From e6c84f28d45730fe3dc74829b8d0a71b8933f4de Mon Sep 17 00:00:00 2001
From: bradfordcondon <bradford.condon@gmail.com>
Date: Sat, 2 Dec 2017 20:51:37 -0500
Subject: [PATCH 1/3] generator now runs without a db connection and create
 basic unit test

---
 tests/GeneratorTest.php | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 tests/GeneratorTest.php

diff --git a/tests/GeneratorTest.php b/tests/GeneratorTest.php
new file mode 100644
index 0000000..ce4bdd7
--- /dev/null
+++ b/tests/GeneratorTest.php
@@ -0,0 +1,34 @@
+<?php
+
+declare(strict_types=1);
+
+use PHPUnit\Framework\TestCase;
+
+require_once(__DIR__ . '/../src/bootstrap.php');
+
+final class GeneratorEngineTest extends TestCase {
+
+	private $generator;
+
+protected function setUp() {
+   
+$this->generator = new StatonLab\FieldGenerator\Generator();
+}
+ protected function tearDown()
+    {
+        $this->generator = NULL;
+    }
+
+/**
+*Assert that the Generator constructs
+*
+**/
+    public function testAdd()
+    {
+        $generator = $this->generator;
+
+        $this->assertInstanceOf("StatonLab\FieldGenerator\Generator", $generator);
+
+    }
+
+}
\ No newline at end of file

From 9a5232bebe00a2442df2ae2a95742690db51f0f2 Mon Sep 17 00:00:00 2001
From: bradfordcondon <bradford.condon@gmail.com>
Date: Sat, 2 Dec 2017 21:26:54 -0500
Subject: [PATCH 2/3] allow creation offline

---
 composer.lock                       | 767 ++++++++++++++++++++++++++++
 s__c_output/g.fields.inc            | 125 +++++
 s__c_output/s__c/s__c.inc           | 128 +++++
 s__c_output/s__c/s__c_formatter.inc | 119 +++++
 s__c_output/s__c/s__c_widget.inc    | 122 +++++
 src/DB.php                          |  33 +-
 src/Generator.php                   |   7 +
 src/bootstrap.php                   |   1 +
 8 files changed, 1298 insertions(+), 4 deletions(-)
 create mode 100644 composer.lock
 create mode 100644 s__c_output/g.fields.inc
 create mode 100644 s__c_output/s__c/s__c.inc
 create mode 100644 s__c_output/s__c/s__c_formatter.inc
 create mode 100644 s__c_output/s__c/s__c_widget.inc

diff --git a/composer.lock b/composer.lock
new file mode 100644
index 0000000..7b3f34f
--- /dev/null
+++ b/composer.lock
@@ -0,0 +1,767 @@
+{
+    "_readme": [
+        "This file locks the dependencies of your project to a known state",
+        "Read more about it at https://getcomposer.org/doc/01-basic-usage.md#composer-lock-the-lock-file",
+        "This file is @generated automatically"
+    ],
+    "content-hash": "73fcac0cb9c94cf50e9803d61ae38ac7",
+    "packages": [
+        {
+            "name": "phpunit/php-code-coverage",
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+            "source": {
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+                "url": "https://github.com/sebastianbergmann/php-code-coverage.git",
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+            },
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+                "reference": "eabf68b476ac7d0f73793aada060f1c1a9bf8979",
+                "shasum": ""
+            },
+            "require": {
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+                "phpunit/php-text-template": "~1.2",
+                "phpunit/php-token-stream": "~1.3",
+                "sebastian/environment": "^1.3.2",
+                "sebastian/version": "~1.0"
+            },
+            "require-dev": {
+                "ext-xdebug": ">=2.1.4",
+                "phpunit/phpunit": "~4"
+            },
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+                "ext-xmlwriter": "*"
+            },
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+            "extra": {
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+                }
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+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
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+            "authors": [
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+                    "email": "sb@sebastian-bergmann.de",
+                    "role": "lead"
+                }
+            ],
+            "description": "Library that provides collection, processing, and rendering functionality for PHP code coverage information.",
+            "homepage": "https://github.com/sebastianbergmann/php-code-coverage",
+            "keywords": [
+                "coverage",
+                "testing",
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+                "url": "https://github.com/sebastianbergmann/php-file-iterator.git",
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+            },
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+                "shasum": ""
+            },
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+            },
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+                    "File/"
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+            "notification-url": "https://packagist.org/downloads/",
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+            ],
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+                {
+                    "name": "Sebastian Bergmann",
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+                    "role": "lead"
+                }
+            ],
+            "description": "FilterIterator implementation that filters files based on a list of suffixes.",
+            "homepage": "https://github.com/sebastianbergmann/php-file-iterator/",
+            "keywords": [
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+                "iterator"
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+        },
+        {
+            "name": "phpunit/php-text-template",
+            "version": "1.2.1",
+            "source": {
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+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
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+            "authors": [
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+            "keywords": [
+                "timer"
+            ],
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+        },
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+                }
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+            "suggest": {
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+                    "email": "whatthejeff@gmail.com"
+                },
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+                    "email": "github@wallbash.com"
+                },
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+                    "email": "bschussek@2bepublished.at"
+                },
+                {
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+                    "email": "sebastian@phpunit.de"
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+            "keywords": [
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+                "equality"
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+                    "email": "mail@kore-nordmann.de"
+                },
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+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                }
+            ],
+            "description": "Diff implementation",
+            "homepage": "https://github.com/sebastianbergmann/diff",
+            "keywords": [
+                "diff"
+            ],
+            "time": "2017-05-22T07:24:03+00:00"
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+            "notification-url": "https://packagist.org/downloads/",
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+            "authors": [
+                {
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+                    "email": "sebastian@phpunit.de"
+                }
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+            "description": "Provides functionality to handle HHVM/PHP environments",
+            "homepage": "http://www.github.com/sebastianbergmann/environment",
+            "keywords": [
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+            "time": "2016-08-18T05:49:44+00:00"
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+                {
+                    "name": "Volker Dusch",
+                    "email": "github@wallbash.com"
+                },
+                {
+                    "name": "Bernhard Schussek",
+                    "email": "bschussek@2bepublished.at"
+                },
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                },
+                {
+                    "name": "Adam Harvey",
+                    "email": "aharvey@php.net"
+                }
+            ],
+            "description": "Provides the functionality to export PHP variables for visualization",
+            "homepage": "http://www.github.com/sebastianbergmann/exporter",
+            "keywords": [
+                "export",
+                "exporter"
+            ],
+            "time": "2016-06-17T09:04:28+00:00"
+        },
+        {
+            "name": "sebastian/recursion-context",
+            "version": "1.0.5",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/recursion-context.git",
+                "reference": "b19cc3298482a335a95f3016d2f8a6950f0fbcd7"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/recursion-context/zipball/b19cc3298482a335a95f3016d2f8a6950f0fbcd7",
+                "reference": "b19cc3298482a335a95f3016d2f8a6950f0fbcd7",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.3.3"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "~4.4"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.0.x-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Jeff Welch",
+                    "email": "whatthejeff@gmail.com"
+                },
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                },
+                {
+                    "name": "Adam Harvey",
+                    "email": "aharvey@php.net"
+                }
+            ],
+            "description": "Provides functionality to recursively process PHP variables",
+            "homepage": "http://www.github.com/sebastianbergmann/recursion-context",
+            "time": "2016-10-03T07:41:43+00:00"
+        },
+        {
+            "name": "sebastian/version",
+            "version": "1.0.6",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/version.git",
+                "reference": "58b3a85e7999757d6ad81c787a1fbf5ff6c628c6"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/version/zipball/58b3a85e7999757d6ad81c787a1fbf5ff6c628c6",
+                "reference": "58b3a85e7999757d6ad81c787a1fbf5ff6c628c6",
+                "shasum": ""
+            },
+            "type": "library",
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de",
+                    "role": "lead"
+                }
+            ],
+            "description": "Library that helps with managing the version number of Git-hosted PHP projects",
+            "homepage": "https://github.com/sebastianbergmann/version",
+            "time": "2015-06-21T13:59:46+00:00"
+        },
+        {
+            "name": "symfony/yaml",
+            "version": "v2.8.31",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/symfony/yaml.git",
+                "reference": "d819bf267e901727141fe828ae888486fd21236e"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/symfony/yaml/zipball/d819bf267e901727141fe828ae888486fd21236e",
+                "reference": "d819bf267e901727141fe828ae888486fd21236e",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.3.9"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "2.8-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "Symfony\\Component\\Yaml\\": ""
+                },
+                "exclude-from-classmap": [
+                    "/Tests/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Fabien Potencier",
+                    "email": "fabien@symfony.com"
+                },
+                {
+                    "name": "Symfony Community",
+                    "homepage": "https://symfony.com/contributors"
+                }
+            ],
+            "description": "Symfony Yaml Component",
+            "homepage": "https://symfony.com",
+            "time": "2017-11-05T15:25:56+00:00"
+        }
+    ],
+    "packages-dev": [],
+    "aliases": [],
+    "minimum-stability": "stable",
+    "stability-flags": {
+        "phpunit/phpunit": 20
+    },
+    "prefer-stable": false,
+    "prefer-lowest": false,
+    "platform": [],
+    "platform-dev": []
+}
diff --git a/s__c_output/g.fields.inc b/s__c_output/g.fields.inc
new file mode 100644
index 0000000..8aac63b
--- /dev/null
+++ b/s__c_output/g.fields.inc
@@ -0,0 +1,125 @@
+<?php
+/**
+ * @file
+ * Contains all field specific code outside the classes.
+ */
+
+/**
+ * Implements hook_bundle_fields_info().
+ *
+ * This hook tells Drupal/Tripal about your new field type. Make sure you've created the
+ * field (handles basic storage of your data), widget (provides user UI to set data),
+ * and formatter (describes display of data on Entity Page) classes. These should be
+ * located in the following directory: [your module]/includes/TripalFields/[classname].inc
+ * with one file per class. Your field name should be [cv name]__[cvterm name] and the
+ * classes should be named [field name], [field_name]_widget, [field name]_formatter
+ * for the field, widget and formatter respectively. MAKE SURE YOU'VE CLEARED THE CACHE
+ * SINCE ADDING THESE FILES so Tripal magic can find them or the following will fail.
+ *
+ * @param $entity_type
+ *   This should be 'TripalEntity' for all Tripal Content.
+ * @param $bundle
+ *   This object describes the Type of Tripal Entity (e.g. Organism or Gene) this hook is
+ *   being called for. However, since this hook creates field types (by definition not
+ *   tied to a specific Tripal Content Type (bundle)) and since a field type will only be
+ *   created if it doesn't already exist, this parameter doesn't actually matter.
+ *   NOTE: If you do need to determine the bundle in this hook, we suggest inspecting
+ *   the data_table since the label can be changed by site administrators.
+ *
+ * @return
+ *   An array of field definitions. Each field in this array will be created if it
+ *   doesn't already exist. To trigger create of fields when developing call
+ *   tripal_refresh_bundle_fields() for the specific bundle.
+ */
+function g_bundle_fields_info($entity_type, $bundle) {
+  $fields = array();
+
+  // Because we are expecting data housed in Chado we can use the 'data_table'
+  // property of the bundle to determine if this bundle is really the one
+  // we want the field to be associated with.
+  if (isset($bundle->data_table) AND ($bundle->data_table == 'organism')) {
+    // First add my term.
+    tripal_insert_cvterm(array(
+      'id' => 's:d',
+      'name' => 'c',
+      'cv_name' => 'd',
+      'definition' => 'f',
+    ));
+
+    // Then describe the field defined by that term.
+    $field_name = 's__c';
+    $field_type = 's__c';
+    $fields[$field_name] = array(
+      'field_name' => $field_name,
+      'type' => $field_type,
+      'cardinality' => 1,
+      'locked' => FALSE,
+      'storage' => array(
+        'type' => 'field_chado_storage',
+      ),
+    );
+  }
+
+  return $fields;
+}
+
+/**
+ * Implements hook_bundle_instances_info().
+ *
+ * This hook tells Drupal/Tripal to create a field instance of a given field type on a
+ * specific Tripal Content type (otherwise known as the bundle). Make sure to implement
+ * hook_bundle_create_fields() to create your field type before trying to create an
+ * instance of that field.
+ *
+ * @param $entity_type
+ *   This should be 'TripalEntity' for all Tripal Content.
+ * @param $bundle
+ *   This object describes the Type of Tripal Entity (e.g. Organism or Gene) the field
+ *   instances are being created for. Thus this hook is called once per Tripal Content Type on your
+ *   site. The name of the bundle is the machine name of the type (e.g. bio_data_1) and
+ *   the label of the bundle (e.g. Organism) is what you see in the interface. Since the
+ *   label can be changed by site admin, we suggest checking the data_table to determine
+ *   if this is the entity you want to add field instances to.
+ * @return
+ *   An array of field instance definitions. This is where you can define the defaults
+ *   for any settings you use in your field. Each entry in this array will be used to
+ *   create an instance of an already existing field.
+ */
+function g_bundle_instances_info($entity_type, $bundle) {
+  $instances = array();
+
+  // ORGANISM.
+  //===============
+  if (isset($bundle->data_table) AND ($bundle->data_table == 'organism')) {
+    $field_name = 's__c';
+    $field_type = 's__c';
+    $instances[$field_name] =  array(
+      'field_name' => $field_name,
+      'entity_type' => $entity_type,
+      'bundle' => $bundle->name,
+      'label' => 'd',
+      'description' => 'f',
+      'required' => FALSE,
+      'settings' => array(
+        'auto_attach' => FALSE,
+        'chado_table' => $bundle->data_table,
+        'chado_column' => 'organism_id',
+        'base_table' => $bundle->data_table,
+      ),
+      'widget' => array(
+        'type' => 's__c_widget',
+        'settings' => array(),
+      ),
+      'display' => array(
+        'default' => array(
+          'label' => 'hidden',
+          'type' => 's__c_formatter',
+          'settings' => array(),
+        ),
+      ),
+    );
+
+  }
+
+  return $instances;
+}
diff --git a/s__c_output/s__c/s__c.inc b/s__c_output/s__c/s__c.inc
new file mode 100644
index 0000000..9298c7a
--- /dev/null
+++ b/s__c_output/s__c/s__c.inc
@@ -0,0 +1,128 @@
+<?php
+/**
+ * @class
+ * Purpose:
+ *
+ * Data:
+ * Assumptions:
+ */
+class s__c extends ChadoField {
+
+  // --------------------------------------------------------------------------
+  //                     EDITABLE STATIC CONSTANTS
+  //
+  // The following constants SHOULD be set for each descendant class.  They are
+  // used by the static functions to provide information to Drupal about
+  // the field and it's default widget and formatter.
+  // --------------------------------------------------------------------------
+
+  // The default label for this field.
+  public static $default_label = 'd';
+
+  // The default description for this field.
+  public static $default_description = 'f';
+
+  // The default widget for this field.
+  public static $default_widget = 's__c_widget';
+
+  // The default formatter for this field.
+  public static $default_formatter = 's__c_formatter';
+
+  // The module that manages this field.
+  public static $module = 'g';
+
+  // A list of global settings. These can be accessed within the
+  // globalSettingsForm.  When the globalSettingsForm is submitted then
+  // Drupal will automatically change these settings for all fields.
+  // Once instances exist for a field type then these settings cannot be
+  // changed.
+  public static $default_settings = array(
+    'storage' => 'field_chado_storage',
+     // It is expected that all fields set a 'value' in the load() function.
+     // In many cases, the value may be an associative array of key/value pairs.
+     // In order for Tripal to provide context for all data, the keys should
+     // be a controlled vocabulary term (e.g. rdfs:type). Keys in the load()
+     // function that are supported by the query() function should be
+     // listed here.
+     'searchable_keys' => array(),
+  );
+
+  // Provide a list of instance specific settings. These can be access within
+  // the instanceSettingsForm.  When the instanceSettingsForm is submitted
+  // then Drupal with automatically change these settings for the instance.
+  // It is recommended to put settings at the instance level whenever possible.
+  // If you override this variable in a child class be sure to replicate the
+  // term_name, term_vocab, term_accession and term_fixed keys as these are
+  // required for all TripalFields.
+  public static $default_instance_settings = array(
+    // The DATABASE name, as it appears in chado.db.  This also builds the link-out url.  In most cases this will simply be the CV name.  In some cases (EDAM) this will be the SUBONTOLOGY.
+    'term_vocabulary' => 's',
+    // The name of the term.
+    'term_name' => 'c',
+    // The unique ID (i.e. accession) of the term.
+    'term_accession' => 'd',
+    // Set to TRUE if the site admin is not allowed to change the term
+    // type, otherwise the admin can change the term mapped to a field.
+    'term_fixed' => FALSE,
+    // Indicates if this field should be automatically attached to display
+    // or web services or if this field should be loaded separately. This
+    // is convenient for speed.  Fields that are slow should for loading
+    // should have auto_attach set to FALSE so tha their values can be
+    // attached asynchronously.
+    'auto_attach' => FALSE,
+    // The table in Chado that the instance maps to.
+    'chado_table' => 'organism',
+    // The column of the table in Chado where the value of the field comes from.
+    'chado_column' => 'organism_id',
+    // The base table.
+    'base_table' => 'organism',
+  );
+
+  // A boolean specifying that users should not be allowed to create
+  // fields and instances of this field type through the UI. Such
+  // fields can only be created programmatically with field_create_field()
+  // and field_create_instance().
+  public static $no_ui = FALSE;
+
+  // A boolean specifying that the field will not contain any data. This
+  // should exclude the field from web services or downloads.  An example
+  // could be a quick search field that appears on the page that redirects
+  // the user but otherwise provides no data.
+  public static $no_data = FALSE;
+
+ /**
+   * Loads the field values from the underlying data store.
+   *
+   * @param $entity
+   *
+   * @return
+   *   An array of the following format:
+   *     $entity->{$field_name}['und'][0]['value'] = $value;
+   *   where:
+   *     - $entity is the entity object to which this field is attached.
+   *     - $field_name is the name of this field
+   *     - 'und' is the language code (in this case 'und' == undefined)
+   *     - 0 is the cardinality.  Increment by 1 when more than one item is
+   *       available.
+   *     - 'value' is the key indicating the value of this field. It should
+   *       always be set.  The value of the 'value' key will be the contents
+   *       used for web services and for downloadable content.  The value
+   *       should be of the follow format types: 1) A single value (text,
+   *       numeric, etc.) 2) An array of key value pair. 3) If multiple entries
+   *       then cardinality should incremented and format types 1 and 2 should
+   *       be used for each item.
+   *   The array may contain as many other keys at the same level as 'value'
+   *   but those keys are for internal field use and are not considered the
+   *   value of the field.
+   *
+   *
+   */
+  public function load($entity) {
+
+    // ChadoFields automatically load the chado column specified in the
+    // default settings above. If that is all you need then you don't even
+    // need to implement this function. However, if you need to add any
+    // additional data to be used in the display, you should add it here.
+    parent::load($entity);
+  }
+}
\ No newline at end of file
diff --git a/s__c_output/s__c/s__c_formatter.inc b/s__c_output/s__c/s__c_formatter.inc
new file mode 100644
index 0000000..bdcd8d0
--- /dev/null
+++ b/s__c_output/s__c/s__c_formatter.inc
@@ -0,0 +1,119 @@
+<?php
+/**
+ * @class
+ * Purpose:
+ *
+ * Display:
+ * Configuration:
+ */
+class s__c_formatter extends ChadoFieldFormatter {
+
+  // The default label for this field.
+  public static $default_label = 'd';
+
+  // The list of field types for which this formatter is appropriate.
+  public static $field_types = array('s__c');
+
+  // The list of default settings for this formatter.
+  public static $default_settings = array(
+    'setting1' => 'default_value',
+  );
+
+  /**
+   * Provides the field's setting form.
+   *
+   * This function corresponds to the hook_field_formatter_settings_form()
+   * function of the Drupal Field API.
+   *
+   * The settings form appears on the 'Manage Display' page of the content
+   * type administration page. This function provides the form that will
+   * appear on that page.
+   *
+   * To add a validate function, please create a static function in the
+   * implementing class, and indicate that this function should be used
+   * in the form array that is returned by this function.
+   *
+   * This form will not be displayed if the formatter_settings_summary()
+   * function does not return anything.
+   *
+   * param $field
+   *   The field structure being configured.
+   * param $instance
+   *   The instance structure being configured.
+   * param $view_mode
+   *   The view mode being configured.
+   * param $form
+   *   The (entire) configuration form array, which will usually have no use
+   *   here.  Typically for reference only.
+   * param $form_state
+   *   The form state of the (entire) configuration form.
+   *
+   * @return
+   *   A Drupal Form array containing the settings form for this field.
+   */
+  public function settingsForm($view_mode, $form, &$form_state) {
+
+  }
+
+  /**
+   *  Provides the display for a field
+   *
+   * This function corresponds to the hook_field_formatter_view()
+   * function of the Drupal Field API.
+   *
+   *  This function provides the display for a field when it is viewed on
+   *  the web page.  The content returned by the formatter should only include
+   *  what is present in the $items[$delta]['values] array. This way, the
+   *  contents that are displayed on the page, via webservices and downloaded
+   *  into a CSV file will always be identical.  The view need not show all
+   *  of the data in the 'values' array.
+   *
+   *  @param $element
+   *  @param $entity_type
+   *  @param $entity
+   *  @param $langcode
+   *  @param $items
+   *  @param $display
+   *
+   *  @return
+   *    An element array compatible with that returned by the
+   *    hook_field_formatter_view() function.
+   */
+  public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
+
+    // Get the settings
+    $settings = $display['settings'];
+  }
+
+  /**
+   * Provides a summary of the formatter settings.
+   *
+   * This function corresponds to the hook_field_formatter_settings_summary()
+   * function of the Drupal Field API.
+   *
+   * On the 'Manage Display' page of the content type administration page,
+   * fields are allowed to provide a settings form.  This settings form can
+   * be used to allow the site admin to define how the field should be
+   * formatted.  The settings are then available for the formatter()
+   * function of this class.  This function provides a text-based description
+   * of the settings for the site developer to see.  It appears on the manage
+   * display page inline with the field.  A field must always return a
+   * value in this function if the settings form gear button is to appear.
+   *
+   * See the hook_field_formatter_settings_summary() function for more
+   * information.
+   *
+   * @param $field
+   * @param $instance
+   * @param $view_mode
+   *
+   * @return string
+   *   A string that provides a very brief summary of the field settings
+   *   to the user.
+   *
+   */
+  public function settingsSummary($view_mode) {
+    return '';
+  }
+
+}
\ No newline at end of file
diff --git a/s__c_output/s__c/s__c_widget.inc b/s__c_output/s__c/s__c_widget.inc
new file mode 100644
index 0000000..25a9a4a
--- /dev/null
+++ b/s__c_output/s__c/s__c_widget.inc
@@ -0,0 +1,122 @@
+<?php
+/**
+ * @class
+ * Purpose:
+ *
+ * Allowing edit?
+ * Data:
+ * Assumptions:
+ */
+class s__c_widget extends ChadoFieldWidget {
+
+  // The default label for this field.
+  public static $default_label = 'd';
+
+  // The list of field types for which this formatter is appropriate.
+  public static $field_types = array('s__c');
+
+  /**
+   * Provides the form for editing of this field.
+   *
+   * This function corresponds to the hook_field_widget_form()
+   * function of the Drupal Field API.
+   *
+   * This form is diplayed when the user creates a new entity or edits an
+   * existing entity.  If the field is attached to the entity then the form
+   * provided by this function will be displayed.
+   *
+   * At a minimum, the form must have a 'value' element.  For Tripal, the
+   * 'value' element of a field always corresponds to the value that is
+   * presented to the end-user either directly on the page (with formatting)
+   * or via web services, or some other mechanism.  However, the 'value' is
+   * sometimes not enough for a field.  For example, the Tripal Chado module
+   * maps fields to table columns and sometimes those columns are foreign keys
+   * therefore, the Tripal Chado modules does not just use the 'value' but adds
+   * additional elements to help link records via FKs.  But even in this case
+   * the 'value' element must always be present in the return form and in such
+   * cases it's value should be set equal to that added in the 'load' function.
+   *
+   * @param $widget
+   * @param $form
+   *   The form structure where widgets are being attached to. This might be a
+   *   full form structure, or a sub-element of a larger form.
+   * @param $form_state
+   *   An associative array containing the current state of the form.
+   * @param $langcode
+   *   The language associated with $items.
+   * @param $items
+   *   Array of default values for this field.
+   * @param $delta
+   *   The order of this item in the array of subelements (0, 1, 2, etc).
+   * @param $element
+   * A form element array containing basic properties for the widget:
+   *  - #entity_type: The name of the entity the field is attached to.
+   *  - #bundle: The name of the field bundle the field is contained in.
+   *  - #field_name: The name of the field.
+   *  - #language: The language the field is being edited in.
+   *  - #field_parents: The 'parents' space for the field in the form. Most
+   *    widgets can simply overlook this property. This identifies the location
+   *    where the field values are placed within $form_state['values'], and is
+   *    used to access processing information for the field through the
+   *    field_form_get_state() and field_form_set_state() functions.
+   *  - #columns: A list of field storage columns of the field.
+   *  - #title: The sanitized element label for the field instance, ready for
+   *    output.
+   *  - #description: The sanitized element description for the field instance,
+   *    ready for output.
+   *  - #required: A Boolean indicating whether the element value is required;
+   *    for required multiple value fields, only the first widget's values are
+   *    required.
+   *  - #delta: The order of this item in the array of subelements; see
+   *    $delta above
+   */
+  public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
+    parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+  }
+
+  /**
+   * Performs validation of the widgetForm.
+   *
+   * Use this validate to ensure that form values are entered correctly.
+   * The 'value' key of this field must be set in the $form_state['values']
+   * array anytime data is entered by the user.  It may be the case that there
+   * are other fields for helping select a value. In the end those helper
+   * fields must be used to set the 'value' field.
+   */
+  public function validate($element, $form, &$form_state, $langcode, $delta) {
+  }
+
+  /**
+   * Performs extra commands when the entity form is submitted.
+   *
+   * Drupal typically does not provide a submit hook for fields.  The
+   * TripalField provides one to allow for behind-the-scenes actions to
+   * occur.   This function should never be used for updates, deletes or
+   * inserts for the Chado table associated with the field.  Rather, the
+   * storage backend should be allowed to handle inserts, updates deletes.
+   * However, it is permissible to perform inserts, updates or deletions within
+   * Chado using this function.  Those operations can be performed if needed but
+   * on other tables not directly associated with the field.
+   *
+   * An example is the chado.feature_synonym table.  The chado_linker__synonym
+   * field allows the user to provide a brand new synonynm and it must add it
+   * to the chado.synonym table prior to the record in the
+   * chado.feature_synonym table.  This insert occurs in the widgetFormSubmit
+   * function.
+   *
+   * @param $form
+   *    The submitted form array.
+   * @param $form_state .
+   *    The form state array.
+   * @param $entity_type
+   *    The type of $entity.
+   * @param $entity
+   *    The entity for the operation.
+   * @param $langcode
+   *    The language associated with $items.
+   * @param $delta
+   */
+  public function submit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
+  }
+
+}
\ No newline at end of file
diff --git a/src/DB.php b/src/DB.php
index e662a8e..f25ab84 100644
--- a/src/DB.php
+++ b/src/DB.php
@@ -48,13 +48,22 @@ class DB {
    */
   protected $sql;
 
+/**
+* True if DB is not connected.
+*
+*/
+  protected $unconnected;
+
+
   /**
    * DB constructor.
    */
   public function __construct($drupal_path = NULL) {
     $settings = $this->getSettingsFilePath($drupal_path);
-    $this->readSettings($settings);
-    $this->createConnection();
+    if ($settings) {
+      $this->readSettings($settings);
+      $this->createConnection();
+    }
   }
 
   /**
@@ -84,11 +93,18 @@ protected function getSettingsFilePath($drupal_root) {
     $settings = "{$drupal_root}/sites/default/settings.php";
 
     if (!file_exists($settings)) {
-      throw  new Exception("The settings file at $settings does not exist.");
+
+      $this->unconnected = true;
+    
+      return null;
+     // throw  new Exception("The settings file at $settings does not exist.");
     }
 
     if (!is_readable($settings)) {
-      throw new Exception("The settings file at $settings is not readable.");
+            $this->unconnected = true;
+
+      return null;
+     // throw new Exception("The settings file at $settings is not readable.");
     }
 
     return $settings;
@@ -152,4 +168,13 @@ public function get() {
   public function count() {
     return intval($this->get()[0]['count']);
   }
+
+
+/**
+*Inform generator if there is no DB connection
+*
+*/
+public function checkOffline() {
+  return $this->unconnected;
+}
 }
\ No newline at end of file
diff --git a/src/Generator.php b/src/Generator.php
index 85324e1..301f9d1 100644
--- a/src/Generator.php
+++ b/src/Generator.php
@@ -187,6 +187,13 @@ protected function validateTerms() {
     $this->prompt->info('Performing DB checks to validate entries ...');
     $failed = FALSE;
 
+    //if no connection, run anyway but let the user know
+    if ($this->db->checkOffline()) {
+          $this->prompt->info('No valid DB connection.  Continuing without querying terms against the DB.');
+          $this->prompt->info("Chosen CV Term ID {$this->db_name}:{$this->field_accession} and CV {$this->cv_name}");
+      return;
+    }
+
     // Validate DB
     $count = $this->count('chado.db', 'name', $this->db_name);
     if ($count <= 0) {
diff --git a/src/bootstrap.php b/src/bootstrap.php
index e14c4e9..3577d3c 100644
--- a/src/bootstrap.php
+++ b/src/bootstrap.php
@@ -8,3 +8,4 @@
 include __DIR__ . '/CLIPrompt.php';
 include __DIR__ . '/Colors.php';
 include __DIR__ . '/Generator.php';
+include __DIR__ . '/DB.php';

From 0b3fa301909ce0741af809439dd98f83c7bcca48 Mon Sep 17 00:00:00 2001
From: bradfordcondon <bradford.condon@gmail.com>
Date: Sat, 2 Dec 2017 21:27:38 -0500
Subject: [PATCH 3/3] successfully create field with no db connection

---
 s__c_output/g.fields.inc            | 125 ---------------------------
 s__c_output/s__c/s__c.inc           | 128 ----------------------------
 s__c_output/s__c/s__c_formatter.inc | 119 --------------------------
 s__c_output/s__c/s__c_widget.inc    | 122 --------------------------
 4 files changed, 494 deletions(-)
 delete mode 100644 s__c_output/g.fields.inc
 delete mode 100644 s__c_output/s__c/s__c.inc
 delete mode 100644 s__c_output/s__c/s__c_formatter.inc
 delete mode 100644 s__c_output/s__c/s__c_widget.inc

diff --git a/s__c_output/g.fields.inc b/s__c_output/g.fields.inc
deleted file mode 100644
index 8aac63b..0000000
--- a/s__c_output/g.fields.inc
+++ /dev/null
@@ -1,125 +0,0 @@
-<?php
-/**
- * @file
- * Contains all field specific code outside the classes.
- */
-
-/**
- * Implements hook_bundle_fields_info().
- *
- * This hook tells Drupal/Tripal about your new field type. Make sure you've created the
- * field (handles basic storage of your data), widget (provides user UI to set data),
- * and formatter (describes display of data on Entity Page) classes. These should be
- * located in the following directory: [your module]/includes/TripalFields/[classname].inc
- * with one file per class. Your field name should be [cv name]__[cvterm name] and the
- * classes should be named [field name], [field_name]_widget, [field name]_formatter
- * for the field, widget and formatter respectively. MAKE SURE YOU'VE CLEARED THE CACHE
- * SINCE ADDING THESE FILES so Tripal magic can find them or the following will fail.
- *
- * @param $entity_type
- *   This should be 'TripalEntity' for all Tripal Content.
- * @param $bundle
- *   This object describes the Type of Tripal Entity (e.g. Organism or Gene) this hook is
- *   being called for. However, since this hook creates field types (by definition not
- *   tied to a specific Tripal Content Type (bundle)) and since a field type will only be
- *   created if it doesn't already exist, this parameter doesn't actually matter.
- *   NOTE: If you do need to determine the bundle in this hook, we suggest inspecting
- *   the data_table since the label can be changed by site administrators.
- *
- * @return
- *   An array of field definitions. Each field in this array will be created if it
- *   doesn't already exist. To trigger create of fields when developing call
- *   tripal_refresh_bundle_fields() for the specific bundle.
- */
-function g_bundle_fields_info($entity_type, $bundle) {
-  $fields = array();
-
-  // Because we are expecting data housed in Chado we can use the 'data_table'
-  // property of the bundle to determine if this bundle is really the one
-  // we want the field to be associated with.
-  if (isset($bundle->data_table) AND ($bundle->data_table == 'organism')) {
-    // First add my term.
-    tripal_insert_cvterm(array(
-      'id' => 's:d',
-      'name' => 'c',
-      'cv_name' => 'd',
-      'definition' => 'f',
-    ));
-
-    // Then describe the field defined by that term.
-    $field_name = 's__c';
-    $field_type = 's__c';
-    $fields[$field_name] = array(
-      'field_name' => $field_name,
-      'type' => $field_type,
-      'cardinality' => 1,
-      'locked' => FALSE,
-      'storage' => array(
-        'type' => 'field_chado_storage',
-      ),
-    );
-  }
-
-  return $fields;
-}
-
-/**
- * Implements hook_bundle_instances_info().
- *
- * This hook tells Drupal/Tripal to create a field instance of a given field type on a
- * specific Tripal Content type (otherwise known as the bundle). Make sure to implement
- * hook_bundle_create_fields() to create your field type before trying to create an
- * instance of that field.
- *
- * @param $entity_type
- *   This should be 'TripalEntity' for all Tripal Content.
- * @param $bundle
- *   This object describes the Type of Tripal Entity (e.g. Organism or Gene) the field
- *   instances are being created for. Thus this hook is called once per Tripal Content Type on your
- *   site. The name of the bundle is the machine name of the type (e.g. bio_data_1) and
- *   the label of the bundle (e.g. Organism) is what you see in the interface. Since the
- *   label can be changed by site admin, we suggest checking the data_table to determine
- *   if this is the entity you want to add field instances to.
- * @return
- *   An array of field instance definitions. This is where you can define the defaults
- *   for any settings you use in your field. Each entry in this array will be used to
- *   create an instance of an already existing field.
- */
-function g_bundle_instances_info($entity_type, $bundle) {
-  $instances = array();
-
-  // ORGANISM.
-  //===============
-  if (isset($bundle->data_table) AND ($bundle->data_table == 'organism')) {
-    $field_name = 's__c';
-    $field_type = 's__c';
-    $instances[$field_name] =  array(
-      'field_name' => $field_name,
-      'entity_type' => $entity_type,
-      'bundle' => $bundle->name,
-      'label' => 'd',
-      'description' => 'f',
-      'required' => FALSE,
-      'settings' => array(
-        'auto_attach' => FALSE,
-        'chado_table' => $bundle->data_table,
-        'chado_column' => 'organism_id',
-        'base_table' => $bundle->data_table,
-      ),
-      'widget' => array(
-        'type' => 's__c_widget',
-        'settings' => array(),
-      ),
-      'display' => array(
-        'default' => array(
-          'label' => 'hidden',
-          'type' => 's__c_formatter',
-          'settings' => array(),
-        ),
-      ),
-    );
-
-  }
-
-  return $instances;
-}
diff --git a/s__c_output/s__c/s__c.inc b/s__c_output/s__c/s__c.inc
deleted file mode 100644
index 9298c7a..0000000
--- a/s__c_output/s__c/s__c.inc
+++ /dev/null
@@ -1,128 +0,0 @@
-<?php
-/**
- * @class
- * Purpose:
- *
- * Data:
- * Assumptions:
- */
-class s__c extends ChadoField {
-
-  // --------------------------------------------------------------------------
-  //                     EDITABLE STATIC CONSTANTS
-  //
-  // The following constants SHOULD be set for each descendant class.  They are
-  // used by the static functions to provide information to Drupal about
-  // the field and it's default widget and formatter.
-  // --------------------------------------------------------------------------
-
-  // The default label for this field.
-  public static $default_label = 'd';
-
-  // The default description for this field.
-  public static $default_description = 'f';
-
-  // The default widget for this field.
-  public static $default_widget = 's__c_widget';
-
-  // The default formatter for this field.
-  public static $default_formatter = 's__c_formatter';
-
-  // The module that manages this field.
-  public static $module = 'g';
-
-  // A list of global settings. These can be accessed within the
-  // globalSettingsForm.  When the globalSettingsForm is submitted then
-  // Drupal will automatically change these settings for all fields.
-  // Once instances exist for a field type then these settings cannot be
-  // changed.
-  public static $default_settings = array(
-    'storage' => 'field_chado_storage',
-     // It is expected that all fields set a 'value' in the load() function.
-     // In many cases, the value may be an associative array of key/value pairs.
-     // In order for Tripal to provide context for all data, the keys should
-     // be a controlled vocabulary term (e.g. rdfs:type). Keys in the load()
-     // function that are supported by the query() function should be
-     // listed here.
-     'searchable_keys' => array(),
-  );
-
-  // Provide a list of instance specific settings. These can be access within
-  // the instanceSettingsForm.  When the instanceSettingsForm is submitted
-  // then Drupal with automatically change these settings for the instance.
-  // It is recommended to put settings at the instance level whenever possible.
-  // If you override this variable in a child class be sure to replicate the
-  // term_name, term_vocab, term_accession and term_fixed keys as these are
-  // required for all TripalFields.
-  public static $default_instance_settings = array(
-    // The DATABASE name, as it appears in chado.db.  This also builds the link-out url.  In most cases this will simply be the CV name.  In some cases (EDAM) this will be the SUBONTOLOGY.
-    'term_vocabulary' => 's',
-    // The name of the term.
-    'term_name' => 'c',
-    // The unique ID (i.e. accession) of the term.
-    'term_accession' => 'd',
-    // Set to TRUE if the site admin is not allowed to change the term
-    // type, otherwise the admin can change the term mapped to a field.
-    'term_fixed' => FALSE,
-    // Indicates if this field should be automatically attached to display
-    // or web services or if this field should be loaded separately. This
-    // is convenient for speed.  Fields that are slow should for loading
-    // should have auto_attach set to FALSE so tha their values can be
-    // attached asynchronously.
-    'auto_attach' => FALSE,
-    // The table in Chado that the instance maps to.
-    'chado_table' => 'organism',
-    // The column of the table in Chado where the value of the field comes from.
-    'chado_column' => 'organism_id',
-    // The base table.
-    'base_table' => 'organism',
-  );
-
-  // A boolean specifying that users should not be allowed to create
-  // fields and instances of this field type through the UI. Such
-  // fields can only be created programmatically with field_create_field()
-  // and field_create_instance().
-  public static $no_ui = FALSE;
-
-  // A boolean specifying that the field will not contain any data. This
-  // should exclude the field from web services or downloads.  An example
-  // could be a quick search field that appears on the page that redirects
-  // the user but otherwise provides no data.
-  public static $no_data = FALSE;
-
- /**
-   * Loads the field values from the underlying data store.
-   *
-   * @param $entity
-   *
-   * @return
-   *   An array of the following format:
-   *     $entity->{$field_name}['und'][0]['value'] = $value;
-   *   where:
-   *     - $entity is the entity object to which this field is attached.
-   *     - $field_name is the name of this field
-   *     - 'und' is the language code (in this case 'und' == undefined)
-   *     - 0 is the cardinality.  Increment by 1 when more than one item is
-   *       available.
-   *     - 'value' is the key indicating the value of this field. It should
-   *       always be set.  The value of the 'value' key will be the contents
-   *       used for web services and for downloadable content.  The value
-   *       should be of the follow format types: 1) A single value (text,
-   *       numeric, etc.) 2) An array of key value pair. 3) If multiple entries
-   *       then cardinality should incremented and format types 1 and 2 should
-   *       be used for each item.
-   *   The array may contain as many other keys at the same level as 'value'
-   *   but those keys are for internal field use and are not considered the
-   *   value of the field.
-   *
-   *
-   */
-  public function load($entity) {
-
-    // ChadoFields automatically load the chado column specified in the
-    // default settings above. If that is all you need then you don't even
-    // need to implement this function. However, if you need to add any
-    // additional data to be used in the display, you should add it here.
-    parent::load($entity);
-  }
-}
\ No newline at end of file
diff --git a/s__c_output/s__c/s__c_formatter.inc b/s__c_output/s__c/s__c_formatter.inc
deleted file mode 100644
index bdcd8d0..0000000
--- a/s__c_output/s__c/s__c_formatter.inc
+++ /dev/null
@@ -1,119 +0,0 @@
-<?php
-/**
- * @class
- * Purpose:
- *
- * Display:
- * Configuration:
- */
-class s__c_formatter extends ChadoFieldFormatter {
-
-  // The default label for this field.
-  public static $default_label = 'd';
-
-  // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('s__c');
-
-  // The list of default settings for this formatter.
-  public static $default_settings = array(
-    'setting1' => 'default_value',
-  );
-
-  /**
-   * Provides the field's setting form.
-   *
-   * This function corresponds to the hook_field_formatter_settings_form()
-   * function of the Drupal Field API.
-   *
-   * The settings form appears on the 'Manage Display' page of the content
-   * type administration page. This function provides the form that will
-   * appear on that page.
-   *
-   * To add a validate function, please create a static function in the
-   * implementing class, and indicate that this function should be used
-   * in the form array that is returned by this function.
-   *
-   * This form will not be displayed if the formatter_settings_summary()
-   * function does not return anything.
-   *
-   * param $field
-   *   The field structure being configured.
-   * param $instance
-   *   The instance structure being configured.
-   * param $view_mode
-   *   The view mode being configured.
-   * param $form
-   *   The (entire) configuration form array, which will usually have no use
-   *   here.  Typically for reference only.
-   * param $form_state
-   *   The form state of the (entire) configuration form.
-   *
-   * @return
-   *   A Drupal Form array containing the settings form for this field.
-   */
-  public function settingsForm($view_mode, $form, &$form_state) {
-
-  }
-
-  /**
-   *  Provides the display for a field
-   *
-   * This function corresponds to the hook_field_formatter_view()
-   * function of the Drupal Field API.
-   *
-   *  This function provides the display for a field when it is viewed on
-   *  the web page.  The content returned by the formatter should only include
-   *  what is present in the $items[$delta]['values] array. This way, the
-   *  contents that are displayed on the page, via webservices and downloaded
-   *  into a CSV file will always be identical.  The view need not show all
-   *  of the data in the 'values' array.
-   *
-   *  @param $element
-   *  @param $entity_type
-   *  @param $entity
-   *  @param $langcode
-   *  @param $items
-   *  @param $display
-   *
-   *  @return
-   *    An element array compatible with that returned by the
-   *    hook_field_formatter_view() function.
-   */
-  public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
-    // Get the settings
-    $settings = $display['settings'];
-  }
-
-  /**
-   * Provides a summary of the formatter settings.
-   *
-   * This function corresponds to the hook_field_formatter_settings_summary()
-   * function of the Drupal Field API.
-   *
-   * On the 'Manage Display' page of the content type administration page,
-   * fields are allowed to provide a settings form.  This settings form can
-   * be used to allow the site admin to define how the field should be
-   * formatted.  The settings are then available for the formatter()
-   * function of this class.  This function provides a text-based description
-   * of the settings for the site developer to see.  It appears on the manage
-   * display page inline with the field.  A field must always return a
-   * value in this function if the settings form gear button is to appear.
-   *
-   * See the hook_field_formatter_settings_summary() function for more
-   * information.
-   *
-   * @param $field
-   * @param $instance
-   * @param $view_mode
-   *
-   * @return string
-   *   A string that provides a very brief summary of the field settings
-   *   to the user.
-   *
-   */
-  public function settingsSummary($view_mode) {
-    return '';
-  }
-
-}
\ No newline at end of file
diff --git a/s__c_output/s__c/s__c_widget.inc b/s__c_output/s__c/s__c_widget.inc
deleted file mode 100644
index 25a9a4a..0000000
--- a/s__c_output/s__c/s__c_widget.inc
+++ /dev/null
@@ -1,122 +0,0 @@
-<?php
-/**
- * @class
- * Purpose:
- *
- * Allowing edit?
- * Data:
- * Assumptions:
- */
-class s__c_widget extends ChadoFieldWidget {
-
-  // The default label for this field.
-  public static $default_label = 'd';
-
-  // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('s__c');
-
-  /**
-   * Provides the form for editing of this field.
-   *
-   * This function corresponds to the hook_field_widget_form()
-   * function of the Drupal Field API.
-   *
-   * This form is diplayed when the user creates a new entity or edits an
-   * existing entity.  If the field is attached to the entity then the form
-   * provided by this function will be displayed.
-   *
-   * At a minimum, the form must have a 'value' element.  For Tripal, the
-   * 'value' element of a field always corresponds to the value that is
-   * presented to the end-user either directly on the page (with formatting)
-   * or via web services, or some other mechanism.  However, the 'value' is
-   * sometimes not enough for a field.  For example, the Tripal Chado module
-   * maps fields to table columns and sometimes those columns are foreign keys
-   * therefore, the Tripal Chado modules does not just use the 'value' but adds
-   * additional elements to help link records via FKs.  But even in this case
-   * the 'value' element must always be present in the return form and in such
-   * cases it's value should be set equal to that added in the 'load' function.
-   *
-   * @param $widget
-   * @param $form
-   *   The form structure where widgets are being attached to. This might be a
-   *   full form structure, or a sub-element of a larger form.
-   * @param $form_state
-   *   An associative array containing the current state of the form.
-   * @param $langcode
-   *   The language associated with $items.
-   * @param $items
-   *   Array of default values for this field.
-   * @param $delta
-   *   The order of this item in the array of subelements (0, 1, 2, etc).
-   * @param $element
-   * A form element array containing basic properties for the widget:
-   *  - #entity_type: The name of the entity the field is attached to.
-   *  - #bundle: The name of the field bundle the field is contained in.
-   *  - #field_name: The name of the field.
-   *  - #language: The language the field is being edited in.
-   *  - #field_parents: The 'parents' space for the field in the form. Most
-   *    widgets can simply overlook this property. This identifies the location
-   *    where the field values are placed within $form_state['values'], and is
-   *    used to access processing information for the field through the
-   *    field_form_get_state() and field_form_set_state() functions.
-   *  - #columns: A list of field storage columns of the field.
-   *  - #title: The sanitized element label for the field instance, ready for
-   *    output.
-   *  - #description: The sanitized element description for the field instance,
-   *    ready for output.
-   *  - #required: A Boolean indicating whether the element value is required;
-   *    for required multiple value fields, only the first widget's values are
-   *    required.
-   *  - #delta: The order of this item in the array of subelements; see
-   *    $delta above
-   */
-  public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
-  }
-
-  /**
-   * Performs validation of the widgetForm.
-   *
-   * Use this validate to ensure that form values are entered correctly.
-   * The 'value' key of this field must be set in the $form_state['values']
-   * array anytime data is entered by the user.  It may be the case that there
-   * are other fields for helping select a value. In the end those helper
-   * fields must be used to set the 'value' field.
-   */
-  public function validate($element, $form, &$form_state, $langcode, $delta) {
-  }
-
-  /**
-   * Performs extra commands when the entity form is submitted.
-   *
-   * Drupal typically does not provide a submit hook for fields.  The
-   * TripalField provides one to allow for behind-the-scenes actions to
-   * occur.   This function should never be used for updates, deletes or
-   * inserts for the Chado table associated with the field.  Rather, the
-   * storage backend should be allowed to handle inserts, updates deletes.
-   * However, it is permissible to perform inserts, updates or deletions within
-   * Chado using this function.  Those operations can be performed if needed but
-   * on other tables not directly associated with the field.
-   *
-   * An example is the chado.feature_synonym table.  The chado_linker__synonym
-   * field allows the user to provide a brand new synonynm and it must add it
-   * to the chado.synonym table prior to the record in the
-   * chado.feature_synonym table.  This insert occurs in the widgetFormSubmit
-   * function.
-   *
-   * @param $form
-   *    The submitted form array.
-   * @param $form_state .
-   *    The form state array.
-   * @param $entity_type
-   *    The type of $entity.
-   * @param $entity
-   *    The entity for the operation.
-   * @param $langcode
-   *    The language associated with $items.
-   * @param $delta
-   */
-  public function submit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-  }
-
-}
\ No newline at end of file