PTFM-17932 remove remaining gtable from app wizard

Summary:
In an effort to move away from gtables, remove the remaining gtable code
from dx-app-wizard.

Test Plan: existing tests

Reviewers: pnguyen

Reviewed By: pnguyen

Differential Revision: https://dnanexus.phacility.com/D934

.arclint

@@ -3,6 +3,7 @@
     "pep8": {
       "type": "pep8",
       "include": "(\\.py$)",
+      "exclude": "(^src/python/dxpy/templating/templates/python/)",
       "flags": ["--max-line-length=119"],
       "severity.rules": {
         "(^E)": "warning",
@@ -11,7 +12,8 @@
     },
     "pyflakes": {
       "type": "pyflakes",
-      "include": "(\\.py$)"
+      "include": "(\\.py$)",
+      "exclude": "(^src/python/dxpy/templating/templates/python/)"
     }
   }
 }

src/python/dxpy/templating/templates/python/parallelized/src/code.py

@@ -84,7 +84,7 @@ def main(DX_APP_WIZARD_INPUT_SIGNATURE):
     # return { "app_output_field": postprocess_job.get_output_ref("answer"), ...}
     #
     # Tip: you can include in your output at this point any open
-    # objects (such as gtables) which will be closed by a job that
+    # objects (such as files) which will be closed by a job that
     # finishes later.  The system will check to make sure that the
     # output object is closed and will attempt to clone it out as
     # output into the parent container only after all subjobs have

src/python/dxpy/templating/utils.py

@@ -197,26 +197,6 @@ def get_pattern(template_dir):
     use_completer()
     return pattern
 
-def get_parallelized_io(required_file_input_names, gtable_input_names, gtable_output_names):
-    input_field = ''
-    output_field = ''
-
-    if required_file_input_names or gtable_input_names:
-        print('')
-        print(fill('Your app template can be initialized to split and process a ' + BOLD() + 'GTable' + ENDC() + ' input.  The following of your input fields are eligible for this template pattern:'))
-        print('  ' + '\n  '.join(gtable_input_names))
-        use_completer(Completer(gtable_input_names))
-        input_field = prompt_for_var('Input field to process (press ENTER to skip)', '', choices=required_file_input_names + gtable_input_names)
-        use_completer()
-
-    if input_field != '' and len(gtable_output_names) > 0:
-        print('')
-        print(fill('Your app template can be initialized to build a ' + BOLD() + 'GTable' + ENDC() + ' in parallel for your output.  The following of your output fields are eligible for this template pattern:'))
-        print('  ' + '\n  '.join(gtable_output_names))
-        use_completer(Completer(gtable_output_names))
-        output_field = prompt_for_var('Output gtable to build in parallel (press ENTER to skip)', '', choices=gtable_output_names)
-    return input_field, output_field
-
 def fill_in_name_and_ver(template_string, name, version):
     '''
     TODO: Rename this?

src/python/scripts/dx-app-wizard

@@ -26,8 +26,7 @@ from collections import OrderedDict
 import dxpy
 from dxpy.templating.utils import (print_intro, get_name, get_version, get_metadata, Completer, get_ordinal_str,
                                    prompt_for_var, prompt_for_yn, use_completer, get_language, language_options,
-                                   get_pattern, get_parallelized_io, fill_in_name_and_ver, clean,
-                                   create_files_from_templates)
+                                   get_pattern, fill_in_name_and_ver, clean, create_files_from_templates)
 from dxpy.utils.printing import fill, BOLD, UNDERLINE, DNANEXUS_LOGO, ENDC
 from dxpy.app_categories import APP_CATEGORIES
 from dxpy.utils.completer import InstanceTypesCompleter
@@ -256,8 +255,6 @@ optional_file_input_names = []
 required_file_array_input_names = []
 optional_file_array_input_names = []
 file_output_names = []
-gtable_input_names = []
-gtable_output_names = []
 
 if 'inputSpec' in app_json:
     for param in app_json['inputSpec']:
@@ -266,16 +263,13 @@ if 'inputSpec' in app_json:
             param_list = optional_file_input_names if may_be_missing else required_file_input_names
         elif param['class'] == 'array:file':
             param_list = optional_file_array_input_names if may_be_missing else required_file_array_input_names
-        elif param['class'] == 'gtable':
-            param_list = gtable_input_names
         else:
             param_list = None
         if param_list is not None:
             param_list.append(param['name'])
 
 if 'outputSpec' in app_json:
     file_output_names = [param['name'] for param in app_json['outputSpec'] if param['class'] == 'file']
-    gtable_output_names = [param['name'] for param in app_json['outputSpec'] if param['class'] == 'gtable']
 
 ########################
 # LANGUAGE AND PATTERN #
@@ -297,19 +291,6 @@ template_dir = os.path.join(os.path.dirname(dxpy.__file__), 'templating', 'templ
 pattern = get_pattern(template_dir)
 template_dir = os.path.join(template_dir, pattern)
 
-pattern_suffix = ''
-parallelized_input_field = ''
-parallelized_output_field = ''
-if pattern == 'parallelized' and len([filename for filename in os.listdir(os.path.join(template_dir, 'src')) if filename.startswith('code-')]) > 0:
-    parallelized_input_field, parallelized_output_field = get_parallelized_io(required_file_input_names,
-                                                                              gtable_input_names,
-                                                                              gtable_output_names)
-    pattern_suffix = ''
-    if parallelized_input_field != '':
-        pattern_suffix += '-input-gtable'
-    if parallelized_output_field != '':
-        pattern_suffix += '-output-gtable'
-
 with open(os.path.join(template_dir, 'dxapp.json'), 'r') as template_app_json_file:
     file_text = fill_in_name_and_ver(template_app_json_file.read(), name, version)
     template_app_json = json.loads(file_text)
@@ -423,9 +404,7 @@ elif pattern == 'scatter-process-gather':
 manifest += create_files_from_templates(template_dir, app_json, language,
                                         required_file_input_names, optional_file_input_names,
                                         required_file_array_input_names, optional_file_array_input_names,
-                                        file_output_names,
-                                        pattern, pattern_suffix,
-                                        parallelized_input_field, parallelized_output_field,
+                                        file_output_names, pattern,
                                         entry_points=entry_points, description=description)
 
 print("Created files:")