Merge pull request #3 from genepattern/Rename

Updating name to ExampleModule

Author: bahill

LICENSE

@@ -1,7 +1,7 @@
 
 BSD 3-Clause License
 
-Copyright (c) 2015-2018, Regents of the University of California & Broad Institute
+Copyright (c) 2015-2021, Regents of the University of California & Broad Institute
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,2 +1,2 @@
-# ABasicModule
-This is a basic GenePattern module written in Python 3. It can be taken as a "blank canvas" for future modules.
+# ExampleModule
+This is an example GenePattern module written in Python 3. It can be used as a template for future modules.

after_you_are_happy_with_your_code_READ_THIS_LIKE_NOW.md

@@ -8,10 +8,10 @@ https://docs.google.com/document/d/1QwpCHFFVAqmPovs515WJujeZuN_91nciK7q-ZDKq6mI/
 Summary:  
 
 #Starting a new Python module from scratch:
-git clone https://github.com/genepattern/ABasicModule.git
+git clone https://github.com/genepattern/ExampleModule.git
 
 # Structure of the blank_canvas_module
-*probably to be called "ABasicModule" to be consistent with the docs and to make sure when sorted alphabetically it shows up at or near the top.*
+*probably to be called "ExampleModule" to be consistent with the docs and to make sure when sorted alphabetically it shows up at or near the top.*
 - after_you_are_happy_with_your_code_READ_THIS_LIKE_NOW.txt
 - build.xml
 - data/
@@ -42,7 +42,7 @@ Before you begin: You may have already done some of these steps, that's okay, ke
 3. Look at the list of LSIDs and add a new entry to the List of modules and visualizers:
 https://github.com/genepattern/common_module_code/blob/master/module.lsid.registry
   - txt2odf became: `LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00372\:1.1.0`
-4. Make sure the manifest file is in the top-most directory (e.g., txt2odf/) -- You may need to remove the manifest that was created for ABasicModule
+4. Make sure the manifest file is in the top-most directory (e.g., txt2odf/) -- You may need to remove the manifest that was created for ExampleModule
   - Double check that the quality has been set to production (as opposed to development, since this module is set to be released), i.e., "quality=production"
 5. Open build.xml and modify the second line "name=**INSERT_MODULE_NAME_HERE** (in this case it is txt2odf)
 6. Open doc.html in a text editor and modify line 4, url=**INSERT_DOCUMENTATION_URL_HERE** to know what address to put there, follow these steps:

build.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project basedir="" default="create-zip" name="ABasicModule">
+<project basedir="" default="create-zip" name="ExampleModule">
 <property name="dirOffset" value="../common_module_code" />
 <import file="${dirOffset}/commontargets.xml" />
 

gpunit/basic_test.yml

@@ -7,8 +7,8 @@
 # Note: this test uses a custom diff command
 #
 
-name: "ABasicModule - Basic test"
-module: ABasicModule
+name: "ExampleModule - Basic test"
+module: ExamplModule
 params:
     filename: "../data/data_placeholder.txt"
     add_custom_message: "True"

manifest

@@ -1,16 +1,16 @@
-#ABasicModule
+#ExampleModule
 #Tue May 01 20:52:13 UTC 2018
 JVMLevel=
-LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00374\:1.0
+LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00374\:2.0
 author=Edwin F. Juarez;UCSD - Mesirov Lab
-categories=Administration
-commandLine=<python_3.6> <libdir>ABasicModule.py -f <filename> -a <add_custom_message> -m <message_to_add> -o <output_filename>
+categories=administration
+commandLine=<python_3.6> <libdir>ExampleModule.py -f <filename> -a <add_custom_message> -m <message_to_add> -o <output_filename>
 job.docker.image=genepattern/docker-python36:0.4
 cpuType=any
-description=This is a basic GenePattern module written in Python 3. It can be taken as a "blank canvas" for future modules. It reads a file and potentially adds a
+description=This is an exmaple GenePattern module written in Python 3. It can be used as a template for future modules. It reads a file and potentially adds a line of tesxt
 fileFormat=txt
 language=Python
-name=ABasicModule
+name=ExampleModule
 os=any
 p1_MODE=IN
 p1_TYPE=FILE
@@ -28,7 +28,7 @@ p1_value=
 p2_MODE=
 p2_TYPE=TEXT
 p2_default_value=False
-p2_description=Wether or not to add a custom message
+p2_description=Whether or not to add a custom message
 p2_fileFormat=
 p2_flag=-a
 p2_name=add_custom_message
@@ -67,6 +67,6 @@ p4_value=
 privacy=public
 quality=production
 taskDoc=doc.html
-taskType=Administration
-userid=edjuaro
-version=Initial version
+taskType=administration
+userid=bhill@broadinstitute.org
+version=Renaming as ExampleModule

src/ABasicModule.py src/ExampleModule.pysrc/ABasicModule.py renamed to src/ExampleModule.py

@@ -1,4 +1,4 @@
-from ABasicModule_functions import *
+from ExampleModule_functions import *
 import argparse
 import humanfriendly
 from timeit import default_timer as timer

src/ABasicModule_command_line_call.py src/ExampleModule_command_line_call.pysrc/ABasicModule_command_line_call.py renamed to src/ExampleModule_command_line_call.py

@@ -7,7 +7,7 @@
 TASKLIB = os.path.join(ROOT, 'src/')
 INPUT_FILE_DIRECTORIES = os.path.join(ROOT, 'data/')
 
-command_line = "python "+TASKLIB+"ABasicModule.py"\
+command_line = "python "+TASKLIB+"ExampleModule.py"\
                 + " -f " + INPUT_FILE_DIRECTORIES+"data_placeholder.txt"\
                 + " -a True"\
                 + ' -m "This message has been added."'\