File access through predefined profiles - Revision history

Daniel Castaño: /* Creation of access profiles */

2018-06-25T14:07:10Z

Creation of access profiles

Daniel Castaño at 14:06, 25 June 2018

2018-06-25T14:06:50Z

Daniel Castaño at 14:05, 25 June 2018

2018-06-25T14:05:31Z

Daniel Castaño at 13:40, 25 June 2018

2018-06-25T13:40:15Z

Daniel Castaño at 13:35, 25 June 2018

2018-06-25T13:35:34Z

Daniel Castaño at 10:33, 25 June 2018

2018-06-25T10:33:21Z

Daniel Castaño at 10:32, 25 June 2018

2018-06-25T10:32:19Z

Daniel Castaño: Created page with " This system is used when you work frequently with filenames that represent the same file as seen by different filesystems. For example, you may have a tomogram stored in a f..."

2018-06-25T10:08:59Z

Created page with " This system is used when you work frequently with filenames that represent the same file as seen by different filesystems. For example, you may have a tomogram stored in a f..."

New page

This system is used when you work frequently with filenames that represent the same file as seen by different filesystems.

For example, you may have a tomogram stored in a fileshare that can be seen in different file systems. Let's say that in your linux machine, you see it as

<tt>/links/tomograms/myTomogram.mrc</tt>

and in your Mac machine, you see it as:

<tt>/Volumes/external/tomograms/myTomogram.mrc</tt>.

In this example,we assume that <tt>/links</tt> and <tt>/Volumes/external</tt> are different mount points (one defined in the unix machine and the other one in the mac machine) that point to the same location.

When you are are working on the different systems, each naming is coherent. The problem occurs when you are working in one system, and you need to refer to file names expressed in the convention of the other system.

In many situations, you can just use string replacing methods of your favorite parsing system (Perl, awk, etc). In Matlab (or ''Dynamo'' standalone) you can just use the convenient <tt>strrep</tt> function. For instance, if you have a text file with file names (viewed from the unix system) to visit in a loop, producing the equivalent list with the names of the same files as viewed from the Mac is trivial.

However, you might have a problem when you use databasing options in ''Dynamo'' that store absolute paths. An examples are the tomograms and models in the [[catalogue]]. If you produced your catalogue in the linux machine, your tomograms will look like:

<pre>/links/tomograms/tomob001ts0001.mrc
/links/tomograms/tomob001ts0002,mrc </tt>

... so that if you access them from your Mac system, the catalogue will think that the files don't exist.

One think that can be done is to use the option in the calatogue gui to "relink" the tomograms (and linking elements in the models) to the mac convention. This works, but is rather tedious. Moreover, it also means that afterwards the catalogue will not recognise the tomogram files when accessed through the linux machine.

@@ Line 40: / Line 40: @@
   <pre>mbsys.access.addProfile('fromUnix','/links/tomograms');
-mbsys.access.addProfile('fromMac','/Volumes/external/tomograms');
+mbsys.access.addProfile('fromMac','/Volumes/external/tomograms'); </pre>
 The profile names <tt>'fromLinux'</tt> and <tt>'fromMac'</tt> are arbitrary.

@@ Line 51: / Line 51: @@
   <tt>mbsys,access.fixProfile('fromMac');</tt>
-=== Using access profile ===
+=== Using access profiles ===
 When a  profile is running, most ''Dynamo'' functions that read or check existence of files will check all available profiles when analysing a file name. For instance, the location  <tt>/links/tomograms/tomob001ts0001.mrc </tt>  will not be recognized by the operative system of your Mac:

@@ Line 57: / Line 57: @@
   <pre>ls /links/tomograms/tomob001ts0001.mrc
 ls: pret: No such file or directory</pre>
 === Removal of  access profiles ===

← Older revision		Revision as of 13:40, 25 June 2018
Line 94:		Line 94:
	Enabled: 1		Enabled: 1
	------------------------------------------------------------</pre>		------------------------------------------------------------</pre>
		+
		+	== Related tools ==
		+
		+	Accessing files through ''repository components'' (documented from release ''Dynamo'' 1.3) has a similar effect, although it is constrained to files that are located and accessible through the repository tree. File accessing profiles can be used for general files in the file system.

@@ Line 25: / Line 25: @@
   <pre>/links/tomograms/tomob001ts0001.mrc
- /links/tomograms/tomob001ts0002.mrc </pre>
+/links/tomograms/tomob001ts0002.mrc </pre>
 ... so that if you access them from your Mac system, the catalogue will think that the files don't exist.
@@ Line 34: / Line 34: @@
 ''Dynamo''  includes a more convenient system to handle this situation: the ''global file access profiles''.  The user can define profiles that express the equivalence of same mount points as viewed in the different machines. Whenever ''Dynamo'' looks for a file expressed with an absolute path, it will automatically test internally every possible registered profile.

@@ Line 1: / Line 1: @@
-This system is used when you work frequently with filenames that represent the same file as seen by different filesystems.
+This system is used when you work frequently with filenames that represent the same file as seen by different file systems.
 For example, you may have a tomogram stored in a fileshare that can be seen in different file systems. Let's say that in your linux machine, you see it as
@@ Line 16: / Line 18: @@
 In many situations, you can just use string replacing methods of your favorite parsing system (Perl, awk, etc). In Matlab  (or ''Dynamo'' standalone) you can just use the convenient <tt>strrep</tt> function. For instance, if you have a text file with file names (viewed from the unix system)  to visit in a loop, producing the equivalent list with the names of the same files as viewed from the Mac is trivial.
-However, you might have a problem when you use databasing options in ''Dynamo''  that store absolute paths. An examples are the tomograms and models in the [[catalogue]]. If you produced your catalogue in the linux machine, your tomograms will look like:
+However, you might have a problem when you use databasing options in ''Dynamo''  that store absolute paths.
   <pre>/links/tomograms/tomob001ts0001.mrc
-  /links/tomograms/tomob001ts0002,mrc </tt>
+  /links/tomograms/tomob001ts0002,mrc </pre>
 ... so that if you access them from your Mac system, the catalogue will think that the files don't exist.
 One think that can be done is to use the option in the  calatogue gui to  "relink" the tomograms (and linking elements in the models) to the mac convention. This works, but is rather tedious. Moreover, it also means that afterwards the catalogue  will not recognise the tomogram files when accessed through the linux machine.