From 99eaa5d14d78f8c1bfc8925550098e774ba73e70 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 22 Oct 2024 14:33:20 +0100 Subject: [PATCH 01/25] Added pycharm .venv hidden folder --- .gcloudignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gcloudignore b/.gcloudignore index b69d3d16..8dfecb33 100644 --- a/.gcloudignore +++ b/.gcloudignore @@ -41,6 +41,7 @@ # Virtual env /venv/ +.venv # Other /rest_api/fixtures/ From 0cbad71784923c80244ba6cf845d817f05013694 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 22 Oct 2024 14:37:43 +0100 Subject: [PATCH 02/25] New validator app backbone --- pgs_web/settings.py | 3 ++- validator/__init__.py | 0 validator/admin.py | 3 +++ validator/apps.py | 6 ++++++ validator/migrations/__init__.py | 0 validator/models.py | 3 +++ validator/tests.py | 3 +++ 7 files changed, 17 insertions(+), 1 deletion(-) create mode 100644 validator/__init__.py create mode 100644 validator/admin.py create mode 100644 validator/apps.py create mode 100644 validator/migrations/__init__.py create mode 100644 validator/models.py create mode 100644 validator/tests.py diff --git a/pgs_web/settings.py b/pgs_web/settings.py index 3782389c..545c3b3a 100644 --- a/pgs_web/settings.py +++ b/pgs_web/settings.py @@ -55,10 +55,11 @@ # Application definition # #------------------------# INSTALLED_APPS = [ - 'catalog.apps.CatalogConfig', + 'catalog.apps.CatalogConfig', 'rest_api.apps.RestApiConfig', 'search.apps.SearchConfig', 'benchmark.apps.BenchmarkConfig', + 'validator.apps.ValidatorConfig', 'django.contrib.admin', 'django.contrib.auth', 'django.contrib.contenttypes', diff --git a/validator/__init__.py b/validator/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/validator/admin.py b/validator/admin.py new file mode 100644 index 00000000..8c38f3f3 --- /dev/null +++ b/validator/admin.py @@ -0,0 +1,3 @@ +from django.contrib import admin + +# Register your models here. diff --git a/validator/apps.py b/validator/apps.py new file mode 100644 index 00000000..49e5efce --- /dev/null +++ b/validator/apps.py @@ -0,0 +1,6 @@ +from django.apps import AppConfig + + +class ValidatorConfig(AppConfig): + default_auto_field = 'django.db.models.BigAutoField' + name = 'validator' diff --git a/validator/migrations/__init__.py b/validator/migrations/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/validator/models.py b/validator/models.py new file mode 100644 index 00000000..71a83623 --- /dev/null +++ b/validator/models.py @@ -0,0 +1,3 @@ +from django.db import models + +# Create your models here. diff --git a/validator/tests.py b/validator/tests.py new file mode 100644 index 00000000..7ce503c2 --- /dev/null +++ b/validator/tests.py @@ -0,0 +1,3 @@ +from django.test import TestCase + +# Create your tests here. From 386576327a945cc19400f4f8721d0224b90c995a Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 22 Oct 2024 16:22:21 +0100 Subject: [PATCH 03/25] Added validator app scripts and static files --- .../static/validator/js/metadata_consumer.js | 116 ++++++++++++++++ validator/static/validator/js/py-worker.js | 31 +++++ .../static/validator/js/scores_consumer.js | 129 ++++++++++++++++++ validator/static/validator/js/webworker.js | 61 +++++++++ .../validator/python/bin/test_services.py | 16 +++ .../python/bin/validation_metadata.py | 91 ++++++++++++ .../validator/python/bin/validation_scores.py | 79 +++++++++++ ..._template_validator-1.1.0-py3-none-any.whl | Bin 0 -> 24486 bytes .../pgscatalog_validate-0.1-py3-none-any.whl | Bin 0 -> 23731 bytes .../template/TemplateColumns2Models.xlsx | Bin 0 -> 17012 bytes .../validator/validate_metadata_client.html | 60 ++++++++ .../validate_scoring_files_client.html | 53 +++++++ validator/urls.py | 7 + validator/views.py | 9 ++ 14 files changed, 652 insertions(+) create mode 100644 validator/static/validator/js/metadata_consumer.js create mode 100644 validator/static/validator/js/py-worker.js create mode 100644 validator/static/validator/js/scores_consumer.js create mode 100644 validator/static/validator/js/webworker.js create mode 100644 validator/static/validator/python/bin/test_services.py create mode 100644 validator/static/validator/python/bin/validation_metadata.py create mode 100644 validator/static/validator/python/bin/validation_scores.py create mode 100644 validator/static/validator/python/wheels/pgs_template_validator-1.1.0-py3-none-any.whl create mode 100644 validator/static/validator/python/wheels/pgscatalog_validate-0.1-py3-none-any.whl create mode 100644 validator/static/validator/template/TemplateColumns2Models.xlsx create mode 100644 validator/templates/validator/validate_metadata_client.html create mode 100644 validator/templates/validator/validate_scoring_files_client.html create mode 100644 validator/urls.py create mode 100644 validator/views.py diff --git a/validator/static/validator/js/metadata_consumer.js b/validator/static/validator/js/metadata_consumer.js new file mode 100644 index 00000000..3e2fa1d8 --- /dev/null +++ b/validator/static/validator/js/metadata_consumer.js @@ -0,0 +1,116 @@ +import "https://cdn.datatables.net/2.0.3/js/dataTables.js" +import { asyncRun } from "./py-worker.js"; + + +const validate_metadata = await fetch(new URL('../python/bin/validation_metadata.py', import.meta.url, null)).then(response => response.text()); +let dirHandle; + + +async function validateFile() { + const fileInput = document.getElementById('myfile'); + const file = fileInput.files[0]; + + if (file) { + const spinner = document.getElementById('pgs_loading'); + spinner.style.visibility = "visible"; + + const reader = new FileReader(); + reader.onload = async function(event) { + const fileContent = new Uint8Array(event.target.result); + let context = { + file_content: fileContent, + file_name: file.name, + dirHandle: dirHandle + } + const { results, error } = await asyncRun(validate_metadata, context); + if(results){ + console.log(results); + spinner.style.visibility = "hidden"; + showResults(results); + } + if(error){ + console.error(error); + spinner.style.visibility = "hidden"; + showSystemError(error); + } + }; + reader.readAsArrayBuffer(file); + } +} + +function report_items_2_html(reports_list) { + let report = '
    '; + $.each(reports_list, function(index, report_item){ + let lines = '' + if (report_item.lines) { + let lines_label = (report_item.lines.length > 1) ? 'Lines' : 'Line'; + lines = lines_label+": "+report_item.lines.join(',')+ ' → '; + } + let message = report_item.message; + // Value highlighting + message = message.replace(/\"(.+?)\"/g, "\"$1\""); + // Leading space + message = message.replace(/\"\s+/g, "\"_"); + // Trailing space + message = message.replace(/\s+<\/b>\"/g, "_\""); + // Column highlighting + message = message.replace(/\'(.+?)\'/g, "\'$1\'"); + report += "
  • "+lines+message+"
    • "; + }); + report += '
'; + return report; +} + +function makeReportTable(data_spreadsheet_items, items_header){ + let table_html = ''+ + ''+ + ''; + $.each(data_spreadsheet_items, function(spreadsheet, reports_list){ + table_html += "'; + }); + table_html += '
Spreadsheet'+items_header+'
"+spreadsheet+""; + table_html += report_items_2_html(reports_list); + table_html += '
'; + return table_html; +} + +function showResults(results){ + let data = JSON.parse(results); + let status_style = (data.status === 'failed') ? ' Failed' : ' Passed'; + let status_html = ''+ + ' '+ + '
File validation'+status_style+'
'; + $('#check_status').html(status_html); + // Error messages + if (data.error) { + let report = '
Error report
' + + makeReportTable(data.error, 'Error message(s)'); + $('#report_error').html(report); + } else { + $('#report_error').html(''); + } + // Warning messages + if (data.warning) { + let report = '
Warning report
' + + makeReportTable(data.warning, 'Warning message(s)'); + $('#report_warning').html(report); + } else { + $('#report_warning').html(''); + } +} + +function showSystemError(errors){ + let status_html = '
File validation: Failed
'; + $('#check_status').html(status_html); + let error_msg = (errors && errors != '') ? errors : 'Internal error'; + let error_html = '
'+ + '
'+ + '
Error: '+error_msg+'
'+ + '
'+ + '
'; + $('#report_error').html(error_html); +} + +document.querySelector('#upload_btn').addEventListener('click', async () => { + await validateFile(); +}); diff --git a/validator/static/validator/js/py-worker.js b/validator/static/validator/js/py-worker.js new file mode 100644 index 00000000..4fddbfde --- /dev/null +++ b/validator/static/validator/js/py-worker.js @@ -0,0 +1,31 @@ +// This script is setting up a way to run Python scripts asynchronously in a web worker. It sends the Python script to the worker and sets up a callback to handle the result when the worker has finished executing the script. +const pyodideWorker = new Worker(new URL("webworker.js", import.meta.url, null)); + +const callbacks = {}; + +pyodideWorker.onmessage = (event) => { + const { id, ...data } = event.data; + const onSuccess = callbacks[id]; + delete callbacks[id]; + onSuccess(data); +}; +//This id is incremented each time the function is invoked and is kept within the safe integer limit. + + +const asyncRun = (() => { + let id = 0; // identify a Promise + return (script, context) => { + // the id could be generated more carefully + id = (id + 1) % Number.MAX_SAFE_INTEGER; + return new Promise((onSuccess) => { + callbacks[id] = onSuccess; + pyodideWorker.postMessage({ + ...context, + python: script, + id, + }); + }); + }; +})(); + +export { asyncRun }; \ No newline at end of file diff --git a/validator/static/validator/js/scores_consumer.js b/validator/static/validator/js/scores_consumer.js new file mode 100644 index 00000000..b864d755 --- /dev/null +++ b/validator/static/validator/js/scores_consumer.js @@ -0,0 +1,129 @@ +import "https://cdn.datatables.net/2.0.3/js/dataTables.js" +import { asyncRun } from "./py-worker.js"; + + +const validate_scores = await fetch(new URL('../python/bin/validation_scores.py', import.meta.url, null)).then(response => response.text()); + +let dirHandle; +let validateFileHandle; + +function startLoading(){ + const spinner = document.getElementById('pgs_loading'); + spinner.style.visibility = "visible"; +} + +function finishLoading(){ + const spinner = document.getElementById('pgs_loading'); + spinner.style.visibility = "hidden"; +} + +function successMount(dirName){ + document.getElementById('grant_message').innerHTML = 'Authorization granted on directory \"'+dirName+"\"."; +} + + +async function mountLocalDirectory() { + // use the same ID crypt4gh to open pickers in the same directory + dirHandle = await showDirectoryPicker(); + + if ((await dirHandle.queryPermission({ mode: "read" })) !== "granted") { + if ( + (await dirHandle.requestPermission({ mode: "read" })) !== "granted" + ) { + throw Error("Unable to read and write directory"); + } + } + return dirHandle.name; +} + +async function validation(validateFileHandle) { + let context; + if (!validateFileHandle) { + console.log('No single scoring file defined'); + context = { + dirHandle: dirHandle, + outputFileName: null, + }; + } else { + context = { + dirHandle: dirHandle, + outputFileName: validateFileHandle.name, + }; + } + + try { + const { results, error } = await asyncRun(validate_scores, context); + if (results) { + let data = JSON.parse(results); + if(data.status === 'success'){ + validation_out.value = data.response; + console.log("pyodideWorker return results: ", data.response); + } else if (data.status === 'error'){ + validation_out.value = ''; + console.error("pyodideWorker returned error: ", data.error); + appendAlertToElement("error",'Error: '+data.error,'danger') + } + return results; + } else if (error) { + validation_out.value = ''; + console.log(typeof error); + console.log("pyodideWorker error: ", error); + appendAlertToElement("error",'Error: '+error,'danger') + } + } catch (e) { + validation_out.value =`Error in pyodideWorker at ${e.filename}, Line: ${e.lineno}, ${e.message}`; + console.log( + `Error in pyodideWorker at ${e.filename}, Line: ${e.lineno}, ${e.message}`, + ); + } +} + +async function appendAlertToElement(elementId, message, type) { + const alertPlaceholder = document.getElementById(elementId); + if (!alertPlaceholder) { + console.error("Element with ID '" + elementId + "' not found."); + return; + } + + const wrapper = document.createElement('div'); + wrapper.innerHTML = [ + `' + ].join(''); + + alertPlaceholder.append(wrapper); +} + +document.querySelector('#validate_directory').addEventListener('click', async () => { + validation_out.value = "Initializing validation...\n"; + //$('#validate').html(' Validating...'); + startLoading(); + await validation(null); + finishLoading(); + //$('#validate').html(''); +}); + +document.querySelector('#mountvalidate').addEventListener('click', async () => { + if (!('showDirectoryPicker' in window)) { + alert('Your browser does not support the File System Access API. Please use a supported browser.'); + return; // Stop execution if the API is not supported + } + else { + let dirName = await mountLocalDirectory(); + //appendAlertToElement('validatediv','Nice, you have granted the permission to the local directory '+dirHandle.name,'success' ) + //document.querySelector('#mount').disabled = true; + successMount(dirName); + document.querySelector('#validate_single').disabled = false; + document.querySelector('#validate_directory').disabled = false; + } +}); + +document.querySelector('#validate_single').addEventListener('click', async () => { + [validateFileHandle] = await window.showOpenFilePicker(); + startLoading(); + await validation(validateFileHandle); + finishLoading(); +}); diff --git a/validator/static/validator/js/webworker.js b/validator/static/validator/js/webworker.js new file mode 100644 index 00000000..f1078ebe --- /dev/null +++ b/validator/static/validator/js/webworker.js @@ -0,0 +1,61 @@ +// webworker.js + +// Setup your project to serve `py-worker.js`. You should also serve +// `pyodide.js`, and all its associated `.asm.js`, `.json`, +// and `.wasm` files as well: +importScripts("https://cdn.jsdelivr.net/pyodide/v0.26.0/full/pyodide.js"); + +const wheels_base_url = "/static/validator/python/wheels/"; + +async function loadPyodideAndPackages() { + self.pyodide = await loadPyodide(); + await pyodide.loadPackage("micropip"); + const micropip = pyodide.pyimport("micropip"); + await micropip.install(['openpyxl','requests','httpx==0.26.0','tenacity','pyliftover', + 'xopen==1.8.0','zstandard','tqdm','natsort','pandas','pandas-schema']); + await micropip.install(wheels_base_url+"pgs_template_validator-1.1.0-py3-none-any.whl", keep_going=true); + await micropip.install(wheels_base_url+"pgscatalog_validate-0.1-py3-none-any.whl", keep_going=true) + await pyodide.FS.createLazyFile('/home/pyodide/', 'TemplateColumns2Models.xlsx', + '/static/validator/template/TemplateColumns2Models.xlsx', true, false); +} +let pyodideReadyPromise = loadPyodideAndPackages(); + + +//This event is fired when the worker receives a message from the main thread via the postMessage method. +self.onmessage = async (event) => { + // make sure loading is done + await pyodideReadyPromise; + // Don't bother yet with this line, suppose our API is built in such a way: + const { id, python, ...context } = event.data; + // The worker copies the context in its own "memory" (an object mapping name to values) + for (const key of Object.keys(context)) { + self[key] = context[key]; + } + // Now is the easy part, the one that is similar to working in the main thread: + try { + let startTime = performance.now(); + + await self.pyodide.loadPackagesFromImports(python); + // mount local directory, make the nativefs as a global vaiable. + if (! self.fsmounted && self.dirHandle){ + self.nativefs = await self.pyodide.mountNativeFS("/data", self.dirHandle); + self.fsmounted = true; + } + // run python script + self.pyodide.globals.set('print', s => console.log(s)) + let results = await self.pyodide.runPythonAsync(python); + // flush new files to disk + if(self.nativefs){ + await self.nativefs.syncfs(); + } + + + let endTime = performance.now(); + + console.log(`Encryption web worker took ${(endTime - startTime) / 1000} seconds`) + self.postMessage({ results, id }); + } catch (error) { + console.log(error); + self.postMessage({ error: error.message, id }); + } + }; diff --git a/validator/static/validator/python/bin/test_services.py b/validator/static/validator/python/bin/test_services.py new file mode 100644 index 00000000..5946a858 --- /dev/null +++ b/validator/static/validator/python/bin/test_services.py @@ -0,0 +1,16 @@ +# from validator.config import OLS_EFO_URL, EUROPMC_URL, GWAS_REST_URL +# from pyodide.http import pyfetch +# +# +# async def test_resource(resource_url): +# response = await pyfetch(resource_url) +# return response.ok +# +# +# resources = { +# 'OLS_EFO': OLS_EFO_URL +# } +# +# for resource in resources.keys(): +# is_ok = await test_resource(resources.get(resource)) +# print(is_ok) \ No newline at end of file diff --git a/validator/static/validator/python/bin/validation_metadata.py b/validator/static/validator/python/bin/validation_metadata.py new file mode 100644 index 00000000..66005faa --- /dev/null +++ b/validator/static/validator/python/bin/validation_metadata.py @@ -0,0 +1,91 @@ +import io +import js +import json +from pyodide.http import open_url +from validator.main_validator import PGSMetadataValidator +from validator.request.connector import Connector, UnknownError, NotFound, Logger + +# Need a proxy for OLS as Pyodide causes a cross-origin issue with the OLS url +OLS_URL = "https://ols-proxy-dot-pgs-catalog.appspot.com/ols-proxy/efo/%s" + +file = io.BytesIO(bytes(js.file_content)) +file_name = js.file_name + + +class PyodideLogger(Logger): + def debug(self, message, name): + print(f'ERROR: {message}') + + +class PyodideConnector(Connector): + def __init__(self): + super().__init__(logger=PyodideLogger()) + + def request(self, url, payload=None) -> dict: + if payload: + query = '&'.join([f"{k}={v}" for k, v in payload.items()]) + url = url + '?' + query + query_result_io = open_url(url) + query_result = query_result_io.read() + + result_json = json.loads(query_result) + return result_json + + def get_efo_trait(self, efo_id) -> dict: + url = OLS_URL % efo_id.replace('_', ':') + response = self.request(url) + # If not found the response should return 404. + if '_embedded' in response and 'terms' in response['_embedded'] and len(response['_embedded']['terms']) == 1: + return response['_embedded']['terms'][0] + elif 'status' in response and response['status'] == 404: + raise NotFound(message=response['error'], url=url) + else: + raise UnknownError(message="Unexpected response from URL: %s" % url, url=url) + + +def validate(): + metadata_validator = PGSMetadataValidator(file, False, PyodideConnector()) + metadata_validator.template_columns_schema_file = '/home/pyodide/TemplateColumns2Models.xlsx' + metadata_validator.parse_spreadsheets() + metadata_validator.parse_publication() + metadata_validator.parse_scores() + metadata_validator.parse_cohorts() + metadata_validator.parse_performances() + metadata_validator.parse_samples() + metadata_validator.post_parsing_checks() + + report_text = 'No error' + + response = {} + + status = 'success' + if metadata_validator.report['error']: + status = 'failed' + response['error'] = {} + error_report = metadata_validator.report['error'] + for error_spreadsheet in error_report: + response['error'][error_spreadsheet] = [] + for error_msg in error_report[error_spreadsheet]: + error_entry = {'message': error_msg} + if error_report[error_spreadsheet][error_msg][0] != None: + error_entry['lines'] = error_report[error_spreadsheet][error_msg] + response['error'][error_spreadsheet].append(error_entry) + + if metadata_validator.report['warning']: + response['warning'] = {} + warning_report = metadata_validator.report['warning'] + for warning_spreadsheet in warning_report: + response['warning'][warning_spreadsheet] = [] + for warning_msg in warning_report[warning_spreadsheet]: + warning_entry = {'message': warning_msg} + if warning_report[warning_spreadsheet][warning_msg][0] != None: + warning_entry['lines'] = warning_report[warning_spreadsheet][warning_msg] + response['warning'][warning_spreadsheet].append(warning_entry) + + response['status'] = status + return response + + +response = validate() + +json.dumps(response) # Is returned by pyodide.runPythonAsync() diff --git a/validator/static/validator/python/bin/validation_scores.py b/validator/static/validator/python/bin/validation_scores.py new file mode 100644 index 00000000..fa32c1b4 --- /dev/null +++ b/validator/static/validator/python/bin/validation_scores.py @@ -0,0 +1,79 @@ +import glob +import json +import tempfile +import os.path +from pathlib import Path + +from js import outputFileName +# from pgscatalog.validate.cli.validate_scorefile import validate_scorefile +from pgscatalog.validate.cli.validate_scorefile import _check_args, _validate_scorefile + + +# local file system is mounted in /data +#input_path = Path("/data") / outputFileName + + +class Args: + dir: str + log_dir: str + t: str + f: str + score_dir: str + check_filename: bool + + +response = '' +error = None + +try: + + # At the moment the results of score validation are stored in individual log files in log_dir + with tempfile.TemporaryDirectory() as log_dir: + + args = Args() + args.t = 'formatted' + args.check_filename = False + args.dir = None + args.f = None + args.log_dir = Path(log_dir) + args.score_dir = None + + if outputFileName: + filename = str(Path("/data") / outputFileName) + if not os.path.exists(filename): + raise FileNotFoundError(filename) + args.f = filename + else: + args.dir = str(Path("/data")) + + # Unconventional use of private functions but temporary + _check_args(args) + _validate_scorefile(args) + + # Getting the validation results from the log files + for log_file in glob.glob(str(log_dir)+'/*_log.txt'): + file_name = log_file.split('/')[-1].removesuffix('_log.txt') + with open(log_file, 'r') as f: + content = f.read() + response = response + file_name + ":\n" + response = response + content + "\n" + +except FileNotFoundError as e: + error = "Could not read input file. Is the selected file in the in the directory with granted rights?" +except Exception as e: + error = str(e) + + +data = {} +if error: + data = { + 'status': 'error', + 'error': error + } +else: + data = { + 'status': 'success', + 'response': response + } + +json.dumps(data) diff --git a/validator/static/validator/python/wheels/pgs_template_validator-1.1.0-py3-none-any.whl b/validator/static/validator/python/wheels/pgs_template_validator-1.1.0-py3-none-any.whl new file mode 100644 index 0000000000000000000000000000000000000000..bf0bbb84dc5f547cc308ebcf9b42683bb653193d GIT binary patch literal 24486 zcmaI;W2`7m)GdrI+qP}nwr$(?Ubb!9w#~h4+qS>`o|Es~`<&d|POAG)&!or9teT@z zW3+-aFbE0&006|lLHKU~008~3I{*Oczo(m_jirg9i@g)QzP_cMrHj5kor5PZfWm)* zDk*3)M*qFM3kU#!@t+_QQ(Jp;CqoAdOXGiWDGD=ifebLcx0G0N@d$YR!C4XZdn4(l zv2vxKgxd`J*P@C#2=Ff}FPE>%qC11K7~A1z6NyU!| zT|4Pt>>{3xL}UPiYe~`$!Etjoq(@_G55$&Ud|b;3k7?e2I`gBaP}JH__xsB{Asx@^ z|01=}ysMmX7k8JN-Tcvjb_4$}_Ea#By2F2%SN~!EZ^BH?>|LA;EnWTrw~ZgL8zMju 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Metadata Template Validation

+ +
+
+
+ + +
+ + +
+
More information about the Template file here.
+
+ +
+ + +
+
+ + +{% endblock %} diff --git a/validator/templates/validator/validate_scoring_files_client.html b/validator/templates/validator/validate_scoring_files_client.html new file mode 100644 index 00000000..2d9b62d7 --- /dev/null +++ b/validator/templates/validator/validate_scoring_files_client.html @@ -0,0 +1,53 @@ +{% extends 'catalog/base.html' %} +{% load static %} + +{% block title %}Metadata Template Validation{% endblock %} + +{% block desc %} + +{% endblock %} + +{% block content %} + + + + +

Scoring Files Validationbeta

+ +
+
+ 1) Please grant the permission to read your local directory that contains your scores to validate: +
+
+
+
+ 2) Then click on to select only one file to validate in this directory, + or click on to validate all scoring files located in this directory. +
+
+ + +
+ +
+ + +{% endblock %} diff --git a/validator/urls.py b/validator/urls.py new file mode 100644 index 00000000..a21f9917 --- /dev/null +++ b/validator/urls.py @@ -0,0 +1,7 @@ +from django.urls import path +from . import views + +urlpatterns = [ + path("validate_metadata_client/", views.validate_metadata_template_client, name="Metadata Template Validation"), + path("validate_scoring_files_client/", views.validate_scoring_files_client, name="Scoring Files Validation"), +] \ No newline at end of file diff --git a/validator/views.py b/validator/views.py new file mode 100644 index 00000000..695c6e80 --- /dev/null +++ b/validator/views.py @@ -0,0 +1,9 @@ +from django.shortcuts import render + + +def validate_metadata_template_client(request): + return render(request, 'validator/validate_metadata_client.html', {}) + + +def validate_scoring_files_client(request): + return render(request, 'validator/validate_scoring_files_client.html', {}) From 1c0a38af1d40f6a2aedd6a737e50093eb7a8ab78 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 22 Oct 2024 16:22:40 +0100 Subject: [PATCH 04/25] Added validator urls --- pgs_web/urls.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pgs_web/urls.py b/pgs_web/urls.py index 3709dd12..5946617c 100755 --- a/pgs_web/urls.py +++ b/pgs_web/urls.py @@ -18,9 +18,10 @@ from search import views as search_views urlpatterns = [ - path('', include('catalog.urls')), + path('', include('catalog.urls')), path('', include('rest_api.urls')), path('', include('benchmark.urls')), + path('', include('validator.urls')), re_path(r'^search/', search_views.search, name="PGS Catalog Search"), re_path(r'^autocomplete/', search_views.autocomplete, name="PGS Catalog Autocomplete") ] From 8cc2d309b0586b736459b384aba5683d9830b74b Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 22 Oct 2024 16:22:56 +0100 Subject: [PATCH 05/25] Added validator static folder --- .gcloudignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gcloudignore b/.gcloudignore index 8dfecb33..900cce52 100644 --- a/.gcloudignore +++ b/.gcloudignore @@ -18,6 +18,7 @@ /catalog/static/ /rest_api/static/ /curation_tracker/static/ +/validator/static/ # Curation and release directories (not needed for the website) /curation/ From 9b6416b12b7429e13be474f90d7c5c85530c1bad Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 22 Oct 2024 17:38:19 +0100 Subject: [PATCH 06/25] Moved score validator to labs --- catalog/static/catalog/pgs.scss | 6 ++++++ catalog/templates/catalog/labs.html | 18 ++++++++++++------ validator/urls.py | 2 +- 3 files changed, 19 insertions(+), 7 deletions(-) diff --git a/catalog/static/catalog/pgs.scss b/catalog/static/catalog/pgs.scss index b29de8e0..c6f99aef 100644 --- a/catalog/static/catalog/pgs.scss +++ b/catalog/static/catalog/pgs.scss @@ -188,6 +188,12 @@ h2 { font-weight:900; } +.score_validator_logo:before { + font-family: 'Font Awesome 6 Free'; + content:"\e5a0"; + font-weight:900; +} + /* Navbar and horizontal menu */ .navbar { diff --git a/catalog/templates/catalog/labs.html b/catalog/templates/catalog/labs.html index 4cd3e765..0bac0132 100644 --- a/catalog/templates/catalog/labs.html +++ b/catalog/templates/catalog/labs.html @@ -20,16 +20,22 @@

Labs
- -
-
+
+ +
Benchmarking PGS
-
- -
+
+ +
+ +
+ +
Score Validator
+
+ {% endblock %} diff --git a/validator/urls.py b/validator/urls.py index a21f9917..1a572a95 100644 --- a/validator/urls.py +++ b/validator/urls.py @@ -3,5 +3,5 @@ urlpatterns = [ path("validate_metadata_client/", views.validate_metadata_template_client, name="Metadata Template Validation"), - path("validate_scoring_files_client/", views.validate_scoring_files_client, name="Scoring Files Validation"), + path("labs/validate_scoring_files_client/", views.validate_scoring_files_client, name="Scoring Files Validation"), ] \ No newline at end of file From 8a08cf782d1317fa024c773f7566a7c68a7442c8 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Tue, 22 Oct 2024 18:02:31 +0100 Subject: [PATCH 07/25] Code cleaning and commenting --- validator/static/validator/js/metadata_consumer.js | 10 +++++----- validator/static/validator/js/scores_consumer.js | 1 - .../static/validator/python/bin/validation_metadata.py | 4 ++++ .../static/validator/python/bin/validation_scores.py | 2 +- 4 files changed, 10 insertions(+), 7 deletions(-) diff --git a/validator/static/validator/js/metadata_consumer.js b/validator/static/validator/js/metadata_consumer.js index 3e2fa1d8..9825afe4 100644 --- a/validator/static/validator/js/metadata_consumer.js +++ b/validator/static/validator/js/metadata_consumer.js @@ -48,13 +48,13 @@ function report_items_2_html(reports_list) { } let message = report_item.message; // Value highlighting - message = message.replace(/\"(.+?)\"/g, "\"$1\""); + message = message.replace(/"(.+?)"/g, "\"$1\""); // Leading space - message = message.replace(/\"\s+/g, "\"_"); + message = message.replace(/"\s+/g, "\"_"); // Trailing space - message = message.replace(/\s+<\/b>\"/g, "_\""); + message = message.replace(/\s+<\/b>"/g, "_\""); // Column highlighting - message = message.replace(/\'(.+?)\'/g, "\'$1\'"); + message = message.replace(/'(.+?)'/g, "\'$1\'"); report += "
  • "+lines+message+"
    • "; }); report += ''; @@ -102,7 +102,7 @@ function showResults(results){ function showSystemError(errors){ let status_html = '
    File validation: Failed
    '; $('#check_status').html(status_html); - let error_msg = (errors && errors != '') ? errors : 'Internal error'; + let error_msg = (errors && errors !== '') ? errors : 'Internal error'; let error_html = '
    '+ '
    '+ '
    Error: '+error_msg+'
    '+ diff --git a/validator/static/validator/js/scores_consumer.js b/validator/static/validator/js/scores_consumer.js index b864d755..b5c9db7b 100644 --- a/validator/static/validator/js/scores_consumer.js +++ b/validator/static/validator/js/scores_consumer.js @@ -66,7 +66,6 @@ async function validation(validateFileHandle) { return results; } else if (error) { validation_out.value = ''; - console.log(typeof error); console.log("pyodideWorker error: ", error); appendAlertToElement("error",'Error: '+error,'danger') } diff --git a/validator/static/validator/python/bin/validation_metadata.py b/validator/static/validator/python/bin/validation_metadata.py index 66005faa..6683b6f9 100644 --- a/validator/static/validator/python/bin/validation_metadata.py +++ b/validator/static/validator/python/bin/validation_metadata.py @@ -18,6 +18,9 @@ def debug(self, message, name): class PyodideConnector(Connector): + """This customised connector is necessary as the 'requests' python module is not supported in WebAssembly. + Moreover, the requests for EFO traits must be redirected to a proxy to avoid cross-origin errors.""" + def __init__(self): super().__init__(logger=PyodideLogger()) @@ -25,6 +28,7 @@ def request(self, url, payload=None) -> dict: if payload: query = '&'.join([f"{k}={v}" for k, v in payload.items()]) url = url + '?' + query + # Using pyodide open_url instead of python requests.get() query_result_io = open_url(url) query_result = query_result_io.read() diff --git a/validator/static/validator/python/bin/validation_scores.py b/validator/static/validator/python/bin/validation_scores.py index fa32c1b4..f33c986f 100644 --- a/validator/static/validator/python/bin/validation_scores.py +++ b/validator/static/validator/python/bin/validation_scores.py @@ -76,4 +76,4 @@ class Args: 'response': response } -json.dumps(data) +json.dumps(data) # Is returned by pyodide.runPythonAsync() From d28671530da452663ca62c24a845fcba81235bee Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Wed, 23 Oct 2024 11:16:55 +0100 Subject: [PATCH 08/25] Removed unused script --- .../static/validator/python/bin/test_services.py | 16 ---------------- 1 file changed, 16 deletions(-) delete mode 100644 validator/static/validator/python/bin/test_services.py diff --git a/validator/static/validator/python/bin/test_services.py b/validator/static/validator/python/bin/test_services.py deleted file mode 100644 index 5946a858..00000000 --- a/validator/static/validator/python/bin/test_services.py +++ /dev/null @@ -1,16 +0,0 @@ -# from validator.config import OLS_EFO_URL, EUROPMC_URL, GWAS_REST_URL -# from pyodide.http import pyfetch -# -# -# async def test_resource(resource_url): -# response = await pyfetch(resource_url) -# return response.ok -# -# -# resources = { -# 'OLS_EFO': OLS_EFO_URL -# } -# -# for resource in resources.keys(): -# is_ok = await test_resource(resources.get(resource)) -# print(is_ok) \ No newline at end of file From 7cf2d8a64da2c8465d3cedd05191fc0fbed68731 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Wed, 23 Oct 2024 17:15:06 +0100 Subject: [PATCH 09/25] Using minified js versions if gae --- .gitignore | 4 +++- validator/static/validator/js/metadata_consumer.js | 3 ++- validator/static/validator/js/py-worker.js | 2 +- validator/static/validator/js/scores_consumer.js | 3 ++- .../templates/validator/validate_metadata_client.html | 7 +++++++ .../templates/validator/validate_scoring_files_client.html | 7 +++++++ 6 files changed, 22 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index daba40ae..35b3e358 100644 --- a/.gitignore +++ b/.gitignore @@ -4,4 +4,6 @@ app.yaml pgs-catalog-cred.json .idea -.vscode \ No newline at end of file +.vscode +*.min.js +*.min.css \ No newline at end of file diff --git a/validator/static/validator/js/metadata_consumer.js b/validator/static/validator/js/metadata_consumer.js index 9825afe4..0e5058db 100644 --- a/validator/static/validator/js/metadata_consumer.js +++ b/validator/static/validator/js/metadata_consumer.js @@ -1,6 +1,7 @@ import "https://cdn.datatables.net/2.0.3/js/dataTables.js" -import { asyncRun } from "./py-worker.js"; +const pyworker = await import((on_gae)?'./py-worker.min.js':'py-worker'); +const asyncRun = pyworker.asynRun; const validate_metadata = await fetch(new URL('../python/bin/validation_metadata.py', import.meta.url, null)).then(response => response.text()); let dirHandle; diff --git a/validator/static/validator/js/py-worker.js b/validator/static/validator/js/py-worker.js index 4fddbfde..d518a04d 100644 --- a/validator/static/validator/js/py-worker.js +++ b/validator/static/validator/js/py-worker.js @@ -1,5 +1,5 @@ // This script is setting up a way to run Python scripts asynchronously in a web worker. It sends the Python script to the worker and sets up a callback to handle the result when the worker has finished executing the script. -const pyodideWorker = new Worker(new URL("webworker.js", import.meta.url, null)); +const pyodideWorker = new Worker(new URL((on_gae) ? "webworker.min.js" : "webworker.js", import.meta.url, null)); const callbacks = {}; diff --git a/validator/static/validator/js/scores_consumer.js b/validator/static/validator/js/scores_consumer.js index b5c9db7b..e93e4a7f 100644 --- a/validator/static/validator/js/scores_consumer.js +++ b/validator/static/validator/js/scores_consumer.js @@ -1,6 +1,7 @@ import "https://cdn.datatables.net/2.0.3/js/dataTables.js" -import { asyncRun } from "./py-worker.js"; +const pyworker = await import((on_gae)?'./py-worker.min.js':'py-worker'); +const asyncRun = pyworker.asynRun; const validate_scores = await fetch(new URL('../python/bin/validation_scores.py', import.meta.url, null)).then(response => response.text()); diff --git a/validator/templates/validator/validate_metadata_client.html b/validator/templates/validator/validate_metadata_client.html index 99d523ce..f290673f 100644 --- a/validator/templates/validator/validate_metadata_client.html +++ b/validator/templates/validator/validate_metadata_client.html @@ -4,7 +4,14 @@ {% block title %}Metadata Template Validation{% endblock %} {% block desc %} + + {% if is_pgs_app_on_gae %} + + {% else %} + {% endif %} {% endblock %} {% block content %} diff --git a/validator/templates/validator/validate_scoring_files_client.html b/validator/templates/validator/validate_scoring_files_client.html index 2d9b62d7..6408342a 100644 --- a/validator/templates/validator/validate_scoring_files_client.html +++ b/validator/templates/validator/validate_scoring_files_client.html @@ -4,7 +4,14 @@ {% block title %}Metadata Template Validation{% endblock %} {% block desc %} + + {% if is_pgs_app_on_gae %} + + {% else %} + {% endif %} {% endblock %} {% block content %} From 9a531f57a9ec7f6077a65e7f673929e2d10ebc00 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Wed, 23 Oct 2024 17:38:08 +0100 Subject: [PATCH 10/25] Fixed wrong script name in import --- validator/static/validator/js/metadata_consumer.js | 2 +- validator/static/validator/js/scores_consumer.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/validator/static/validator/js/metadata_consumer.js b/validator/static/validator/js/metadata_consumer.js index 0e5058db..4eb83089 100644 --- a/validator/static/validator/js/metadata_consumer.js +++ b/validator/static/validator/js/metadata_consumer.js @@ -1,6 +1,6 @@ import "https://cdn.datatables.net/2.0.3/js/dataTables.js" -const pyworker = await import((on_gae)?'./py-worker.min.js':'py-worker'); +const pyworker = await import((on_gae)?'./py-worker.min.js':'./py-worker.js'); const asyncRun = pyworker.asynRun; const validate_metadata = await fetch(new URL('../python/bin/validation_metadata.py', import.meta.url, null)).then(response => response.text()); diff --git a/validator/static/validator/js/scores_consumer.js b/validator/static/validator/js/scores_consumer.js index e93e4a7f..205ff118 100644 --- a/validator/static/validator/js/scores_consumer.js +++ b/validator/static/validator/js/scores_consumer.js @@ -1,6 +1,6 @@ import "https://cdn.datatables.net/2.0.3/js/dataTables.js" -const pyworker = await import((on_gae)?'./py-worker.min.js':'py-worker'); +const pyworker = await import((on_gae)?'./py-worker.min.js':'./py-worker.js'); const asyncRun = pyworker.asynRun; const validate_scores = await fetch(new URL('../python/bin/validation_scores.py', import.meta.url, null)).then(response => response.text()); From 5901bdb5cdbc9b31522c2fb47186f6d4471d4b52 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Wed, 23 Oct 2024 17:43:42 +0100 Subject: [PATCH 11/25] Fixed typo --- validator/static/validator/js/metadata_consumer.js | 2 +- validator/static/validator/js/scores_consumer.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/validator/static/validator/js/metadata_consumer.js b/validator/static/validator/js/metadata_consumer.js index 4eb83089..17d9bc2c 100644 --- a/validator/static/validator/js/metadata_consumer.js +++ b/validator/static/validator/js/metadata_consumer.js @@ -1,7 +1,7 @@ import "https://cdn.datatables.net/2.0.3/js/dataTables.js" const pyworker = await import((on_gae)?'./py-worker.min.js':'./py-worker.js'); -const asyncRun = pyworker.asynRun; +const asyncRun = pyworker.asyncRun; const validate_metadata = await fetch(new URL('../python/bin/validation_metadata.py', import.meta.url, null)).then(response => response.text()); let dirHandle; diff --git a/validator/static/validator/js/scores_consumer.js b/validator/static/validator/js/scores_consumer.js index 205ff118..29a1a077 100644 --- a/validator/static/validator/js/scores_consumer.js +++ b/validator/static/validator/js/scores_consumer.js @@ -1,7 +1,7 @@ import "https://cdn.datatables.net/2.0.3/js/dataTables.js" const pyworker = await import((on_gae)?'./py-worker.min.js':'./py-worker.js'); -const asyncRun = pyworker.asynRun; +const asyncRun = pyworker.asyncRun; const validate_scores = await fetch(new URL('../python/bin/validation_scores.py', import.meta.url, null)).then(response => response.text()); From 7cae096ba37d75a131e8ae7c28be5452436eec80 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Wed, 23 Oct 2024 17:46:16 +0100 Subject: [PATCH 12/25] Removed unused import --- validator/static/validator/js/metadata_consumer.js | 2 -- validator/static/validator/js/scores_consumer.js | 2 -- 2 files changed, 4 deletions(-) diff --git a/validator/static/validator/js/metadata_consumer.js b/validator/static/validator/js/metadata_consumer.js index 17d9bc2c..1d7f7d03 100644 --- a/validator/static/validator/js/metadata_consumer.js +++ b/validator/static/validator/js/metadata_consumer.js @@ -1,5 +1,3 @@ -import "https://cdn.datatables.net/2.0.3/js/dataTables.js" - const pyworker = await import((on_gae)?'./py-worker.min.js':'./py-worker.js'); const asyncRun = pyworker.asyncRun; diff --git a/validator/static/validator/js/scores_consumer.js b/validator/static/validator/js/scores_consumer.js index 29a1a077..3f716223 100644 --- a/validator/static/validator/js/scores_consumer.js +++ b/validator/static/validator/js/scores_consumer.js @@ -1,5 +1,3 @@ -import "https://cdn.datatables.net/2.0.3/js/dataTables.js" - const pyworker = await import((on_gae)?'./py-worker.min.js':'./py-worker.js'); const asyncRun = pyworker.asyncRun; From 810e7fbe8362b2d8c84288ccb82a05b7ed31e8f8 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Thu, 24 Oct 2024 10:20:17 +0100 Subject: [PATCH 13/25] Fixed typo --- validator/static/validator/python/bin/validation_scores.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/validator/static/validator/python/bin/validation_scores.py b/validator/static/validator/python/bin/validation_scores.py index f33c986f..755376f3 100644 --- a/validator/static/validator/python/bin/validation_scores.py +++ b/validator/static/validator/python/bin/validation_scores.py @@ -59,7 +59,7 @@ class Args: response = response + content + "\n" except FileNotFoundError as e: - error = "Could not read input file. Is the selected file in the in the directory with granted rights?" + error = "Could not read input file. Is the selected file in the directory with granted rights?" except Exception as e: error = str(e) From 3f8fa88eec1b16373acd70c0f95f42e7189e22bb Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Thu, 24 Oct 2024 10:53:10 +0100 Subject: [PATCH 14/25] Removed unused commented code --- validator/static/validator/js/scores_consumer.js | 4 ---- 1 file changed, 4 deletions(-) diff --git a/validator/static/validator/js/scores_consumer.js b/validator/static/validator/js/scores_consumer.js index 3f716223..d158e72b 100644 --- a/validator/static/validator/js/scores_consumer.js +++ b/validator/static/validator/js/scores_consumer.js @@ -97,11 +97,9 @@ async function appendAlertToElement(elementId, message, type) { document.querySelector('#validate_directory').addEventListener('click', async () => { validation_out.value = "Initializing validation...\n"; - //$('#validate').html(' Validating...'); startLoading(); await validation(null); finishLoading(); - //$('#validate').html(''); }); document.querySelector('#mountvalidate').addEventListener('click', async () => { @@ -111,8 +109,6 @@ document.querySelector('#mountvalidate').addEventListener('click', async () => { } else { let dirName = await mountLocalDirectory(); - //appendAlertToElement('validatediv','Nice, you have granted the permission to the local directory '+dirHandle.name,'success' ) - //document.querySelector('#mount').disabled = true; successMount(dirName); document.querySelector('#validate_single').disabled = false; document.querySelector('#validate_directory').disabled = false; From d166fd8e4f40e7b0c1cf97400eea4c01ac7dc441 Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Thu, 24 Oct 2024 14:59:04 +0100 Subject: [PATCH 15/25] Bumped metadata validator version to 1.1.1 --- validator/static/validator/js/webworker.js | 2 +- ...gs_template_validator-1.1.0-py3-none-any.whl | Bin 24486 -> 0 bytes ...gs_template_validator-1.1.1-py3-none-any.whl | Bin 0 -> 24620 bytes 3 files changed, 1 insertion(+), 1 deletion(-) delete mode 100644 validator/static/validator/python/wheels/pgs_template_validator-1.1.0-py3-none-any.whl create mode 100644 validator/static/validator/python/wheels/pgs_template_validator-1.1.1-py3-none-any.whl diff --git a/validator/static/validator/js/webworker.js b/validator/static/validator/js/webworker.js index f1078ebe..06562376 100644 --- a/validator/static/validator/js/webworker.js +++ b/validator/static/validator/js/webworker.js @@ -13,7 +13,7 @@ async function loadPyodideAndPackages() { const micropip = pyodide.pyimport("micropip"); await micropip.install(['openpyxl','requests','httpx==0.26.0','tenacity','pyliftover', 'xopen==1.8.0','zstandard','tqdm','natsort','pandas','pandas-schema']); - await micropip.install(wheels_base_url+"pgs_template_validator-1.1.0-py3-none-any.whl", keep_going=true); + await micropip.install(wheels_base_url+"pgs_template_validator-1.1.1-py3-none-any.whl", keep_going=true); await 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zgO;~RGhbqvKjBwH z3Y?0s$?C*HpAA23&Pl1Rsu{E3OHj+ch1;JcN-CA!$g|3bnN!?T82y2bTRsdc?mhsE z5%boSF2#zsY_E%hF^mHJ-Fwp)Lw3c15SNhKBmc@1>a=lq~nz&{dS{BtFryoN8^$xSHhVb$W6 zFGuGu?{%oVmPwwA%bletzs_hX8~?OsnjHPh+ToX2aa8oo{Tv;5$qQ-OZ?el?c5q!y zDX~n5NiOOXXGGYd1Q3tj*<}^%A7dUK=Y;Otu4N;^N=Y2=b9w|l6Cer2t^crVwLJ7` zGC?I3{u5a^)VsUyF9WH-+gju00)5i^Vi=sBy4JTc=2YgfjiJv9&%7)Q6AR^$1$?&f z2X5^UrEte%LyU#)9_)Nj&#P z#GmokPbp8MqaP`(4-(8{M}7;Eeu{XSv;2sVdQfm45s#_MPYF-6H6IBn5B9c4!ei3r zQ^M0Uxkthl>hFaA%9eWydg`=%1YxrO0s6P^@+sh{CGinJ$MHMhPlMu9%2RvaBjv@z z*?k-l$3M(|Pbq)3dN>9DIR5fZ{re~kMCJLN@^3TLZ}I9+QBR#zk0{yyiTaPP>M7`{ zujvs4%lp6j^t;RHDeI{K{>Y*c`knP3Is7T$snqxgxEJ{Y@Gs%M~!e`F)6{cZNYX97>*PYaYsc(>-?hX12nc|!iL;^IGKC?l=EP5x)8p)3dc UFz@+G1jYn#KGZ5}x_|xqKhK6%{{R30 literal 0 HcmV?d00001 From 7cccb4e08675b6480c1b6ed24e6f66aae5f56cdd Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Mon, 28 Oct 2024 15:00:55 +0000 Subject: [PATCH 16/25] Removed "_client" suffix from validators urls --- catalog/templates/catalog/labs.html | 2 +- curation_tracker/urls.py | 2 +- validator/urls.py | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/catalog/templates/catalog/labs.html b/catalog/templates/catalog/labs.html index 0bac0132..1ce398e3 100644 --- a/catalog/templates/catalog/labs.html +++ b/catalog/templates/catalog/labs.html @@ -30,7 +30,7 @@

    Labs
    - +
    Score Validator
     diff --git a/curation_tracker/urls.py b/curation_tracker/urls.py index e6b265f7..3385ce6d 100644 --- a/curation_tracker/urls.py +++ b/curation_tracker/urls.py @@ -6,6 +6,6 @@ path('curation_tracker/l2_curation', views.browse_l2_waiting, name='L2 Curation'), path('curation_tracker/release_ready', views.browse_release_ready, name='Release Ready'), # e.g. /upload/ - path("validate_metadata/", views.validate_metadata_template, name="Metadata Template Validation"), + path("validate_metadata_legacy/", views.validate_metadata_template, name="Metadata Template Validation"), path('curation_tracker/stats/', views.stats, name='Curation Stats') ] diff --git a/validator/urls.py b/validator/urls.py index 1a572a95..cc6a2bac 100644 --- a/validator/urls.py +++ b/validator/urls.py @@ -2,6 +2,6 @@ from . import views urlpatterns = [ - path("validate_metadata_client/", views.validate_metadata_template_client, name="Metadata Template Validation"), - path("labs/validate_scoring_files_client/", views.validate_scoring_files_client, name="Scoring Files Validation"), + path("validate_metadata/", views.validate_metadata_template_client, name="metadata_template_validation"), + path("labs/validate_scoring_files/", views.validate_scoring_files_client, name="scoring_files_validation"), ] \ No newline at end of file From f06b88ce63f324f50d629d8f7c8b6ed44e2cc7ce Mon Sep 17 00:00:00 2001 From: Florent Yvon Date: Mon, 28 Oct 2024 15:02:53 +0000 Subject: [PATCH 17/25] Fixed title --- .../templates/validator/validate_scoring_files_client.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/validator/templates/validator/validate_scoring_files_client.html b/validator/templates/validator/validate_scoring_files_client.html index 6408342a..c58c7f25 100644 --- a/validator/templates/validator/validate_scoring_files_client.html +++ b/validator/templates/validator/validate_scoring_files_client.html @@ -1,7 +1,7 @@ {% extends 'catalog/base.html' %} {% load static %} -{% block title %}Metadata Template Validation{% endblock %} +{% block title %}Scoring Files Validation{% endblock %} {% block desc %}