pre_process: reup pre_process files lost during rebase

server/web2py/applications/vidjil/controllers/pre_process.py

+# coding: utf8
+import gluon.contrib.simplejson
+if request.env.http_origin:
+    response.headers['Access-Control-Allow-Origin'] = request.env.http_origin  
+    response.headers['Access-Control-Allow-Credentials'] = 'true'
+    response.headers['Access-Control-Max-Age'] = 86400
+
+    
+ACCESS_DENIED = "access denied"
+
+def index():
+    if not auth.user : 
+        res = {"redirect" : "default/user/login"}
+        return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
+
+    query = db((auth.accessible_query('read', db.pre_process) | auth.accessible_query('admin', db.pre_process) ) ).select(orderby=~db.pre_process.name)
+
+    return dict(message=T('Pre-process list'),
+               query=query,
+               isAdmin = auth.is_admin())
+
+
+def add(): 
+    return dict(message=T('Add pre-process'))
+
+
+def add_form(): 
+    error =""
+
+    required_fields = ['config_name', 'config_command', 'config_fuse_command', 'config_program']
+    for field in required_fields:
+        if request.vars[field] == "" :
+            error += field+" needed, "
+
+    if error=="" :
+        
+        db.config.insert(name=request.vars['config_name'],
+                        info=request.vars['config_info'],
+                        command=request.vars['config_command'],
+                        fuse_command=request.vars['config_fuse_command'],
+                        program=request.vars['config_program']
+                        )
+
+        res = {"redirect": "config/index",
+               "message": "config '%s' added" % request.vars['config_name']}
+        log.admin(res)
+        return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
+        
+    else :
+        res = {"success" : "false", "message" : error}
+        log.error(res)
+        return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
+
+
+def edit(): 
+    return dict(message=T('edit config'))
+
+
+def edit_form(): 
+    error =""
+
+    required_fields = ['id', 'config_name', 'config_command', 'config_fuse_command', 'config_program']
+    for field in required_fields:
+        if request.vars[field] == "" :
+            error += field+" needed, "
+
+    if error=="" :
+
+        db.config[request.vars["id"]] = dict(name=request.vars['config_name'],
+                                             info=request.vars['config_info'],
+                                             command=request.vars['config_command'],
+                                             fuse_command=request.vars['config_fuse_command'],
+                                             program=request.vars['config_program']
+                                             )
+
+        res = {"redirect": "config/index",
+               "message": "config '%s' updated" % request.vars['config_name']}
+
+        log.admin(res)
+        return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
+
+    else :
+        res = {"success" : "false", "message" : error}
+        log.error(res)
+        return gluon.contrib.simplejson.dumps(res, separators=(',',':'))
+
+def confirm():
+    return dict(message=T('confirm config deletion'))
+
+def delete():
+    #delete results_file using this config
+    db(db.results_file.config_id==request.vars["id"]).delete()
+    
+    #delete config
+    db(db.config.id==request.vars["id"]).delete() 
+    
+    res = {"redirect": "config/index",
+           "message": "config '%s' deleted" % request.vars["id"]}
+    log.admin(res)
+    return gluon.contrib.simplejson.dumps(res, separators=(',',':'))

server/web2py/applications/vidjil/views/pre_process/add.html

+{{extend 'db_layout.html'}}
+
+<form id="data_form" action="DB_ADDRESS/pre_process/add_form" enctype="multipart/form-data" method="post">
+    <table>
+        <tbody>
+            <tr>
+                <td > <label for="pre_process_name" id="pre_process_name__label">Name: </label> </td>
+                <td > <input class="string" id="pre_process_name" name="pre_process_name" type="text" value=""> </td> 
+                <td > </td>
+            </tr>
+
+            
+            <tr>
+                <td> <label for="pre_process_command" id="pre_process_command__label">Command: </label> </td>
+                <td> <textarea class="text" cols="60" id="pre_process_command" name="pre_process_command" rows="10"></textarea> </td> 
+                <td> Describe the command usage of your script to help Vidjil to use it correctly.</br>
+                     replace in your command input file paths with &file1& and &file2& and result file path with &result& <br>
+                     for exemple the command: <br>
+            <span style="font-family: 'courier'" >python myReadMergerScript.py -n 50 sample_r1.fastq sample_r2.fastq -o result.fastq</span><br>
+                     must be described as: <br>
+            <span style="font-family: 'courier'">python myReadMergerScript.py -n 50 &file1& &file2& -o &result&</span><br>
+        </td>
+            </tr>
+            <tr>
+                <td> <label for="pre_process_info" id="pre_process_info__label">Info: </label> </td>
+                <td> <textarea class="text" cols="60" id="pre_process_info" name="pre_process_info" rows="10"></textarea> </td> 
+                <td> </td>
+            </tr>
+            <tr>
+                <td> </td>
+                <td ><input type="submit" value="Soumettre" class="btn"> </td>
+                <td> </td>
+            </tr>
+        </tbody>
+    </table>
+</form>

server/web2py/applications/vidjil/views/pre_process/edit.html

+{{extend 'db_layout.html'}}
+
+{{
+info = db.pre_process[request.vars["id"]]
+}}
+
+<form id="data_form" action="DB_ADDRESS/pre_process/edit_form" enctype="multipart/form-data" method="post">
+    <input type="HIDDEN" id="pre_process_id" name="id" value="{{=request.vars["id"]}}"> 
+    <table>
+        <tbody>
+            <tr>
+                <td > <label for="pre_process_name" id="pre_process_name__label">Name: </label> </td>
+                <td > <input class="string" id="pre_process_name" name="pre_process_name" type="text" value="{{=info.name}}"> </td> 
+                <td > </td>
+            </tr>
+            <tr>
+                <td> <label for="pre_process_command" id="pre_process_command__label">Command: </label> </td>
+                <td> <textarea class="text" cols="60" id="pre_process_command" name="pre_process_command" rows="10">{{=info.command}}</textarea> </td> 
+                <td> </td>
+            </tr>
+            <tr>
+ 
+            <tr>
+                <td> <label for="pre_process_info" id="pre_process_info__label">Info: </label> </td>
+                <td> <textarea class="text" cols="80" id="pre_process_info" name="pre_process_info" rows="10">{{=info.info}}</textarea> </td> 
+                <td> </td>
+            </tr>
+            <tr>
+                <td> </td>
+                <td ><input type="submit" value="Soumettre" class="btn"> </td>
+                <td> </td>
+            </tr>
+        </tbody>
+    </table>
+</form>

server/web2py/applications/vidjil/views/pre_process/index.html

+{{extend 'db_layout.html'}}
+
+{{('message' in globals())}}
+{{if 'message' in globals():}}
+
+<h3>{{=message}}</h3>
+
+<div id="db_table_container">
+    <table class="db_table" id="table">
+        <thead>
+            <tr><td class="column_50"></td>
+                <td class="column2"> name </td>
+                <td> command </td>
+                <td> info </td>
+
+                <td class="column5"> </td>
+                <td class="column5"> </td>
+                <td class="column5"> </td>
+            </tr>
+        </thead>
+       {{ for row in query :}}
+            <tr>
+                <td> {{=row.id }} </td>
+                <td> {{=row.name }} </td>
+                <td> {{=row.command }} </td>
+                <td> {{=row.info }} </td>
+
+{{if isAdmin:}} <td onclick="db.call('pre_process/permission', {'id' :'{{=row.id}}'} )" > <i class="icon-key" title="set permissions"></i> </td> {{else:}} <td></td> {{pass}}
+                <td onclick="db.call('pre_process/edit', {'id' :'{{=row.id}}'} )" > <i class="icon-pencil-2" title="edit pre-process"></i> </td>
+                <td onclick="db.call('pre_process/confirm', {'id' :'{{=row.id}}'} )" > <i class="icon-erase" title="delete pre-process"></i> </td>
+            </tr>
+        {{pass}}
+    </table>
+    <table class="db_table" id="db_fixed_header"></table>
+</div>
+
+<span class="button2" onclick="db.call('pre_process/add')"> + new pre-process </span>
+
+
+{{elif 'content' in globals():}}
+{{=content}}
+{{else:}}
+{{=BEAUTIFY(response._vars)}}
+{{pass}}