Mercurial > repos > yating-l > gonramp_apollo_tools
diff apolloUserManager.xml @ 0:ce4f91831680 draft default tip
planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894
| author | yating-l |
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| date | Fri, 16 Feb 2018 10:57:13 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/apolloUserManager.xml Fri Feb 16 10:57:13 2018 -0500 @@ -0,0 +1,290 @@ +<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 + + "test1@demo.com", "test1", "demo", "1234" + "test2@demo.com", "test2", "demo", "1234" + "test3@demo.com", "test3", "demo", "1234" + + +Text file for deleting multiple users: + +.. csv-table:: + :header: "useremail" + :widths: 20 + + "test1@demo.com" + "test2@demo.com" + "test3@demo.com" + + +Text file for adding / removing multiple users from a group: + +.. csv-table:: + :header: "useremail", "group" + :widths: 20, 20 + + "test1@demo.com", "annotation_group1" + "test2@demo.com", "annotation_group1" + "test3@demo.com", "annotation_group1" + + </help> + <citations> + </citations> +</tool> \ No newline at end of file