn

then

$DATA = /Users/garyt
$INSIDE = /Users/garyt/projects/abc.ccpn
$OUTSIDE = /Users/garyt/projects

Other directories with common path roots that are not contained by $INSIDE or $OUTSIDE are named remoteData<_some_number>

so if you had /Users/garyt/spectra/hsqc.spc thaty might be [remoteData]/spectra.hsqc

But /Users/garyt/projects/spectra/hsqc.spc would be $OUTSIDE/spectra/hsqc.spc

remoteData directories appear in the upper section which should allow them to be edited and changed (but note [remoteData] not sure why

In the Lower part of the dialog paths are shown which I believe can include $DATA $INSIDE etc

If the path exists and it is a recognised data file the field is green if its yellow the file / directory exists but it isn’t a valid data file and if its red it doesn’t exist

I have noticed that the dialog can be incredibly laggy and plan to investigate soon!

Regards
Gary

#3

Hi Gary,
Thanks for the response. That kind of helps, at least enough to realise that this dialog in fact does not replace the functionality of the v2 path/directory editor function (where you could change the paths of many files at once).
Would it be possible to re-introduce this functionality? It is really important, as we are often accessing the same data from different access points (via remote mounting a shared network folder).A related question: it is starting to look to me like the new version is no longer beta, but maybe not quite operational yet. Should we stick with version 2 for now?

Thanks,
Patrick

#4

Hi Patrick,

V3 is now at a bit of an `in-between` stage. If you are starting a new assignment project, it works nicely and is functional and certainly beyond beta. But although V3 has some features that V2 doesn`t have (e.g. phasing), there are still many V2 features that it lacks. You can see a list of things at https://www.ccpn.ac.uk/forums/misc.php?a...elp&hid=64.
So for the moment you may be better off staying with V2. I certainly know a number of people who are waiting for specific functionality before they are willing to switch.
In the mean time I`ll see what we can do about changing lots of paths at once.

Best wishes,

Vicky

#5

Hi Patrick,

worth adding that if you wanted to change lots of paths in one go, you could do it with a macro. e.g. the following would change the relative path for all your spectra:

Python
  1. specPath = `/New/File/Path/`
  2. for spectrum in project.spectra:
  3.     specFileName = spectrum.filePath.split(`/`)[-1]
  4.     spectrum.filePath = specPath+specFileName



For Bruker data you would probably want to adjust the specFileName part so you don`t just keep the file name, but some of the data structure, too.

If you wanted to something for spectra individually (e.g. with copy/paste), the following might be useful:

Python
  1. sp=project.getByPid(`SP:hsqc`)
  2. sp.filePath=(`/New/File/Path/Filename)



Best wishes,

Vicky

#6

Hi Vicky,

Thanks for the information on this script. For now it seems a bit of a moot point until we can actually import our projects. Once that works we can give it a try.

Patrick