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updated invitro
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Newatia authored and Newatia committed Jun 7, 2024
1 parent 00a4b1c commit 2e6e030
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Showing 14 changed files with 633 additions and 405 deletions.
426 changes: 242 additions & 184 deletions ...itro-pharmacology-assay-data-import/invitro-pharmacology-assay-data-import.component.html
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12 changes: 12 additions & 0 deletions ...itro-pharmacology-assay-data-import/invitro-pharmacology-assay-data-import.component.scss
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Original file line number Diff line number Diff line change
Expand Up @@ -289,10 +289,18 @@
margin-top: 20px;
}

.margintop30px {
margin-top: 30px;
}

.margintop90px {
margin-top: 90px;
}

.margintop120px {
margin-top: 120px;
}

.margintop150px {
margin-top: 150px;
}
Expand Down Expand Up @@ -369,6 +377,10 @@
font-size: 13px;
}

.font15px {
font-size: 15px;
}

.font16px {
font-size: 16px;
}
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282 changes: 247 additions & 35 deletions ...nvitro-pharmacology-assay-data-import/invitro-pharmacology-assay-data-import.component.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -37,17 +37,43 @@ import { InvitroAssayInformation, InvitroAssaySet, ValidationMessage } from '../
})
export class InvitroPharmacologyAssayDataImportComponent implements OnInit {

private TARGET_NAME = "TARGET_NAME";
private HUMAN_HOMOLOG_TARGET = "HUMAN_HOMOLOG_TARGET";
private LIGAND_SUBSTRATE = "LIGAND_SUBSTRATE";
private ANALYTE = "ANALYTE";

substanceKeyTypeForInvitroPharmacologyConfig = null;

private subscriptions: Array<Subscription> = [];

importDataList: Array<any> = [];
importedBulkAssayJson: Array<InvitroAssayInformation> = [];
importedAssayJson: any;
message = '';
submitMessage = '';
disabled = "true";

disableValidateButton = "true";
disableImportButton = "true";

importValidateMessageArray: Array<any> = [];
importSaveMessageArray: Array<any> = [];

willDownload = false;

name = 'This is XLSX TO JSON CONVERTER';
isAllRecordValid: boolean;

isAllRecordValidated = false;
isAllRecordSaved = false;

isLoading = false;

errorMessage: string;
serverError: boolean;
submissionMessage: string;
showSubmissionMessages = false;
validationResult = false;
validationMessages: Array<ValidationMessage> = [];
message = '';
submitMessage = '';
isAdmin = false;

constructor(
private activatedRoute: ActivatedRoute,
Expand All @@ -66,6 +92,15 @@ export class InvitroPharmacologyAssayDataImportComponent implements OnInit {

ngOnInit(): void {
this.titleService.setTitle("IVP Import Assay Data");

// Check if user has either Admin or Updater role
this.authService.hasAnyRolesAsync('DataEntry', 'SuperDataEntry', 'Admin').subscribe(response => {
this.isAdmin = response;
});

// Get Invitro Pharmacology Substance Key Type from the configuration file
this.substanceKeyTypeForInvitroPharmacologyConfig = this.generalService.getSubstanceKeyTypeForInvitroPharmacologyConfig();

}

ngOnDestroy(): void {
Expand Down Expand Up @@ -102,6 +137,11 @@ export class InvitroPharmacologyAssayDataImportComponent implements OnInit {
return;
}
else {
this.importValidateMessageArray = [];
this.disableImportButton = 'true';
this.isAllRecordValidated = false;
this.submitMessage = '';

// Empty the list
this.importDataList.length = 0;

Expand Down Expand Up @@ -182,44 +222,29 @@ export class InvitroPharmacologyAssayDataImportComponent implements OnInit {
delete element["Standard Ligand/Substrate Concentration"]
delete element["Standard Ligand/Substrate Concentration Units"]

// delete element["Assay Set"]
// delete element["Assay Set"]

// Add to list
this.importDataList.push(element);
} // element

}); // LOOP: importedAssayJson

// Un-disable the import button
this.disabled = "false";
this.disableValidateButton = 'false';
// this.disableImportButton = 'false';

} // reader.onload

reader.readAsBinaryString(target.files[0]);


} // else

// let datafirstrow = (XLSX.utils.sheet_to_json(ws, {skipHeader: true, origin: "A2"}));
// console.log(datafirstrow);
}

replaceUndefinedValue(value): string {
return (value === undefined || value == null || value.length <= 0) ? "": value;
return (value === undefined || value == null || value.length <= 0) ? "" : value;
}

/*
setDownload(data) {
this.willDownload = true;
setTimeout(() => {
const el = document.querySelector("#download");
el.setAttribute("href", `data:text/json;charset=utf-8,${encodeURIComponent(data)}`);
el.setAttribute("download", 'xlsxtojson.json');
}, 1000)
}
*/

createAssaySet(element: any) {
const newAssaySet: InvitroAssaySet = {};

Expand All @@ -230,28 +255,215 @@ export class InvitroPharmacologyAssayDataImportComponent implements OnInit {
element["invitroAssaySets"] = sets;
}

importAssayJSONIntoDatabase() {
validate(): void {
this.isLoading = true;
this.serverError = false;
this.loadingService.setLoading(true);

this.submitMessage = "Validating Assay records, please wait .....";

this.importValidateMessageArray = [];
// Loop through each Assay JSON Record, and save into the database
this.importedAssayJson.forEach((element, index) => {

setTimeout(() => {
// NEED THIS, otherwise the index value is getting changed before validation comes back
const localIndex = index;
// setTimeout(() => {
if (element) {
// console.log("index: " + index + " " + JSON.stringify(element));
this.message = this.message + "index: " + index + " " + JSON.stringify(element) + "\n\n";
this.invitroPharmacologyService.assay = JSON.parse(JSON.stringify(element));
this.invitroPharmacologyService.saveAssay().subscribe(response => {
if (response) {
if (response.id) {

const assay = JSON.parse(JSON.stringify(element));
this.invitroPharmacologyService.assay = assay;

// Validate Assay
this.invitroPharmacologyService.validateAssay().pipe(take(1)).subscribe(results => {
this.submissionMessage = null;

// NEED this two fields to check if valid or not
this.validationMessages = results.validationMessages.filter(
message => message.messageType.toUpperCase() === 'ERROR' || message.messageType.toUpperCase() === 'WARNING');
this.validationResult = results.valid;

const saved = { 'indexRecord': index, 'externalAssaySource': assay.externalAssaySource, 'externalAssayId': assay.externalAssayId, validationMessages: this.validationMessages, 'valid': results.valid }
this.importValidateMessageArray.push(saved);

if (this.importDataList.length == this.importValidateMessageArray.length) {

// Get the index if the value exists in the array
// if index returns -1, all records are Valid
const indexAllRecordValid = this.importValidateMessageArray.findIndex(record => record.valid === false);

// Not all records are valid, has ERROR
if (indexAllRecordValid >= 0) {
this.isAllRecordValid = false;
} else {
// ALL RECORDS VALID
this.isAllRecordValid = true;
}
this.message = "";
this.submitMessage = "Import Successful";

// SORT the validation array by id
this.importValidateMessageArray.sort((a, b) => {
return a.indexRecord - b.indexRecord;
});

if (this.isAllRecordValid == true) {
this.disableImportButton = 'false';
}

this.isAllRecordValidated = true;
this.submitMessage = '';

this.loadingService.setLoading(false);
this.isLoading = false;
}

}, error => {
this.addServerError(error);
this.loadingService.setLoading(false);
this.isLoading = false;
});
}
}, 10000); // timeout

})
}); // for import data list
}

addServerError(error: any): void {
this.serverError = true;
this.validationResult = false;
this.validationMessages = null;

const message: ValidationMessage = {
actionType: 'server failure',
links: [],
appliedChange: false,
suggestedChange: false,
messageType: 'ERROR',
message: 'Unknown Server Error'
};
if (error && error.error && error.error.message) {
message.message = 'Server Error ' + (error.status + ': ' || ': ') + error.error.message;
} else if (error && error.error && (typeof error.error) === 'string') {
message.message = 'Server Error ' + (error.status + ': ' || '') + error.error;
} else if (error && error.message) {
message.message = 'Server Error ' + (error.status + ': ' || '') + error.message;
}
this.validationMessages = [message];
this.showSubmissionMessages = true;
}

importAssayJSONIntoDatabase() {
this.importValidateMessageArray = [];
this.importSaveMessageArray = [];
this.isAllRecordSaved = false;
this.submitMessage = '';

this.isLoading = true;
this.loadingService.setLoading(this.isLoading);

this.submitMessage = "Saving Assay records into the database, please wait .....";

// Loop through each Assay JSON Record, and save into the database
this.importedAssayJson.forEach((element, index) => {

setTimeout(() => {
if (element) {
this.invitroPharmacologyService.assay = JSON.parse(JSON.stringify(element));

// this.populateSubstanceKey(this.invitroPharmacologyService.assay.targetName, this.TARGET_NAME);
// this.populateSubstanceKey(this.invitroPharmacologyService.assay.targetName, this.TARGET_NAME);
// this.populateSubstanceKey(this.invitroPharmacologyService.assay.targetName, this.TARGET_NAME);

// Save Into the database
this.invitroPharmacologyService.saveAssay().subscribe(response => {
if (response) {
if (response.id) {

const saved = { 'indexRecord': index, 'externalAssaySource': response.externalAssaySource, 'externalAssayId': response.externalAssayId, 'saved': 'Yes', 'savedId': response.id }
this.importSaveMessageArray.push(saved);
}

// All records saved
if (index == this.importedAssayJson.length - 1) {
this.message = "";
this.submitMessage = "Import Successful";

// Clear Validation variables
this.importValidateMessageArray = [];
this.isAllRecordValid = false;
this.isAllRecordValidated = false;

this.disableValidateButton = 'true';
this.disableImportButton = 'true';

this.isAllRecordSaved = true;

// SORT the validation array by id
this.importSaveMessageArray.sort((a, b) => {
return a.indexRecord - b.indexRecord;
});

this.isLoading = false;
this.loadingService.setLoading(this.isLoading);
}
}
}, error => {

this.submitMessage = "";

this.isLoading = false;
this.loadingService.setLoading(this.isLoading);
});
}
}, 10000); // timeout
});
}

populateSubstanceKey(ingredientName: string, fieldName: string) {

/****************************************************************/
/* SUBSTANCE KEY RESOLVER BEGIN */
/****************************************************************/
// Get Substance record by Ingredient/Substance Name, to get Substance UUID and Approval ID
const substanceSubscribe = this.generalService.getSubstanceByName(ingredientName).subscribe(response => {
if (response) {
if (response.content && response.content.length > 0) {

// Loop through the search results and if the Substance/Ingredient name is same as name in the search
// result, select that substance
response.content.forEach(substance => {

if (substance) {
if (substance._name) {

// If Substance Name is same as in the Search Result
if (substance._name === ingredientName) {

/****************************************************************/
/* SUBSTANCE KEY RESOLVER BEGIN */
/****************************************************************/
let substanceKey = this.generalService.getSubstanceKeyBySubstanceResolver(substance, this.substanceKeyTypeForInvitroPharmacologyConfig);

// Set the Substance Key and Substance Key Type
if (fieldName && fieldName === this.TARGET_NAME) {
// this.assay.targetNameApprovalId = substance.approvalID;
// this.assay.targetNameSubstanceKey = substanceKey;
//this.assay.targetNameSubstanceKeyType = this.substanceKeyTypeForInvitroPharmacologyConfig;
}
/* SUBSTANCE KEY RESOLVER END */

} // if substance._name === ingredientName

} // if substance._name is not null
} // if Substance exists

}); // LOOP Substance search result

} // if response content > 0
} // if response
});
this.subscriptions.push(substanceSubscribe);

/* SUBSTANCE KEY RESOLVER END */

}

showJSON(): void {
Expand Down
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