From cc5894656ffc89e9313988e44087f383f5c5dcf1 Mon Sep 17 00:00:00 2001
From: Lacey Sanderson <laceyannesanderson@gmail.com>
Date: Sun, 31 Mar 2024 14:22:50 -0600
Subject: [PATCH] Add missing services for blast programs.

---
 src/Services/TripalBlastProgramBlastp.php  | 63 ++++++++++++++++++++++
 src/Services/TripalBlastProgramBlastx.php  | 62 +++++++++++++++++++++
 src/Services/TripalBlastProgramTblastn.php | 63 ++++++++++++++++++++++
 tripal_blast.services.yml                  | 12 +++--
 4 files changed, 197 insertions(+), 3 deletions(-)
 create mode 100644 src/Services/TripalBlastProgramBlastp.php
 create mode 100644 src/Services/TripalBlastProgramBlastx.php
 create mode 100644 src/Services/TripalBlastProgramTblastn.php

diff --git a/src/Services/TripalBlastProgramBlastp.php b/src/Services/TripalBlastProgramBlastp.php
new file mode 100644
index 0000000..83d39e9
--- /dev/null
+++ b/src/Services/TripalBlastProgramBlastp.php
@@ -0,0 +1,63 @@
+<?php
+/**
+ * @file
+ * Form definition of BLASTp program.
+ */
+
+namespace Drupal\tripal_blast\Services;
+
+use Drupal\tripal_blast\Services\TripalBlastProgramHelper;
+
+/**
+ * BLASTp program class.
+ */
+class TripalBlastProgramBlastp {
+  const BLASTp = 'blastp';
+
+  /**
+   * Advanced field names used - refer to this value when
+   * validating and submitting fields under advanced options.
+   */
+  public function formFieldNames() {
+    // Keys match field names used in form definition below.
+    $field_name_validator = [];
+    return $field_name_validator;
+  }
+
+  /**
+   * Adds the BLASTp Advanced Options to the passed in form.
+   * This form function is meant to be called within another form definition.
+   *
+   * @param $blast_cache
+   *   BLAST job history to reference information information contained.
+   *
+   * @return array
+   *   Additional form field definitions.
+   */
+  public function formOptions($blast_cache) {
+    $blast = self::BLASTp;
+
+    // Edit and Resubmit functionality.
+    // We want to pull up the details from a previous blast and fill them in as defaults
+    // for this blast.
+    $options = (isset($blast_cache)) ? $blast_cache : [];
+    $defaults = TripalBlastProgramHelper::programGetDefaultValues($options, $blast);
+
+    $form_alter = [];
+
+    return $form_alter;
+  }
+
+  /**
+   * Map advanced options specific to this program to BLAST keywords.
+   *
+   * @param $advanced_field_names
+   *   Values set from form ($form_state).
+   *
+   * @return array
+   *   Form values mapped to BLAST keywords.
+   */
+  public function formFieldBlastKey($advanced_field_values) {
+    return [];
+  }
+}
diff --git a/src/Services/TripalBlastProgramBlastx.php b/src/Services/TripalBlastProgramBlastx.php
new file mode 100644
index 0000000..8b11752
--- /dev/null
+++ b/src/Services/TripalBlastProgramBlastx.php
@@ -0,0 +1,62 @@
+<?php
+/**
+ * @file
+ * Form definition of BLASTx program.
+ */
+
+namespace Drupal\tripal_blast\Services;
+
+use Drupal\tripal_blast\Services\TripalBlastProgramHelper;
+
+/**
+ * BLASTx program class.
+ */
+class TripalBlastProgramBlastx {
+  const BLASTx = 'blastx';
+
+  /**
+   * Advanced field names used - refer to this value when
+   * validating and submitting fields under advanced options.
+   */
+  public function formFieldNames() {
+    // Keys match field names used in form definition below.
+    $field_name_validator = [];
+    return $field_name_validator;
+  }
+
+  /**
+   * Adds the BLASTx Advanced Options to the passed in form.
+   * This form function is meant to be called within another form definition.
+   *
+   * @param $blast_cache
+   *   BLAST job history to reference information information contained.
+   *
+   * @return array
+   *   Additional form field definitions.
+   */
+  public function formOptions($blast_cache) {
+    $blast = self::BLASTx;
+
+    // Edit and Resubmit functionality.
+    // We want to pull up the details from a previous blast and fill them in as defaults
+    // for this blast.
+    $options = (isset($blast_cache)) ? $blast_cache : [];
+    $defaults = TripalBlastProgramHelper::programGetDefaultValues($options, $blast);
+
+    $form_alter = [];
+    return $form_alter;
+  }
+
+  /**
+   * Map advanced options specific to this program to BLAST keywords.
+   *
+   * @param $advanced_field_names
+   *   Values set from form ($form_state).
+   *
+   * @return array
+   *   Form values mapped to BLAST keywords.
+   */
+  public function formFieldBlastKey($advanced_field_values) {
+    return [];
+  }
+}
diff --git a/src/Services/TripalBlastProgramTblastn.php b/src/Services/TripalBlastProgramTblastn.php
new file mode 100644
index 0000000..dd3ac6a
--- /dev/null
+++ b/src/Services/TripalBlastProgramTblastn.php
@@ -0,0 +1,63 @@
+<?php
+/**
+ * @file
+ * Form definition of tBLASTn program.
+ */
+
+namespace Drupal\tripal_blast\Services;
+
+use Drupal\tripal_blast\Services\TripalBlastProgramHelper;
+
+/**
+ * tBLASTn program class.
+ */
+class TripalBlastProgramTblastn {
+  const tBLASTn = 'tblastn';
+
+  /**
+   * Advanced field names used - refer to this value when
+   * validating and submitting fields under advanced options.
+   */
+  public function formFieldNames() {
+    // Keys match field names used in form definition below.
+    $field_name_validator = [];
+    return $field_name_validator;
+  }
+
+  /**
+   * Adds the tBLASTn Advanced Options to the passed in form.
+   * This form function is meant to be called within another form definition.
+   *
+   * @param $blast_cache
+   *   BLAST job history to reference information information contained.
+   *
+   * @return array
+   *   Additional form field definitions.
+   */
+  public function formOptions($blast_cache) {
+    $blast = self::tBLASTn;
+
+    // Edit and Resubmit functionality.
+    // We want to pull up the details from a previous blast and fill them in as defaults
+    // for this blast.
+    $options = (isset($blast_cache)) ? $blast_cache : [];
+    $defaults = TripalBlastProgramHelper::programGetDefaultValues($options, $blast);
+
+    $form_alter = [];
+
+    return $form_alter;
+  }
+
+  /**
+   * Map advanced options specific to this program to BLAST keywords.
+   *
+   * @param $advanced_field_names
+   *   Values set from form ($form_state).
+   *
+   * @return array
+   *   Form values mapped to BLAST keywords.
+   */
+  public function formFieldBlastKey($advanced_field_values) {
+    return [];
+  }
+}
diff --git a/tripal_blast.services.yml b/tripal_blast.services.yml
index 93f36e1..449ead3 100644
--- a/tripal_blast.services.yml
+++ b/tripal_blast.services.yml
@@ -3,8 +3,14 @@
 
 services:
   tripal_blast.database_service:
-    class: Drupal\tripal_blast\Services\TripalBlastDatabaseService  
+    class: Drupal\tripal_blast\Services\TripalBlastDatabaseService
   tripal_blast.job_service:
-    class: Drupal\tripal_blast\Services\TripalBlastJobService    
+    class: Drupal\tripal_blast\Services\TripalBlastJobService
   tripal_blast.program_blastn:
-    class: Drupal\tripal_blast\Services\TripalBlastProgramBlastn
\ No newline at end of file
+    class: Drupal\tripal_blast\Services\TripalBlastProgramBlastn
+  tripal_blast.program_blastx:
+    class: Drupal\tripal_blast\Services\TripalBlastProgramBlastx
+  tripal_blast.program_tblastn:
+    class: Drupal\tripal_blast\Services\TripalBlastProgramTblastn
+  tripal_blast.program_blastp:
+    class: Drupal\tripal_blast\Services\TripalBlastProgramBlastp