source: trunk/doc/src/docbook/userdoc/file_system.xml @ 3219

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References #528. More text in File management doc/handling files and /file types.
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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: file_system.xml 3219 2007-03-30 14:32:55Z martin $
7 
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27-->
28
29<chapter id="file_system">
30  <title>File management</title>
31  <sect1 id="file_system.system">
32    <title>File system</title>
33    <para>
34      Files in BASE2 are managed from the page at
35      <menuchoice>
36        <guimenu>View</guimenu>
37        <guimenuitem>Files</guimenuitem>
38      </menuchoice>
39      . The basic layout on the page is the same as for all the other list pages in BASE2 but
40      there are some differences e.g. there is a navigation tree to the left, used to browse
41      the directory structure, and there are some buttons in the toolbar, that are special for
42      files and directories. The figure below is a representation of the files and
43      directories-page and is followed with a short description to some of the special
44      fucntions.
45    </para>
46    <figure id="file.system.figures.filepage">
47      <title>The file page</title>
48      <screenshot>
49        <mediaobject>
50          <imageobject>
51            <imagedata fileref="figures/filepage.png" format="PNG" />
52          </imageobject>
53        </mediaobject>
54      </screenshot>
55    </figure>
56    <variablelist>
57      <varlistentry>
58        <term>
59          <interface>1. User's home directory</interface>
60        </term>
61        <listitem>
62          <para>
63            This is the logged in user's home directory with sub directories. It is
64            visible if current user has a home directory and is then always located at
65            the top of the navigation tree. More about this can be read in
66            <xref linkend="file_system.system.browse.tree.home" />
67          </para>
68        </listitem>
69      </varlistentry>
70
71      <varlistentry>
72        <term>
73          <interface>2. Other users</interface>
74        </term>
75        <listitem>
76          <para>
77            The other users' home directories that the current user has read permission
78            on are listed here, including his/her own.
79          </para>
80        </listitem>
81      </varlistentry>
82
83      <varlistentry>
84        <term>
85          <interface>3. Refresh button</interface>
86        </term>
87        <listitem>
88          <para>
89            This button, which is located at the bottom of the navigation tree,
90            refreshes/updates the directory tree. It can for example be used to get a
91            recently created directory to appear in the tree.
92          </para>
93        </listitem>
94      </varlistentry>
95
96      <varlistentry>
97        <term>
98          <interface>4. Current directory</interface>
99        </term>
100        <listitem>
101          <para>Shows the full BASE2-path to current directory.</para>
102        </listitem>
103      </varlistentry>
104
105      <varlistentry>
106        <term>
107          <interface>5. View a file's contents</interface>
108        </term>
109        <listitem>
110          <para>
111            A click on this icon will open the file's contents in a new window. If the
112            browser doesn't has support to view the file there will be possibilities to
113            download the file instead.
114          </para>
115        </listitem>
116      </varlistentry>
117
118      <varlistentry>
119        <term>
120          <interface>6. Download file</interface>
121        </term>
122        <listitem>
123          <para>
124            This icon lets the user to download a file by clicking on it. The download
125            will start in a new dialog window.
126          </para>
127        </listitem>
128      </varlistentry>
129
130      <varlistentry>
131        <term>
132          <interface>7. Re-upload a file</interface>
133        </term>
134        <listitem>
135          <para>
136            This icon is only visible for those files that have been moved offline and
137            should be used to reload the file into BASE2's filesystem. Start to upload
138            the file to the same position by clicking on the icon.
139          </para>
140        </listitem>
141      </varlistentry>
142
143      <varlistentry>
144        <term>
145          <interface>8. Contents in current directory</interface>
146        </term>
147        <listitem>
148          <para>
149            This area contains the files and sub directories that are located in the
150            current directory that is choosen in the navigation tree.
151          </para>
152        </listitem>
153      </varlistentry>
154
155      <varlistentry>
156        <term>
157          <interface>9. Navigation tree</interface>
158        </term>
159        <listitem>
160          <para>
161            This sidebar displays the tree of directories that the current user has
162            permission to read. Click on a directory to display it's contents in the
163            list or click on the plus sign to the left to expand directory and view the
164            subdirectories (no plus sign - no subdirectories).
165          </para>
166        </listitem>
167      </varlistentry>
168    </variablelist>
169
170    <sect2 id="file_system.system.browse">
171      <title>Browse the file system</title>
172      <para>
173        Browsing BASE2's filesystem is done from the navigation bar by clicking on a
174        directory to view it's contents in the list. Both subdirectories and files in the
175        selected directory are showed.
176      </para>
177      <note>
178        <title>Browse a directory</title>
179        <para>
180          A directory can only be open from the navigation tree and never from the list. A
181          click on a directory's name in the list will open the directory's edit window.
182        </para>
183      </note>
184      <sect3 id="file_system.system.browse.tree">
185        <title>Navigation tree</title>
186        <para>
187          The navigation tree contains of folders/directories that the logged in user has
188          permission to read. At the top is the current user's home directory and under it
189          is a folder with all home directories.
190        </para>
191        <para>
192          The tree can be updated with the refresh-button at the bottom of the panel (the
193          tree isn't self-refreshing).
194        </para>
195        <sect4 id="file_system.system.browse.tree.home">
196          <title>Home directory - 'My home'</title>
197          <para>
198            To make it easier for the logged in user to find his/her directory without
199            having to scroll through the whole list of home directories, his or hers
200            home directory is located at the top of the navigation tree under the
201            <interface>My home</interface>
202            folder .
203          </para>
204          <note>
205            <title>No home directory</title>
206            <para>
207              Not all users have a home directory connected to their accounts. If
208              <interface>My home</interface>
209              is missing, it most certainly depends on that the current user account
210              doesn't have got a home directory. Home directories are managed by the
211              user administrator on the BASE2 server.
212            </para>
213          </note>
214        </sect4>
215      </sect3>
216    </sect2>
217    <sect2 id="file_system.system.qouta">
218      <title>Disk space quota</title>
219      <para>
220        Normally is the user accounts assigned with limited quota of disk space used to
221        store files, raw data or experiments at a location. The three categories have, in
222        case of disk quota, a total limit of space to use and it's also possible for them to
223        have a limit by their own too.
224        <example>
225          <title>Disk quota</title>
226          <para>
227            The user account has a total quota of 1GB but there is also a limitation of
228            raw data to be at maximum 500MB. This will prevent the raw data to take more
229            then 500 MB of the total quota.
230          </para>
231        </example>
232        More information about how much quota the current account has and how much that is
233        occupied of it can be found at account's home page, described in
234        <xref linkend="webclient.intro.homepage" />
235        .
236      </para>
237    </sect2>
238    <sect2 id="file_system.system.locaiton">
239      <title>Location</title>
240      <para>TODO</para>
241    </sect2>
242  </sect1>
243
244  <sect1 id="file_system.handling">
245    <title>Handling files</title>
246    <para></para>
247    <sect2 id="file_system.handling.actions">
248      <title>Actions</title>
249      <para></para>
250      <sect3 id="file_system.handling.actions.download">
251        <title>Download</title>
252        <para></para>
253      </sect3>
254      <sect3 id="file_system.handling.actions.view">
255        <title>View file</title>
256        <para>Properties or file contents</para>
257      </sect3>
258    </sect2>
259    <sect2 id="file_system.handling.upload">
260      <title>Upload a file</title>
261      <helptext external_id="file.upload" title="Upload a file">
262        <para></para>
263      </helptext>
264    </sect2>
265    <sect2 id="file_system.handling.edit">
266      <title>Edit a file</title>
267      <para>
268        The edit window to set a file's property in can either be open with
269        <guibutton>Edit&hellip;</guibutton>
270        in the toolbar at the file's view page or by holding down
271        <keycap>ctrl</keycap>
272        ,
273        <keycap>alt</keycap>
274        or
275        <keycap>shift</keycap>
276        when clicking on the name of the file. It requires that the current user has write
277        permission on the file to be able to edit and set the properties.
278      </para>
279
280      <helptext external_id="file.edit" title="Edit file properties">
281        <para>These are the file's properties that are displayed in the popup window.</para>
282        <variablelist>
283          <title>Properties</title>
284          <varlistentry>
285            <term>
286              <guilabel>Path</guilabel>
287            </term>
288            <listitem>
289              <para>
290                This is the path where a file is located. This can only be changed
291                by moving the file, read more about how this is done in
292                <xref linkend="file_system.handling.move" />
293                .
294              </para>
295            </listitem>
296          </varlistentry>
297          <varlistentry>
298            <term>
299              <guilabel>Name</guilabel>
300            </term>
301            <listitem>
302              <para>
303                The file's name, which can't be left empty and must be unique in
304                current directory. The maximum length of the file name is 255
305                charaters and it can contain blank spaces but not any of
306                <keycap>~</keycap>
307                ,
308                <keycap>\</keycap>
309                ,
310                <keycap>/</keycap>
311                ,
312                <keycap>:</keycap>
313                ,
314                <keycap>;</keycap>
315                ,
316                <keycap>*</keycap>
317                ,
318                <keycap>&#63;</keycap>
319                ,
320                <keycap>&lt;</keycap>
321                ,
322                <keycap>&gt;</keycap>
323                or
324                <keycap>|</keycap>
325                .
326              </para>
327            </listitem>
328          </varlistentry>
329          <varlistentry>
330            <term>
331              <guilabel>Type</guilabel>
332            </term>
333            <listitem>
334              <para>
335                Shows which kind of type the file is. Select the file type to use
336                from the drop down list with available types. The option
337                <guilabel>-none-</guilabel>
338                should be used if the file shouldn't be associated with any kind of
339                file type.
340              </para>
341            </listitem>
342          </varlistentry>
343          <varlistentry>
344            <term>
345              <guilabel>MIME type</guilabel>
346            </term>
347            <listitem>
348              <para>
349                The file's content/media type. This is normally set automatically
350                when uploading the file into BASE2 but it can be changed by an user,
351                that has write permissions, at any time.
352              </para>
353            </listitem>
354          </varlistentry>
355          <varlistentry>
356            <term>
357              <guilabel>Description</guilabel>
358            </term>
359            <listitem>
360              <para>
361                This text area can be used to store relevant information about file
362                and it's contents. Use the magnifying glass, located to the right
363                under the text area, to edit the text in a larger window.
364              </para>
365            </listitem>
366          </varlistentry>
367        </variablelist>
368        <para>
369          Finish the editing process by pressing either
370          <guibutton>Save</guibutton>
371          to save the properties to the database or
372          <guibutton>Cancel</guibutton>
373          to abort and discard the changes.
374        </para>
375      </helptext>
376
377    </sect2>
378    <sect2 id="file_system.handling.remove">
379      <title>Delete, restore and move offline</title>
380      <para>
381        These functions are used to manage the directories and files' existance on the
382        server, to keep the list of files and directories up-to-date and release disk space
383        on server.
384      </para>
385      <sect3 id="file_system.handling.remove.delete">
386        <title>Delete</title>
387        <para>
388          A deleted file/directory is moved to the account's trash can and is marked to be
389          removed. Those items that have been marked as deleted can't be used in analysis
390          or other activities in BASE2 but they are not removed from the server and can be
391          restored again by the users that have write permission on the items.
392        </para>
393        <para>
394          Before a file or directory can be deleted it first needs to be selected, this is
395          done by ticking the checkbox in front of it's name in the list. Click then on
396          <guibutton>Delete</guibutton>
397          to mark the item as deleted.
398        </para>
399        <tip>
400          <title>Delete many directories/files</title>
401          <para>
402            Select all those items, that should be deleted in a list to flag them all
403            for deletion at the same time.
404          </para>
405        </tip>
406        <para>
407          Files and directories that are marked for deletion can be included in the list
408          by selecting
409          <guilabel>Removed</guilabel>
410          from the drop-down list with presets, see
411          <xref linkend="webclient.figures.viewpresets" />
412          .Those which have been deleted are marked with a trash can icon in front of
413          their names.
414        </para>
415      </sect3>
416      <sect3 id="file_system.handling.remove.restore">
417        <title>Restore</title>
418        <para>
419          Files and directories that have been marked for deletion, and not yet removed
420          from the trash can, can be restored again without any loss of information. To do
421          that, the removed items have to be made visible in the list and which is done by
422          selecting
423          <guilabel>Removed</guilabel>
424          in the drop down list of presets, see
425          <xref linkend="webclient.figures.viewpresets" />
426          .
427        </para>
428        <para>
429          Select the file or directory that should be restored, by ticking the check box
430          to the left of the item. Then click on
431          <guibutton>Restore</guibutton>
432          in the toolbar to restore and remove the deletion flag. The trash can has now
433          disappeared infront of the item that was restored and it's possible to use the
434          item in BASE2 again.
435        </para>
436        <tip>
437          <title>Restoring multiple directories/files</title>
438          <para>
439            Multiple files and directories can be restored at the same time. This is
440            done by selecting all the items that should be restored before pressing the
441            restore button.
442          </para>
443        </tip>
444      </sect3>
445      <sect3 id="file_system.handling.remove.move_offline">
446        <title>Move offline</title>
447        <para>
448          Moving a file offline means that the fysical file is deleted from the server's
449          disk space but the file will still exist as an item in the database. This makes
450          it possible to save disk space but still be able to asociate the file with other
451          items in BASE2.
452        </para>
453        <para>
454          Tick the checkbox for those files that should be moved offline and press then
455          <menuchoice>
456            <guibutton>Move&hellip;</guibutton>
457            <guisubmenu>Offline&hellip;</guisubmenu>
458          </menuchoice>
459          . The selected files will be moved immediatley and disk space will be released.
460        </para>
461        <sect4>
462          <title>Upload a file that is offline</title>
463          <para>
464            A file that has been moved offline can be uploaded again by clicking on the
465            icon in the actions-column, see number 7 in
466            <xref linkend="file.system.figures.filepage" />
467            . The procedure to upload the file is the same that is described in
468            <xref linkend="file_system.handling.upload" />
469            <important>
470              <para>
471                There will not be any check to confirm that the file to upload is
472                the same that was originally stored in BASE2.
473              </para>
474            </important>
475          </para>
476        </sect4>
477      </sect3>
478    </sect2>
479    <sect2 id="file_system.handling.directories">
480      <title>Directories</title>
481      <para>
482        Directories in BASE2 are folders where files can be organized into. Click on
483        <guibutton>New directory&hellip;</guibutton>
484        in the toolbar to create a directory in current path and edit the properties as
485        described below.
486      </para>
487      <sect3 id="file_system.handling.directories.edit">
488        <title>Edit a directory</title>
489        <para>
490          The window to edit a directory's properties is opened either by clicking on the
491          directory's name in the list or when creating a new directory.
492        </para>
493        <helptext external_id="directory.edit" title="Edit directory">
494          <para>
495            <variablelist>
496              <title>Properties</title>
497              <varlistentry>
498                <term>
499                  <guilabel>Path</guilabel>
500                </term>
501                <listitem>
502                  <para>
503                    This property is read-only in the edit window but can be
504                    change instead by moving the directory, described in
505                    <xref linkend="file_system.handling.move" />
506                  </para>
507                </listitem>
508              </varlistentry>
509              <varlistentry>
510                <term>
511                  <guilabel>Name</guilabel>
512                </term>
513                <listitem>
514                  <para>
515                    The directory's name to identify it with in the list. This
516                    field must have a value and it must be an unique name in the
517                    current directory.
518                  </para>
519                </listitem>
520              </varlistentry>
521              <varlistentry>
522                <term>
523                  <guilabel>Description</guilabel>
524                </term>
525                <listitem>
526                  <para>
527                    Any relevant information about the directory can be written
528                    in this text area. The magnifying glass down to the right
529                    can be used to edit the description text in a larger text
530                    area, just click on the icon to open it in a separate pop-up
531                    window.
532                  </para>
533                </listitem>
534              </varlistentry>
535            </variablelist>
536          </para>
537          <para>
538            The editing process is completed with either
539            <guibutton>Save</guibutton>
540            , to save the properties into the database, or with
541            <guibutton>Cancel</guibutton>
542            to discard the changes. Both of the buttons will close the edit window and
543            if the directory is updated the list will be reloaded with the directory's
544            new properties.
545          </para>
546        </helptext>
547      </sect3>
548    </sect2>
549    <sect2 id="file_system.handling.move">
550      <title>Move file/directory</title>
551      <para>
552        Files and directories can be moved to other directories to re-organize the items.
553      </para>
554      <para>
555        Select first of all those files and directories in current path that should be moved
556        and click then on
557        <menuchoice>
558          <guibutton>Move&hellip;</guibutton>
559          <guisubmenu>To another directory</guisubmenu>
560        </menuchoice>
561        to open a window with directories to choose from.
562      </para>
563      <para>
564        Choose a directory where the selected items should be moved to. Doesn't the
565        directory exist, it can be created in the popup window's current path, with
566        <guibutton>New&hellip;</guibutton>
567        .
568      </para>
569      <para>
570        Click on
571        <guibutton>Ok</guibutton>
572        to carry out the move or
573        <guibutton>Cancel</guibutton>
574        to abort.
575      </para>
576    </sect2>
577  </sect1>
578
579  <sect1 id="file_system.filetypes">
580    <title>File types</title>
581    <para>
582      A file can be associated with one of many file types that exists in BASE2. File types
583      make it possible to sort the files depending of what the files should be use for in the
584      program.
585    </para>
586    <para>
587      Following file types exists in BASE2.
588      <variablelist>
589        <title>File types</title>
590        <varlistentry>
591          <term>Image</term>
592          <listitem>
593            <para>Indicates that the file is an image file.</para>
594          </listitem>
595        </varlistentry>
596        <varlistentry>
597          <term>Plate</term>
598          <listitem>
599            <para>
600              The asociated file is a file with information about plate/plates.
601            </para>
602          </listitem>
603        </varlistentry>
604        <varlistentry>
605          <term>Plate mapping</term>
606          <listitem>
607            <para>Files with information about plate mapping</para>
608          </listitem>
609        </varlistentry>
610        <varlistentry>
611          <term>Print map</term>
612          <listitem>
613            <para>Print map files</para>
614          </listitem>
615        </varlistentry>
616        <varlistentry>
617          <term>Protocol</term>
618          <listitem>
619            <para>files with protocol information</para>
620          </listitem>
621        </varlistentry>
622        <varlistentry>
623          <term>Raw data</term>
624          <listitem>
625            <para>Raw data files</para>
626          </listitem>
627        </varlistentry>
628        <varlistentry>
629          <term>Reporter</term>
630          <listitem>
631            <para>Files with information about reporters</para>
632          </listitem>
633        </varlistentry>
634        <varlistentry>
635          <term>Reporter map</term>
636          <listitem>
637            <para>
638              Files of this type contain information about how the reporters are
639              mapped.
640            </para>
641          </listitem>
642        </varlistentry>
643        <varlistentry>
644          <term>Spot images</term>
645          <listitem>
646            <para>A zip-file containing generated spot images in png format.</para>
647          </listitem>
648        </varlistentry>
649      </variablelist>
650    </para>
651  </sect1>
652</chapter>
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