Add Custom Default Annotation Value Filters at Project Level

These override the Search level Default Annotation Value Filters set in the Proxl XML file and set at import.
yeastrc · Jun 20, 2019 · 7193993 · 7193993
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commit 7193993
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diff --git a/database_scripts/MySQL_Workbench_Model/Proxl_Database_MySQL_Workbench_Model.mwb b/database_scripts/MySQL_Workbench_Model/Proxl_Database_MySQL_Workbench_Model.mwb
diff --git a/database_scripts/install/create_empty_database.sql b/database_scripts/install/create_empty_database.sql
@@ -2559,9 +2559,101 @@ CREATE TABLE  proxl_xml_file_import_submit_import_program_key_per_user_history (
 ENGINE = InnoDB;
 
 
-SET SQL_MODE=@OLD_SQL_MODE;
-SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS;
-SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS;
+-- -----------------------------------------------------
+-- Table project_level_default_fltr_ann_cutoffs_tbl
+-- -----------------------------------------------------
+DROP TABLE IF EXISTS project_level_default_fltr_ann_cutoffs_tbl ;
+
+CREATE TABLE  project_level_default_fltr_ann_cutoffs_tbl (
+  id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+  project_id INT(10) UNSIGNED NOT NULL,
+  search_program_name VARCHAR(200) NOT NULL,
+  psm_peptide_type ENUM('psm', 'peptide', 'psm_per_peptide') NOT NULL,
+  annotation_type_name VARCHAR(255) NOT NULL,
+  annotation_cutoff_value DOUBLE NOT NULL,
+  created_auth_user_id INT UNSIGNED NOT NULL,
+  created_date_time DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+  last_updated_auth_user_id INT NOT NULL,
+  last_updated_date_time DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
+  PRIMARY KEY (id),
+  CONSTRAINT prj_lvl_dfltfltr_ann_ctffs
+    FOREIGN KEY (project_id)
+    REFERENCES project (id)
+    ON DELETE CASCADE
+    ON UPDATE NO ACTION)
+ENGINE = InnoDB
+COMMENT = 'User Entered Annotation Cutoffs that apply to all searches in the project';
+
+CREATE UNIQUE INDEX unique_record_index ON project_level_default_fltr_ann_cutoffs_tbl (project_id ASC, search_program_name ASC, psm_peptide_type ASC, annotation_type_name ASC);
+
+
+-- -----------------------------------------------------
+-- Table project_level_default_fltr_ann_cutoffs_cutoff_as_string_tbl
+-- -----------------------------------------------------
+DROP TABLE IF EXISTS project_level_default_fltr_ann_cutoffs_cutoff_as_string_tbl ;
+
+CREATE TABLE  project_level_default_fltr_ann_cutoffs_cutoff_as_string_tbl (
+  project_level_default_fltr_ann_cutoffs_id INT(10) UNSIGNED NOT NULL,
+  annotation_cutoff_value_string VARCHAR(45) NOT NULL,
+  PRIMARY KEY (project_level_default_fltr_ann_cutoffs_id),
+  CONSTRAINT prj_lvl_dfltfltr_ann_ctffs_as_str_fk
+    FOREIGN KEY (project_level_default_fltr_ann_cutoffs_id)
+    REFERENCES project_level_default_fltr_ann_cutoffs_tbl (id)
+    ON DELETE CASCADE
+    ON UPDATE NO ACTION)
+ENGINE = InnoDB;
+
+
+-- -----------------------------------------------------
+-- Table project_level_default_fltr_ann_cutoffs_prev_tbl
+-- -----------------------------------------------------
+DROP TABLE IF EXISTS project_level_default_fltr_ann_cutoffs_prev_tbl ;
+
+CREATE TABLE  project_level_default_fltr_ann_cutoffs_prev_tbl (
+  id INT(10) UNSIGNED NOT NULL,
+  project_id INT(10) UNSIGNED NOT NULL,
+  psm_peptide_type ENUM('psm', 'peptide', 'psm_per_peptide') NOT NULL,
+  search_program_name VARCHAR(200) NOT NULL,
+  annotation_type_name VARCHAR(255) NOT NULL,
+  annotation_cutoff_value DOUBLE NOT NULL,
+  created_auth_user_id INT UNSIGNED NOT NULL,
+  created_date_time DATETIME NOT NULL,
+  last_updated_auth_user_id INT NOT NULL,
+  last_updated_date_time DATETIME NOT NULL,
+  id_prev_record INT NOT NULL AUTO_INCREMENT,
+  copy_create_date DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+  PRIMARY KEY (id_prev_record),
+  CONSTRAINT prj_lvl_dfltfltr_ann_ctffs_prv
+    FOREIGN KEY (project_id)
+    REFERENCES project (id)
+    ON DELETE CASCADE
+    ON UPDATE NO ACTION)
+ENGINE = InnoDB
+COMMENT = 'Prev data - User Entered Annotation Cutoffs that apply to all searches in the project';
+
+CREATE INDEX id_idex ON project_level_default_fltr_ann_cutoffs_prev_tbl (id ASC);
+
+
+-- -----------------------------------------------------
+-- Table project_level_default_fltr_ann_cutoffs_cutoff_as_string_prev_tbl
+-- -----------------------------------------------------
+DROP TABLE IF EXISTS project_level_default_fltr_ann_cutoffs_cutoff_as_string_prev_tbl ;
+
+CREATE TABLE  project_level_default_fltr_ann_cutoffs_cutoff_as_string_prev_tbl (
+  project_level_default_fltr_ann_cutoffs_id INT(10) UNSIGNED NOT NULL,
+  annotation_cutoff_value_string VARCHAR(45) NOT NULL,
+  id_prev_record INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+  project_id INT(10) UNSIGNED NOT NULL,
+  PRIMARY KEY (id_prev_record),
+  CONSTRAINT prj_lvl_dfltfltr_ann_ctffs_as_str_prev_fk
+    FOREIGN KEY (project_id)
+    REFERENCES project (id)
+    ON DELETE CASCADE
+    ON UPDATE NO ACTION)
+ENGINE = InnoDB;
+
+CREATE INDEX prj_lvl_dfltfltr_ann_ctffs_as_str_prev_fk_idx ON project_level_default_fltr_ann_cutoffs_cutoff_as_string_prev_tbl (project_id ASC);
+
 
 
 DELIMITER $$
@@ -2583,3 +2675,7 @@ END$$
 
 DELIMITER ;
 
+SET SQL_MODE=@OLD_SQL_MODE;
+SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS;
+SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS;
+
diff --git a/database_scripts/upgrades/2019_06_Update_1__add__project_level_default_fltr_ann_cutoffs.txt b/database_scripts/upgrades/2019_06_Update_1__add__project_level_default_fltr_ann_cutoffs.txt
@@ -0,0 +1,75 @@
+
+--  2019_06_Update_1__add__project_level_default_fltr_ann_cutoffs.txt
+
+CREATE TABLE  project_level_default_fltr_ann_cutoffs_tbl (
+  id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+  project_id INT(10) UNSIGNED NOT NULL,
+  search_program_name VARCHAR(200) NOT NULL,
+  psm_peptide_type ENUM('psm', 'peptide', 'psm_per_peptide') NOT NULL,
+  annotation_type_name VARCHAR(255) NOT NULL,
+  annotation_cutoff_value DOUBLE NOT NULL,
+  created_auth_user_id INT UNSIGNED NOT NULL,
+  created_date_time DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+  last_updated_auth_user_id INT NOT NULL,
+  last_updated_date_time DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
+  PRIMARY KEY (id),
+  UNIQUE INDEX unique_record_index (project_id ASC, search_program_name ASC, psm_peptide_type ASC, annotation_type_name ASC),
+  CONSTRAINT prj_lvl_dfltfltr_ann_ctffs
+    FOREIGN KEY (project_id)
+    REFERENCES project (id)
+    ON DELETE CASCADE
+    ON UPDATE NO ACTION)
+ENGINE = InnoDB
+COMMENT = 'User Entered Annotation Cutoffs that apply to all searches i' /* comment truncated */ /*n the project*/;
+
+
+CREATE TABLE  project_level_default_fltr_ann_cutoffs_cutoff_as_string_tbl (
+  project_level_default_fltr_ann_cutoffs_id INT(10) UNSIGNED NOT NULL,
+  annotation_cutoff_value_string VARCHAR(45) NOT NULL,
+  PRIMARY KEY (project_level_default_fltr_ann_cutoffs_id),
+  CONSTRAINT prj_lvl_dfltfltr_ann_ctffs_as_str_fk
+    FOREIGN KEY (project_level_default_fltr_ann_cutoffs_id)
+    REFERENCES project_level_default_fltr_ann_cutoffs_tbl (id)
+    ON DELETE CASCADE
+    ON UPDATE NO ACTION)
+ENGINE = InnoDB;
+
+
+CREATE TABLE  project_level_default_fltr_ann_cutoffs_prev_tbl (
+  id INT(10) UNSIGNED NOT NULL,
+  project_id INT(10) UNSIGNED NOT NULL,
+  psm_peptide_type ENUM('psm', 'peptide', 'psm_per_peptide') NOT NULL,
+  search_program_name VARCHAR(200) NOT NULL,
+  annotation_type_name VARCHAR(255) NOT NULL,
+  annotation_cutoff_value DOUBLE NOT NULL,
+  created_auth_user_id INT UNSIGNED NOT NULL,
+  created_date_time DATETIME NOT NULL,
+  last_updated_auth_user_id INT NOT NULL,
+  last_updated_date_time DATETIME NOT NULL,
+  id_prev_record INT NOT NULL AUTO_INCREMENT,
+  copy_create_date DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+  PRIMARY KEY (id_prev_record),
+  INDEX id_idex (id ASC),
+  CONSTRAINT prj_lvl_dfltfltr_ann_ctffs_prv
+    FOREIGN KEY (project_id)
+    REFERENCES project (id)
+    ON DELETE CASCADE
+    ON UPDATE NO ACTION)
+ENGINE = InnoDB
+COMMENT = 'Prev data - User Entered Annotation Cutoffs that apply to al' /* comment truncated */ /*l searches in the project*/;
+
+CREATE TABLE project_level_default_fltr_ann_cutoffs_cutoff_as_string_prev_tbl (
+  project_level_default_fltr_ann_cutoffs_id INT(10) UNSIGNED NOT NULL,
+  annotation_cutoff_value_string VARCHAR(45) NOT NULL,
+  id_prev_record INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
+  project_id INT(10) UNSIGNED NOT NULL,
+  PRIMARY KEY (id_prev_record),
+  INDEX prj_lvl_dfltfltr_ann_ctffs_as_str_prev_fk_idx (project_id ASC),
+  CONSTRAINT prj_lvl_dfltfltr_ann_ctffs_as_str_prev_fk
+    FOREIGN KEY (project_id)
+    REFERENCES project (id)
+    ON DELETE CASCADE
+    ON UPDATE NO ACTION)
+ENGINE = InnoDB;
+
+
diff --git a/proxl_web_app/front_end/build.gradle b/proxl_web_app/front_end/build.gradle
@@ -159,13 +159,16 @@ task createHandlebarsOutputDirs {
 
   	  dirToCreate = rootDir + "project_page__saved_views_section"
   	  mkdirSuccess = project.file( dirToCreate ).mkdirs()
-
-  	  dirToCreate = rootDir + "project_page__saved_views_section_loggedin_users"
+  	    	  
+  	  dirToCreate = rootDir + "project_page__saved_views_section"
   	  mkdirSuccess = project.file( dirToCreate ).mkdirs()
 
   	  dirToCreate = rootDir + "project_page__share_data_section_loggedin_users"
   	  mkdirSuccess = project.file( dirToCreate ).mkdirs()
 
+  	  dirToCreate = rootDir + "project_page__ann_cutoff_defaults_project_level"
+  	  mkdirSuccess = project.file( dirToCreate ).mkdirs()
+
   	  dirToCreate = rootDir + "project_list"
   	  mkdirSuccess = project.file( dirToCreate ).mkdirs()
 
@@ -689,6 +692,29 @@ task handlebarsPrecompile_project_page__share_data_section_loggedin_users(type:
    ]
 }
 
+//  Handlebars Precompile for input handlebars_templates/project_page__ann_cutoff_defaults_project_level
+
+task handlebarsPrecompile_project_page__ann_cutoff_defaults_project_level(type: NodeTask) {
+
+  def precompile_Input_Directory = "handlebars_templates/project_page__ann_cutoff_defaults_project_level"
+  def precompile_Output_File = "handlebars_templates_precompiled/project_page__ann_cutoff_defaults_project_level/project_page__ann_cutoff_defaults_project_level_template-bundle.js"
+
+  // Gradle Build Avoidance information.  Must specify correct inputs and outputs.
+  inputs.dir( precompile_Input_Directory )
+  outputs.file( precompile_Output_File )
+
+  def osName = System.getProperty("os.name").toLowerCase();
+  if (osName.contains("windows")) {
+    script = project.file('node_modules/handlebars/bin/handlebars')
+  } else {
+    script = project.file('node_modules/.bin/handlebars')
+  }
+  args = [ '--amd' , // parameters must be before file list
+  '--min',
+  '-f', precompile_Output_File,
+   precompile_Input_Directory
+   ]
+}
 
 //  Handlebars Precompile for input handlebars_templates/project_list
 
@@ -844,6 +870,7 @@ task frontEndBuild(type: GradleBuild) {
      'handlebarsPrecompile_project_page__share_data_section_loggedin_users',
      'handlebarsPrecompile_project_page__saved_views_section',
      'handlebarsPrecompile_project_page__saved_views_section_loggedin_users',
+     'handlebarsPrecompile_project_page__ann_cutoff_defaults_project_level',
      'handlebarsPrecompile_save_view',
      'handlebarsPrecompile_merged_pages_shared',
      'handlebarsPrecompile_peptide_page',

diff --git a/...t_level/project_page__ann_cutoff_defaults_project_level_overlay_ann_type_entry.handlebars b/...t_level/project_page__ann_cutoff_defaults_project_level_overlay_ann_type_entry.handlebars
@@ -0,0 +1,30 @@
+{{!-- project_page__ann_cutoff_defaults_project_level_overlay_ann_type_entry.handlebars in 'project_page__ann_cutoff_defaults_project_level'
+
+	Project Page - Set Annotation Defaults at Project Level Overlay Root
+
+    Annotation Type Entry
+	
+--}}
+
+<tr class=" selector_ann_type_containing_row ">
+    <td  style="padding-left: 20px;">{{ annType_Entry.annTypeName }}</td>
+    <td style="padding-right: 10px;">
+        <input type="text" maxlength="30" style="width: 150px;"
+            data-peptide_psm="{{ peptidePSM }}"
+            data-index_per_type="{{ annType_Entry.indexPerType }}" 
+            data-index_overall="{{ annType_Entry.indexOverall }}"
+            class=" {{ cssSelectorClasses }} "
+            value="{{ annType_Entry.existingCutoffValue  }}">
+    </td>
+    <td>
+        <div class=" selector_found_values ">
+            {{#if annType_Entry.foundValuesString }}
+                Found: 
+                {{ annType_Entry.foundValuesString }}
+            {{/if}}
+        </div>
+        <div class=" error-text selector_invalid_entry " style=" display: none;" >
+            value has to be a decimal number
+        </div>
+    </td>
+</tr>
diff --git a/...oject_level/project_page__ann_cutoff_defaults_project_level_overlay_background.handlebars b/...oject_level/project_page__ann_cutoff_defaults_project_level_overlay_background.handlebars
@@ -0,0 +1,8 @@
+{{!-- project_page__ann_cutoff_defaults_project_level_overlay_background.handlebars in 'project_page__ann_cutoff_defaults_project_level'
+
+	Project Page - Set Annotation Defaults at Project Level Overlay Background
+	
+--}}
+<div id="project_page__ann_cutoff_defaults_project_level_overlay_background"
+     class="project-level-ann-cutoff-defaults-modal-dialog-overlay-background" >
+</div>
diff --git a/...ject_page__ann_cutoff_defaults_project_level_overlay_peptide_list_header_entry.handlebars b/...ject_page__ann_cutoff_defaults_project_level_overlay_peptide_list_header_entry.handlebars
@@ -0,0 +1,14 @@
+{{!-- project_page__ann_cutoff_defaults_project_level_overlay_peptide_list_header_entry.handlebars in 'project_page__ann_cutoff_defaults_project_level'
+
+	Project Page - Set Annotation Defaults at Project Level Overlay Root
+
+    Peptide List Entry
+	
+--}}
+<tr>
+    <td colspan="3">
+        <div style="margin-left: 10px; font-weight: bold;">
+            Peptide filters
+        </div>
+    </td>
+</tr>
diff --git a/.../project_page__ann_cutoff_defaults_project_level_overlay_psm_list_header_entry.handlebars b/.../project_page__ann_cutoff_defaults_project_level_overlay_psm_list_header_entry.handlebars
@@ -0,0 +1,14 @@
+{{!-- project_page__ann_cutoff_defaults_project_level_overlay_psm_list_header_entry.handlebars in 'project_page__ann_cutoff_defaults_project_level'
+
+	Project Page - Set Annotation Defaults at Project Level Overlay Root
+
+    PSM List Entry
+	
+--}}
+<tr>
+    <td colspan="3">
+        <div style="margin-left: 10px; font-weight: bold;">
+            PSM filters
+        </div>
+    </td>
+</tr>
diff --git a/...lts_project_level/project_page__ann_cutoff_defaults_project_level_overlay_root.handlebars b/...lts_project_level/project_page__ann_cutoff_defaults_project_level_overlay_root.handlebars
@@ -0,0 +1,43 @@
+{{!-- project_page__ann_cutoff_defaults_project_level_overlay_root.handlebars in 'project_page__ann_cutoff_defaults_project_level'
+
+	Project Page - Set Annotation Defaults at Project Level Overlay Root
+	
+--}}
+<div id="project_page__ann_cutoff_defaults_project_level_overlay_root"
+    class=" project-level-ann-cutoff-defaults-modal-dialog-overlay-div overlay-outer-div  "
+    style=" width: 600px; "  >
+
+    <div class="project-level-ann-cutoff-defaults-modal-dialog-overlay-header" style="width:100%; " >
+
+        <h1 id="project_page__ann_cutoff_defaults_project_level_x_exit"
+             class="project-level-ann-cutoff-defaults-modal-dialog-overlay-X-for-exit-overlay " 
+            >X</h1>
+
+        <h1 class="project-level-ann-cutoff-defaults-modal-dialog-overlay-header-text" >Set Custom Filters for Project</h1>
+    </div>
+    <div class="project-level-ann-cutoff-defaults-modal-dialog-overlay-body selector_project_page__ann_cutoff_defaults_project_level_body " 
+        style="max-height: 630px; overflow-y: auto;">
+
+        <div style="margin-top: 10px; margin-bottom: 10px;">
+            <div >
+                All data in project will be filtered using these values.
+            </div>
+            <div >
+                Remove all values to disable project-level filtering.
+            </div>
+        </div>
+      <table border="0" id="project_page__ann_cutoff_defaults_project_level_main_table" class=" main-cutoffs-table " >
+        <tbody >
+        </tbody>            
+      </table>
+
+        <div style="margin-top: 10px;">
+            <input type="button" value="Save" 
+                id="project_page__ann_cutoff_defaults_project_level_save_button">&nbsp;
+
+            <input type="button" value="Cancel" 
+                id="project_page__ann_cutoff_defaults_project_level_cancel_button">
+        </div>
+    </div>
+
+</div>
diff --git a/...l/project_page__ann_cutoff_defaults_project_level_overlay_search_program_entry.handlebars b/...l/project_page__ann_cutoff_defaults_project_level_overlay_search_program_entry.handlebars
@@ -0,0 +1,15 @@
+{{!-- project_page__ann_cutoff_defaults_project_level_overlay_search_program_entry.handlebars in 'project_page__ann_cutoff_defaults_project_level'
+
+	Project Page - Set Annotation Defaults at Project Level Overlay Root
+
+    Search Program Entry
+	
+--}}
+
+<tr>
+    <td colspan="3">
+        <div style="margin-top: 10px; margin-bottom: 5px; font-weight: bold;">
+            {{ dataPerSearchProgramName_Entry.searchProgramName }}
+        </div>
+    </td>
+</tr>