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Add Default Min PSMs at Project Level
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@danjasuw
danjasuw committed Jun 25, 2019
1 parent a3983cb commit ed3bcff
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Showing 35 changed files with 950 additions and 180 deletions.
Binary file modified database_scripts/MySQL_Workbench_Model/Proxl_Database_MySQL_Workbench_Model.mwb
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41 changes: 41 additions & 0 deletions database_scripts/upgrades/2019_06_Update_2__add__project_level_default_fltr_min_psms.txt
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@@ -0,0 +1,41 @@

-- 2019_06_Update_2__add__project_level_default_fltr_min_psms.txt

CREATE TABLE IF NOT EXISTS project_level_default_fltr_min_psms_tbl (
id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
project_id INT(10) UNSIGNED NOT NULL,
min_psms INT 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 project_level_default_fltr_min_psms_tbl
FOREIGN KEY (project_id)
REFERENCES project (id)
ON DELETE CASCADE
ON UPDATE NO ACTION)
ENGINE = InnoDB
COMMENT = 'User Entered Min PSMs that apply to all searches in the proj' /* comment truncated */ /*ect*/;


CREATE TABLE project_level_default_fltr_min_psms_prev_tbl (
id INT(10) UNSIGNED NOT NULL,
project_id INT(10) UNSIGNED NOT NULL,
min_psms INT 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 UNSIGNED NOT NULL AUTO_INCREMENT,
copy_create_date DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
PRIMARY KEY (id_prev_record),
CONSTRAINT project_level_default_fltr_min_psms_prev_tbl
FOREIGN KEY (project_id)
REFERENCES project (id)
ON DELETE CASCADE
ON UPDATE NO ACTION)
ENGINE = InnoDB
COMMENT = 'User Entered Min PSMs that apply to all searches in the proj' /* comment truncated */ /*ect*/;


21 changes: 20 additions & 1 deletion ...lts_project_level/project_page__ann_cutoff_defaults_project_level_overlay_root.handlebars
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Expand Up @@ -18,16 +18,35 @@
<div class="project-level-ann-cutoff-defaults-modal-dialog-overlay-body selector_project_page__ann_cutoff_defaults_project_level_body "
style="max-height: {{ mainBodyMaxHeight }}px; overflow-y: auto;">

<div style="margin-top: 10px; margin-bottom: 10px;">
<div style="margin-top: 10px; margin-bottom: 20px;">
<div >
All data in project will be filtered using these values.
</div>
<div >
Remove all values to disable project-level filtering.
</div>
</div>

<style >
#project_page__ann_cutoff_defaults_project_level_main_table td { padding-left: 0px; }
</style>

<table border="0" id="project_page__ann_cutoff_defaults_project_level_main_table" class=" main-cutoffs-table " >
<tbody >
<tr>
<td style="font-weight: bold;">
Min PSMs
</td>
<td>
<input type="text" maxlength="30" style="width: 150px;"
id="project_page__ann_cutoff_defaults_project_level_psms_min">
</td>
<td>
<div id="project_page__ann_cutoff_defaults_project_level_psms_min_invalid_entry" class=" error-text " style=" display: none;" >
Invalid value. Must be positive integer or empty field.
</div>
</td>
</tr>
</tbody>
</table>

Expand Down
111 changes: 104 additions & 7 deletions ...js/page_js/data_pages/project_page/projectPg_setAnnotationCutoffsDefaults_ProjectLevel.js
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Original file line number Diff line number Diff line change
Expand Up @@ -297,6 +297,8 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {

const displayObjects = this._createDisplayObjectsFromWebserviceResponseData({ responseData });

const minPSMs = responseData.existingEntriesResponse.minPSMs;

const $body = $( "body" );

{
Expand Down Expand Up @@ -334,6 +336,15 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {
$overlay.appendTo( $body );
}

{
const $project_page__ann_cutoff_defaults_project_level_psms_min = $("#project_page__ann_cutoff_defaults_project_level_psms_min");
if ( $project_page__ann_cutoff_defaults_project_level_psms_min.length === 0 ) {
throw Error("No DOM element with id 'project_page__ann_cutoff_defaults_project_level_psms_min'");
}
$project_page__ann_cutoff_defaults_project_level_psms_min.val( minPSMs );
this._add_MinPSM_InputField__OnChange_Processing({ $project_page__ann_cutoff_defaults_project_level_psms_min });
}

const $project_page__ann_cutoff_defaults_project_level_main_table = $overlay.find("#project_page__ann_cutoff_defaults_project_level_main_table");
if ( $project_page__ann_cutoff_defaults_project_level_main_table.length === 0 ) {
throw Error("No DOM element with id 'project_page__ann_cutoff_defaults_project_level_main_table'");
Expand Down Expand Up @@ -449,6 +460,76 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {
}
}

////////// Validate Min PSM Value

/**
*
*/
_add_MinPSM_InputField__OnChange_Processing({ $project_page__ann_cutoff_defaults_project_level_psms_min }) {

const project_page__ann_cutoff_defaults_project_level_psms_min_DOM = $project_page__ann_cutoff_defaults_project_level_psms_min[ 0 ];

project_page__ann_cutoff_defaults_project_level_psms_min_DOM.addEventListener('input', ( eventObject ) => {
try {
eventObject.preventDefault();
// console.log("'input' fired");
const eventTarget = eventObject.target;
// const inputBoxValue = eventTarget.value;
// console.log("'input' fired. inputBoxValue: " + inputBoxValue );
const $eventTarget = $( eventTarget );
const $selector_invalid_entry = $("#project_page__ann_cutoff_defaults_project_level_psms_min_invalid_entry");
var fieldValue = $eventTarget.val();
if ( ! this._isFieldValueValidMinimumPSMValue({ fieldValue }) ) {
$selector_invalid_entry.show();

if ( this._minPSMs_Entry_Valid ) {
this._minPSMs_Entry_Valid = false;

// Value changed so update dependent items
this._update_enable_disable_SaveButton();
}
} else {
$selector_invalid_entry.hide();

if ( ! this._minPSMs_Entry_Valid ) {
this._minPSMs_Entry_Valid = true;

// Value changed so update dependent items
this._update_enable_disable_SaveButton();
}
}
return false;
} catch( e ) {
reportWebErrorToServer.reportErrorObjectToServer( { errorException : e } );
throw e;
}
});
}

_isFieldValueValidMinimumPSMValue({ fieldValue }) {
if ( fieldValue === "" ) {
return true;
}
if ( fieldValue === "0" ) {
return false;
}
// only test for valid cutoff value if not empty string
if ( ! /^[+]?(\d+)$/.test( fieldValue ) ) {
// cutoff value is not a valid integer number
return false;
}
const valueNumber = Number.parseInt( fieldValue );
if ( Number.isNaN( valueNumber ) ) {
return false;
}
if ( valueNumber < 1 ) {
return false;
}
return true;
};

////////// Validate Filterable Annotation Cutoff Value

/**
*
*/
Expand All @@ -475,7 +556,7 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {
const $selector_ann_type_containing_row = $eventTarget.closest(".selector_ann_type_containing_row");
const $selector_invalid_entry = $selector_ann_type_containing_row.find(".selector_invalid_entry");
var fieldValue = $eventTarget.val();
if ( ! this._isFieldValueValidNumber({ fieldValue }) ) {
if ( ! this._isFieldValueValidDecimalNumber({ fieldValue }) ) {
$selector_invalid_entry.show();

const indexOverall = annType_Entry.indexOverall;
Expand Down Expand Up @@ -504,7 +585,7 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {
});
}

_isFieldValueValidNumber({ fieldValue }) {
_isFieldValueValidDecimalNumber({ fieldValue }) {
if ( fieldValue === "" ) {
return true;
}
Expand All @@ -526,6 +607,8 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {
const annotationTypeDataResponse = responseData.annotationTypeDataResponse;
const existingEntriesResponse = responseData.existingEntriesResponse;

const minPSMs = existingEntriesResponse.minPSMs;

// Use objects for index so can increment the index property in called methods

const annotationTypes_Overall_Entries_AllTypes_Index_Container= { index : 0 };
Expand Down Expand Up @@ -744,7 +827,7 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {
throw Error("No DOM element with id 'project_page__ann_cutoff_defaults_project_level_save_button'");
}

if ( this._annotationTypes_Entries_UserDataError.size === 0 ) {
if ( this._annotationTypes_Entries_UserDataError.size === 0 && this._minPSMs_Entry_Valid ) {
if ( ! this._saveButton_IsEnabled ) {

project_page__ann_cutoff_defaults_project_level_save_buttonDOM.disabled = false;
Expand All @@ -765,8 +848,10 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {
_save() {

const cutoffValuesFromPage = this._getCutoffValuesFromPage();

const minPSMs = this._get_minPSMs_FromPage();

const promise_save_ValuesToServer = this._save_ValuesToServer({ cutoffValuesFromPage });
const promise_save_ValuesToServer = this._save_ValuesToServer({ cutoffValuesFromPage, minPSMs });

promise_save_ValuesToServer.catch( ( ) => { } );

Expand All @@ -779,8 +864,19 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {
var $element = $("#set_project_level_default_cutoffs_button_success_message_values_updated");
showErrorMsg( $element ); // Used for success messages as well
});
}

/**
*
*/
_get_minPSMs_FromPage() {

const $project_page__ann_cutoff_defaults_project_level_psms_min = $("#project_page__ann_cutoff_defaults_project_level_psms_min");
let minPSMs = $project_page__ann_cutoff_defaults_project_level_psms_min.val();
if ( minPSMs === "" ) {
minPSMs = undefined;
}
return minPSMs;
}

/**
Expand Down Expand Up @@ -844,7 +940,7 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {
// No value so skip to next
return; // EARLY RETURN
}
if ( ! this._isFieldValueValidNumber({ fieldValue : fieldValueString }) ) {
if ( ! this._isFieldValueValidDecimalNumber({ fieldValue : fieldValueString }) ) {
throw Error("_getCutoffValuesFromPage_ForType(...) '! this._isFieldValueValidNumber( fieldValueString )' fieldValueString: " + fieldValueString );
}
const fieldValue = Number.parseFloat( fieldValueString );
Expand Down Expand Up @@ -877,13 +973,14 @@ class ProjectPg_setAnnotationCutoffsDefaults_ProjectLevel_Overlay {
/**
*
*/
_save_ValuesToServer({ cutoffValuesFromPage }) {
_save_ValuesToServer({ cutoffValuesFromPage, minPSMs }) {

return new Promise( (resolve, reject) => {
try {
let requestObj = {
projectId : this._projectId,
cutoffValues : cutoffValuesFromPage
cutoffValues : cutoffValuesFromPage,
minPSMs
};

const url = "services/projectLevelDefaultCutoffs_SaveUpdateEntries_ForProjectId";
Expand Down
65 changes: 44 additions & 21 deletions ...s/page_js/data_pages/project_search_ids_driven_pages/image_page/crosslink-image-viewer.js
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Original file line number Diff line number Diff line change
Expand Up @@ -699,6 +699,8 @@ var ImagePagePrimaryRootCodeClass = function() {
var _projectSearchIds;
var _projectSearchIdsUserOrdered = "";

let _defaultsCutoffsAndOthers = undefined;

// Loaded data:

var _allLinkersSupportedForLinkablePositions = undefined; // true or false returned from webservice
Expand Down Expand Up @@ -870,7 +872,7 @@ var ImagePagePrimaryRootCodeClass = function() {
if ( windowHash === "" || windowHash === "#" ) {
// No Hash value so set defaults and return
jsonFromHash = {
cutoffs : getCutoffDefaultsFromPage(),
cutoffs : getCutoffDefaults(),
'excludeType' : EXCLUDE_LINK_TYPE_DEFAULT
};
return jsonFromHash;
Expand Down Expand Up @@ -944,13 +946,13 @@ var ImagePagePrimaryRootCodeClass = function() {
}
if ( json.cutoffs === undefined || json.cutoffs === null ) {
// Set cutoff defaults if not in JSON
json.cutoffs = getCutoffDefaultsFromPage();
json.cutoffs = getCutoffDefaults();
}
// START: Special update to allow projectSearchId values to be added or removed from URL
// Update cutoffs to add defaults for search ids in defaults but not in cutoffs
// Update cutoffs to remove search ids not in defaults but in cutoffs
var cutoffs_Searches = json.cutoffs.searches;
var cutoffDefaultsFromPage = getCutoffDefaultsFromPage();
var cutoffDefaultsFromPage = getCutoffDefaults();
var cutoffDefaultsFromPage_Searches = cutoffDefaultsFromPage.searches;
// Update cutoffs_Searches with values from cutoffDefaultsFromPage
// for any searches in cutoffDefaultsFromPage but not in cutoffs_Searches
Expand Down Expand Up @@ -983,24 +985,6 @@ var ImagePagePrimaryRootCodeClass = function() {
return json;
}

/**
*
*/
function getCutoffDefaultsFromPage() {
var $cutoffValuesRootLevelCutoffDefaults = $("#cutoffValuesRootLevelCutoffDefaults");
var cutoffValuesRootLevelCutoffDefaultsString = $cutoffValuesRootLevelCutoffDefaults.val();
try {
var cutoffValuesRootLevelCutoffDefaults = JSON.parse( cutoffValuesRootLevelCutoffDefaultsString );
} catch( e2 ) {
throw Error( "Failed to parse cutoffValuesRootLevelCutoffDefaults string as JSON. " +
"Error Message: " + e2.message +
". cutoffValuesRootLevelCutoffDefaultsString: |" +
cutoffValuesRootLevelCutoffDefaultsString +
"|" );
}
return cutoffValuesRootLevelCutoffDefaults;
}

/**
*
*/
Expand Down Expand Up @@ -6141,13 +6125,52 @@ var ImagePagePrimaryRootCodeClass = function() {
} );
}


/**
* Get the defaults out of the DOM placed by the Server Side Code and store in Javascript variables
*/
let getDefaultsFromPage = function() {

const $default_values_cutoffs_others = $("#default_values_cutoffs_others");
const default_values_cutoffs_othersString = $default_values_cutoffs_others.val();

try {
const default_values_cutoffs_others = JSON.parse( default_values_cutoffs_othersString );

// Copy only the properties that are set in the server side code
_defaultsCutoffsAndOthers = { cutoffs: default_values_cutoffs_others.cutoffs, minPSMs : default_values_cutoffs_others.minPSMs };

} catch( e2 ) {
throw Error( "Failed to parse default_values_cutoffs_othersString as JSON. " +
"Error Message: " + e2.message +
". default_values_cutoffs_othersString: |" +
default_values_cutoffs_othersString +
"|." );
}
}

/**
*
*/
let getCutoffDefaults = function() {

const default_values_cutoffs = _defaultsCutoffsAndOthers.cutoffs;

return default_values_cutoffs;
}



//////////////////////////////////////////////////

/**
* Initialize the page and load the data
*/
function initPage() {
console.log( "Initializing the page." );

getDefaultsFromPage();

// convert old JSON
console.log( "\tPerforming necessary legacy JSON updates." );
var _legacyJSONUpdater = new LegacyJSONUpdater();
Expand Down

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