annotate apolloUserManager.xml @ 0:ce4f91831680 draft default tip

planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894

<tool id="apollo_user_manager" name="Apollo User Manager" version="1.0.0">
    <description>
        This Galaxy tool is used to manage Apollo users. 
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <requirements>
        <requirement type="package" version="3.0.3">apollo_api</requirement>
    </requirements>

    <stdio>
    </stdio>

    <command detect_errors="exit_code"><![CDATA[
        mkdir -p $output.extra_files_path;
        ## Dump the tool parameters into a JSON file 
        python $json_file parameters.json;
        python $__tool_directory__/apolloUserManager.py --data_json parameters.json -o $output
    ]]></command>
    <configfiles>
        <configfile name="json_file">
import json
import sys

file_path = sys.argv[1]
#set global data_parameter_dict = {"operations": dict()}
## Function to retrieve the data of the inputs
#def prepare_json($operation_type, $data_dict, $batch)
    #silent $data_dict.update({"batch": str($batch)})
    #if $operation_type in $data_parameter_dict["operations"]
        #silent $data_parameter_dict["operations"][$operation_type].append($data_dict)
    #else
        #set array_inputs = []
        #silent $array_inputs.append($data_dict)
        #silent $data_parameter_dict["operations"].update({$operation_type: $array_inputs})
    #end if 
#end def




#for $i, $f in enumerate($operation)
    #if $f.operation_type_selector.operation_type == "create"
        #set batch = $f.operation_type_selector.batch_selector.batch
        #if $batch == "false"
            #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email), 
                            "firstname": str($f.operation_type_selector.batch_selector.firstname),
                            "lastname": str($f.operation_type_selector.batch_selector.lastname),
                            "password": str($f.operation_type_selector.batch_selector.password)}
            
        #else 
            #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format), 
                                "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
        #end if 
        #silent $prepare_json("create", $data_dict, $batch)
    
    #elif $f.operation_type_selector.operation_type == "delete"
        #set batch = $f.operation_type_selector.batch_selector.batch
        #if $batch == "false"
            #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email)}
        #else 
            #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format), 
                                "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
        #end if 
        #silent $prepare_json("delete", $data_dict, $batch)
    #elif $f.operation_type_selector.operation_type == "add"
        #set batch = $f.operation_type_selector.batch_selector.batch
        #if $batch == "false"
            #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email),
                        "group": str($f.operation_type_selector.batch_selector.group_name)}
        #else 
            #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format), 
                                "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
        #end if 
        #silent $prepare_json("add", $data_dict, $batch)
    #elif $f.operation_type_selector.operation_type == "remove"
        #set batch = $f.operation_type_selector.batch_selector.batch
        #if $batch == "false"
            #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email),
                        "group": str($f.operation_type_selector.batch_selector.group_name)}
        #else 
            #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format), 
                                "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
        #end if 
        #silent $prepare_json("remove", $data_dict, $batch)
    #end if
#end for


#set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)}
#silent $data_parameter_dict.update({"apollo_admin": $apollo_admin})
#silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
#silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
#silent $data_parameter_dict.update({"port": str($advanced_options.port)})
#silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
with open(file_path, 'w') as f:
    json.dump($data_parameter_dict, f)
        </configfile>
    </configfiles>


    <inputs>
        <param name="admin_username" type="text" label="Admin username" help="Login in with Apollo admin account">
            <sanitizer>
                <valid initial="string.letters,string.digits">
                    <add value="@-=_.()/+*^,:?!"/>
                </valid>
            </sanitizer>
        </param>

        <param
            name="admin_password"
            type="text"
            label="Admin password"
        />
        
        <repeat name="operation" title="New operation">
            <conditional name="operation_type_selector" >
                <param name="operation_type" type="select" label="Create a user, delete a user, add a user to a group or remove a user from a group">
                    <option value="create">Create a user</option>
                    <option value="delete">Delete a users</option>
                    <option value="add">Add a user to a group</option>
                    <option value="remove">Remove a user from a group</option>
                </param>
                <when value="create">
                    <conditional name="batch_selector">
                        <param name="batch" type="select" label="Manipulate a single user or multiple users">
                            <option value="false" selected="true">Single user</option>
                            <option value="true">Multiple users</option>
                        </param>
                        <when value="false">
                            <param name="user_email" type="text" label="User email" help="Specify the user email">
                                <sanitizer>
                                    <valid initial="string.letters,string.digits">
                                        <add value="@-=_.()/+*^,:?!"/>
                                    </valid>
                                </sanitizer>
                            </param>
                            <param name="firstname" type="text" label="First name" />
                            <param name="lastname" type="text" label="Last name" />
                            <param name="password" type="text" label="Password" />
                        </when>
                        <when value="true">
                            <expand macro="upload_text_file" />
                        </when>
                    </conditional>
                </when>
                <when value="delete">
                    <conditional name="batch_selector">
                        <param name="batch" type="select" label="Manipulate a single user or multiple users">
                            <option value="false" selected="true">Single user</option>
                            <option value="true">Multiple users</option>
                        </param>
                        <when value="false">
                            <param name="user_email" type="text" label="User email" help="Specify the user email">
                                <sanitizer>
                                    <valid initial="string.letters,string.digits">
                                        <add value="@-=_.()/+*^,:?!"/>
                                    </valid>
                                </sanitizer>
                            </param>
                        </when>
                        <when value="true">
                            <expand macro="upload_text_file" />
                        </when>
                    </conditional>
                </when>
                <when value="add">
                    <conditional name="batch_selector">
                        <param name="batch" type="select" label="Manipulate a single user or multiple users">
                            <option value="false" selected="true">Single user</option>
                            <option value="true">Multiple users</option>
                        </param>
                        <when value="false">
                            <param name="user_email" type="text" label="User email" help="Specify the user email">
                                <sanitizer>
                                    <valid initial="string.letters,string.digits">
                                        <add value="@-=_.()/+*^,:?!"/>
                                    </valid>
                                </sanitizer>
                            </param>
                            <param type="text" name="group_name" size="30" value="unknown" label="Group name" />
                        </when>
                        <when value="true">
                            <expand macro="upload_text_file" />                        
                        </when>
                    </conditional>
                </when>
                <when value="remove">
                    <conditional name="batch_selector">
                        <param name="batch" type="select" label="Manipulate a single user or multiple users">
                            <option value="false" selected="true">Single user</option>
                            <option value="true">Multiple users</option>
                        </param>
                        <when value="false">
                            <param name="user_email" type="text" label="User email" help="Specify the user email">
                                <sanitizer>
                                    <valid initial="string.letters,string.digits">
                                        <add value="@-=_.()/+*^,:?!"/>
                                    </valid>
                                </sanitizer>
                            </param>
                            <param type="text" name="group_name" size="30" value="unknown" label="Group name" />
                        </when>
                        <when value="true">
                            <expand macro="upload_text_file" />                        
                        </when>
                    </conditional>
                </when>
            </conditional>
        </repeat>

        <conditional name="advanced_options">
            <param name="advanced_options_selector" type="select" label="Advanced options">
                <option value="off" selected="true">Hide advanced options</option>
                <option value="on">Display advanced options</option>
            </param>
            <!-- TODO: Avoid redundancy here -->
            <when value="on">
                <param name="port" type="integer" min="8000" max="8888" value="8080" label="Port number of Apollo" />
                <param name="debug_mode" type="select" label="Activate debug mode"> 
                    <option value="false" selected="true">No</option>
                    <option value="true">Yes</option>
                    <help>
                        Use this option if you are a G-OnRamp developer
                    </help>
                </param>
            </when>
            <when value="off">
                <param name="port" type="hidden" value="8080" />
                <param name="debug_mode" type="hidden"
                       value="false">
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="output" label="${tool.name} on ${on_string}" />
    </outputs>

    <help>
        This Galaxy tool is used to manage Apollo users.The currently supported operation including:

  - Create a new user 
  - Delete a user
  - Add a user to a group (If the group doesn't exist, create the group)
  - Remove a user to a group

The tool can do these operations on one student at a time. It can also do the operations on multiple students at a time by uploading a text file, which including students information.

The text file can be either CSV (comma-delimited) or Tabular (tab-delimited). It should have a header line, including names for each column. Example text files: 

Text file for creating multiple users:

.. csv-table:: 
   :header: "useremail", "firstname", "lastname", "password"
   :widths: 20, 10, 10, 10

   "[e-mail]", "test1", "demo", "1234"
   "[e-mail]", "test2", "demo", "1234"
   "[e-mail]", "test3", "demo", "1234"


Text file for deleting multiple users:

.. csv-table:: 
    :header: "useremail"
    :widths: 20

    "[e-mail]"
    "[e-mail]"
    "[e-mail]"


Text file for adding / removing multiple users from a group:

.. csv-table:: 
   :header: "useremail", "group"
   :widths: 20, 20

   "[e-mail]", "annotation_group1"
   "[e-mail]", "annotation_group1"
   "[e-mail]", "annotation_group1"

    </help>
    <citations>
    </citations>
</tool>