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comparison apolloUserManager.xml @ 0:1da8b9042af4 draft

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planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
author yating-l
date Mon, 27 Nov 2017 14:47:03 -0500
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1 <tool id="apollo_user_manager" name="Apollo User Manager" version="1.0.0">
2 <description>
3 This Galaxy tool is used to manage Apollo users.
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <requirements>
10 <requirement type="package" version="3.0.3">apollo_api</requirement>
11 </requirements>
12
13 <stdio>
14 </stdio>
15
16 <command detect_errors="exit_code"><![CDATA[
17
18 ## Dump the tool parameters into a JSON file
19 python $json_file parameters.json;
20 python $__tool_directory__/apolloUserManager.py --data_json parameters.json -o $output
21 ]]></command>
22 <configfiles>
23 <configfile name="json_file">
24 import json
25 import sys
26
27 file_path = sys.argv[1]
28 #set global data_parameter_dict = {"operations": dict()}
29 ## Function to retrieve the data of the inputs
30 #def prepare_json($operation_type, $data_dict, $batch)
31 #silent $data_dict.update({"batch": str($batch)})
32 #if $operation_type in $data_parameter_dict["operations"]
33 #silent $data_parameter_dict["operations"][$operation_type].append($data_dict)
34 #else
35 #set array_inputs = []
36 #silent $array_inputs.append($data_dict)
37 #silent $data_parameter_dict["operations"].update({$operation_type: $array_inputs})
38 #end if
39 #end def
40
41
42
43
44 #for $i, $f in enumerate($operation)
45 #if $f.operation_type_selector.operation_type == "create"
46 #set batch = $f.operation_type_selector.batch_selector.batch
47 #if $batch == "false"
48 #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email),
49 "firstname": str($f.operation_type_selector.batch_selector.firstname),
50 "lastname": str($f.operation_type_selector.batch_selector.lastname),
51 "password": str($f.operation_type_selector.batch_selector.password)}
52
53 #else
54 #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format),
55 "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
56 #end if
57 #silent $prepare_json("create", $data_dict, $batch)
58
59 #elif $f.operation_type_selector.operation_type == "delete"
60 #set batch = $f.operation_type_selector.batch_selector.batch
61 #if $batch == "false"
62 #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email)}
63 #else
64 #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format),
65 "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
66 #end if
67 #silent $prepare_json("delete", $data_dict, $batch)
68 #elif $f.operation_type_selector.operation_type == "add"
69 #set batch = $f.operation_type_selector.batch_selector.batch
70 #if $batch == "false"
71 #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email),
72 "group": str($f.operation_type_selector.batch_selector.group_name)}
73 #else
74 #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format),
75 "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
76 #end if
77 #silent $prepare_json("add", $data_dict, $batch)
78 #elif $f.operation_type_selector.operation_type == "remove"
79 #set batch = $f.operation_type_selector.batch_selector.batch
80 #if $batch == "false"
81 #set data_dict = {"useremail": str($f.operation_type_selector.batch_selector.user_email),
82 "group": str($f.operation_type_selector.batch_selector.group_name)}
83 #else
84 #set data_dict = {"format": str($f.operation_type_selector.batch_selector.format),
85 "false_path": str($f.operation_type_selector.batch_selector.user_info_file)}
86 #end if
87 #silent $prepare_json("remove", $data_dict, $batch)
88 #end if
89 #end for
90
91
92 #set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)}
93 #silent $data_parameter_dict.update({"apollo_admin": $apollo_admin})
94 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
95 #silent $data_parameter_dict.update({"port": str($advanced_options.port)})
96 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
97 with open(file_path, 'w') as f:
98 json.dump($data_parameter_dict, f)
99 </configfile>
100 </configfiles>
101
102
103 <inputs>
104 <param name="admin_username" type="text" label="Admin username" help="Login in with Apollo admin account">
105 <sanitizer>
106 <valid initial="string.letters,string.digits">
107 <add value="@-=_.()/+*^,:?!"/>
108 </valid>
109 </sanitizer>
110 </param>
111
112 <param
113 name="admin_password"
114 type="text"
115 label="Admin password"
116 />
117
118 <repeat name="operation" title="New operation">
119 <conditional name="operation_type_selector" >
120 <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">
121 <option value="create">Create a user</option>
122 <option value="delete">Delete a users</option>
123 <option value="add">Add a user to a group</option>
124 <option value="remove">Remove a user from a group</option>
125 </param>
126 <when value="create">
127 <conditional name="batch_selector">
128 <param name="batch" type="select" label="Manipulate a single user or multiple users">
129 <option value="false" selected="true">Single user</option>
130 <option value="true">Multiple users</option>
131 </param>
132 <when value="false">
133 <param name="user_email" type="text" label="User email" help="Specify the user email">
134 <sanitizer>
135 <valid initial="string.letters,string.digits">
136 <add value="@-=_.()/+*^,:?!"/>
137 </valid>
138 </sanitizer>
139 </param>
140 <param name="firstname" type="text" label="First name" />
141 <param name="lastname" type="text" label="Last name" />
142 <param name="password" type="text" label="Password" />
143 </when>
144 <when value="true">
145 <expand macro="upload_text_file" />
146 </when>
147 </conditional>
148 </when>
149 <when value="delete">
150 <conditional name="batch_selector">
151 <param name="batch" type="select" label="Manipulate a single user or multiple users">
152 <option value="false" selected="true">Single user</option>
153 <option value="true">Multiple users</option>
154 </param>
155 <when value="false">
156 <param name="user_email" type="text" label="User email" help="Specify the user email">
157 <sanitizer>
158 <valid initial="string.letters,string.digits">
159 <add value="@-=_.()/+*^,:?!"/>
160 </valid>
161 </sanitizer>
162 </param>
163 </when>
164 <when value="true">
165 <expand macro="upload_text_file" />
166 </when>
167 </conditional>
168 </when>
169 <when value="add">
170 <conditional name="batch_selector">
171 <param name="batch" type="select" label="Manipulate a single user or multiple users">
172 <option value="false" selected="true">Single user</option>
173 <option value="true">Multiple users</option>
174 </param>
175 <when value="false">
176 <param name="user_email" type="text" label="User email" help="Specify the user email">
177 <sanitizer>
178 <valid initial="string.letters,string.digits">
179 <add value="@-=_.()/+*^,:?!"/>
180 </valid>
181 </sanitizer>
182 </param>
183 <param type="text" name="group_name" size="30" value="unknown" label="Group name" />
184 </when>
185 <when value="true">
186 <expand macro="upload_text_file" />
187 </when>
188 </conditional>
189 </when>
190 <when value="remove">
191 <conditional name="batch_selector">
192 <param name="batch" type="select" label="Manipulate a single user or multiple users">
193 <option value="false" selected="true">Single user</option>
194 <option value="true">Multiple users</option>
195 </param>
196 <when value="false">
197 <param name="user_email" type="text" label="User email" help="Specify the user email">
198 <sanitizer>
199 <valid initial="string.letters,string.digits">
200 <add value="@-=_.()/+*^,:?!"/>
201 </valid>
202 </sanitizer>
203 </param>
204 <param type="text" name="group_name" size="30" value="unknown" label="Group name" />
205 </when>
206 <when value="true">
207 <expand macro="upload_text_file" />
208 </when>
209 </conditional>
210 </when>
211 </conditional>
212 </repeat>
213
214 <conditional name="advanced_options">
215 <param name="advanced_options_selector" type="select" label="Advanced options">
216 <option value="off" selected="true">Hide advanced options</option>
217 <option value="on">Display advanced options</option>
218 </param>
219 <!-- TODO: Avoid redundancy here -->
220 <when value="on">
221 <param name="port" type="integer" min="8000" max="8888" value="8080" label="Port number of Apollo" />
222 <param name="debug_mode" type="select" label="Activate debug mode">
223 <option value="false" selected="true">No</option>
224 <option value="true">Yes</option>
225 <help>
226 Use this option if you are a G-OnRamp developer
227 </help>
228 </param>
229 </when>
230 <when value="off">
231 <param name="port" type="hidden" value="8080" />
232 <param name="debug_mode" type="hidden"
233 value="false">
234 </param>
235 </when>
236 </conditional>
237 </inputs>
238 <outputs>
239 <data format="html" name="output" label="${tool.name}" />
240 </outputs>
241
242 <help>
243 This Galaxy tool is used to manage Apollo users.The currently supported operation including:
244
245 - Create a new user
246 - Delete a user
247 - Add a user to a group (If the group doesn't exist, create the group)
248 - Remove a user to a group
249
250 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.
251
252 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:
253
254 Text file for creating multiple users:
255
256 .. csv-table::
257 :header: "useremail", "firstname", "lastname", "password"
258 :widths: 20, 10, 10, 10
259
260 "test1@demo.com", "test1", "demo", "1234"
261 "test2@demo.com", "test2", "demo", "1234"
262 "test3@demo.com", "test3", "demo", "1234"
263
264
265 Text file for deleting multiple users:
266
267 .. csv-table::
268 :header: "useremail"
269 :widths: 20
270
271 "test1@demo.com"
272 "test2@demo.com"
273 "test3@demo.com"
274
275
276 Text file for adding / removing multiple users from a group:
277
278 .. csv-table::
279 :header: "useremail", "group"
280 :widths: 20, 20
281
282 "test1@demo.com", "annotation_group1"
283 "test2@demo.com", "annotation_group1"
284 "test3@demo.com", "annotation_group1"
285
286 </help>
287 <citations>
288 </citations>
289 </tool>