doc: move user database help to doc/browser.org, updated help

doc/browser.org

@@ -113,6 +113,45 @@ obtained:
    - You can visualize results by IMGT/V-QUEST and IgBlast on the selected sequences, in another window, by clicking on the corresponding buttons.
    - You can unselect all sequences by clicking on the background of the scatterplot.
 
+
+** The database / server connection (experimental)
+
+A *server* is currently developed to link the browser and the
+algorithmic part. The goal is that the clinicians will be able to
+upload, manage and process their runs directly on the browser (with
+authentication).
+
+
+*** Patients
+      
+Once you are authentified, this page show the patient list. Here you
+can see your patients and patients whose permission has been given to you.
+
+New patients can be added ('add patient'), edited ('e') or deleted ('X').
+By default, you are the only one who can see/access this new patient.
+You can grant access to other people or group ('P'),
+people will be able to see your patient and make some action depending of the access granted.
+
+
+*** Samples
+
+Clicking on a patient give acccess the "samples" page. Each sample is
+a .fasta/.fastq file that will be processed by one or several
+pipelines.
+You can see which samples have been processed with the selected
+config, and download the sequence files if they are available ("dl").
+
+Depending on your granted accesses, you can 
+add a new sample to the list ("add file"), 
+schedule a processing for a sequence file (select a config and "run"),
+or delete a sample ("X").
+
+The processing can take a few seconds to a few hours, depending on the
+software lauched, its options and the size of the sample.
+Once the processing is finished, click on the button "see result" and
+the browser will load the data of the processed files. The first click
+on this button can take a few seconds.
+
 * Assessing the quality of your data and of the analysis
 
 To make sure that the PCR, the sequencing and the Vidjil analysis went well, several elements can be controlled.

server/web2py/applications/vidjil/views/db_layout.html

@@ -9,7 +9,6 @@
         <a class="button" onclick="db.call('user/index');">users</a>
         - - -
         {{pass}}
-        <a class="button" onclick="db.call('default/help');">help</a>
     </div>
     
     <div id="db_auth">

server/web2py/applications/vidjil/views/default/help.html

@@ -4,100 +4,7 @@
     <h2>{{=message}}</h2>
     
     <div id="db_table_container">
-        
-        <h3>
-            Patients
-        </h3>
-        This page will show you the patient list, here you can see your patients and patients whose permission has been given to you.</br>
     
-        <div class="db_help_p">
-            <div class="db_help_action">Add patient </div>
-                <div class="db_help_desc">You can add a new patient to the list by clicking the "add patient" button and complete the form. 
-                    By default you are the only one who can see/access this new patient (admin right).</div>
-
-            <div class="db_help_action">Permission (admin)</div>
-                 <div class="db_help_desc">You can share permission with other people or group with the "P" button,
-                    people will be able to see your patient and make some action depending of the acces right given.
-                    Even if you don't have admin right you can see who have access to the patient</div>
-
-            <div class="db_help_action">Delete (admin)</div>
-                 <div class="db_help_desc">Just use the "X" button, you need to confirm your choice before the deletion.</div>
-
-            <div class="db_help_action">Edit (admin)</div>
-                <div class="db_help_desc">If you want to change some information use the "e" button to reopen the form.</div>
-        </div>
-
-        <h3>
-            Configs
-        </h3>
-        This page will show you the config list, config are just parameters for Vidjil runs. everybody can use config (no permission acces needed, TODO)
-        <div class="db_help_p">
-            <div class="db_help_action">Add config </div>
-                <div class="db_help_desc">You can add a new config to the list by clicking the "add config" button and complete the form.</div>
-
-            <div class="db_help_action">Delete</div>
-                 <div class="db_help_desc">Just use the "X" button, you need to confirm your choice before the deletion.</div>
-
-            <div class="db_help_action">Edit</div>
-                <div class="db_help_desc">If you want to change some information use the "e" button to reopen the form.</div>
-        </div>
-
-
-
-        <h3>
-            Patient files
-        </h3>
-        To acces the file list of a patient just click on it in the patient list, you need at least one config to access the patient list.
-        You can see which file have been runned with the selected config
-        <div class="db_help_p">
-            <div class="db_help_action">Add file (admin) </div>
-                <div class="db_help_desc">You can add a new file to the list by clicking the "add file" button and complete the form.</div>
-
-            <div class="db_help_action">Run </div>
-                <div class="db_help_desc">You can schedule a Vidjil run for a sequence file, select a config and click the "run" button.</div>
-
-            <div class="db_help_action">Download</div>
-                <div class="db_help_desc">You can download the sequence file, select a config and click the "run" button.</div>
-
-            <div class="db_help_action">Delete (admin)</div>
-                 <div class="db_help_desc">Just use the "X" button, you need to confirm your choice before the deletion.</div>
-
-            <div class="db_help_action">Edit (admin)</div>
-                <div class="db_help_desc">If you want to change some information use the "e" button to reopen the form.</div>
-
-            <div class="db_help_action">See result</div>
-                <div class="db_help_desc">click the button "see result" and the browser will load the data of all the sequence 
-                    files who have been processed by vidjil with the current selected config (can take a few seconds)</div>
-
-        </div>
-
-        <h3>
-            Groups
-        </h3>
-        Group list, group member share permission about patient
-        <div class="db_help_p">
-            <div class="db_help_action">New group</div>
-                <div class="db_help_desc">click this button if you want to create a new group, everybody can create a group, by default the group creator become admin of the group.</div>
-            
-            <div class="db_help_action">Permission</div>
-                <div class="db_help_desc">You can give Admin right to some member of the group with the "P" button,
-                    Admin can invite people to become member of the group or revoke membership</div>
-            
-            <div class="db_help_action">Member list</div>
-                <div class="db_help_desc">You can see the member list by clicking on the group name.</br>
-                    (admin) here you can invite people or revoke member.</div>
-
-            <div class="db_help_action">Delete (admin)</div>
-                 <div class="db_help_desc">Just use the "X" button, you need to confirm your choice before the deletion.</div>
-        </div>
-
-        <h3>
-            Users
-        </h3>
-        TODO
-        <div class="db_help_p">
-            
-        </div>
         
     </div>