diff --git a/public/imports.js b/public/imports.js index 7bf9d733a..7ce2f624e 100755 --- a/public/imports.js +++ b/public/imports.js @@ -42,7 +42,6 @@ document.addEventListener('DOMContentLoaded', async function () { } if (allPresentInDom) { clearInterval(interval) - console.log("Finished loading html") resolve() } else { console.log('Nothing in DOM yet, waiting 100ms') diff --git a/public/nav.js b/public/nav.js index 040e655eb..767a4f603 100755 --- a/public/nav.js +++ b/public/nav.js @@ -4,7 +4,6 @@ import Swal from "sweetalert2"; while (!window.htmlPagesAdded) { await new Promise((resolve) => setTimeout(resolve, 100)) } -console.log("Going for it") // this variable is here to keep track of when the Organize datasets/Continue button is enabled or disabled @@ -82,7 +81,6 @@ const handleSectionTrigger = async (event) => { } if (sectionId === "guided_mode-section") { - console.log("IN this section") // Disallow the transition if an upload is in progress if (document.getElementById("returnButton") !== null) { Swal.fire({ @@ -226,10 +224,8 @@ const handleSectionTrigger = async (event) => { ]; if (showSidebarSections.includes(sectionId)) { - console.log("Here?") forceActionSidebar("show"); } else { - console.log("In elese statement") forceActionSidebar("hide"); } @@ -254,7 +250,6 @@ const handleSectionTrigger = async (event) => { }; function showMainContent() { - console.log(document.querySelector(".js-nav").classList) document.querySelector(".js-nav").classList.add("is-shown"); document.querySelector(".js-content").classList.add("is-shown"); } diff --git a/src/main/strain.js b/src/main/strain.js index 3d8dcd21b..95a0923a3 100644 --- a/src/main/strain.js +++ b/src/main/strain.js @@ -8,7 +8,6 @@ ipcMain.handle("getStrainData", async (event, rridInfo) => { let data = ""; let dataReady = false; if (res.statusCode === 200) { - console.log("Status code is 200?") res.setEncoding("utf8"); res.on("data", (d) => { data += d; @@ -29,7 +28,6 @@ ipcMain.handle("getStrainData", async (event, rridInfo) => { }) }) - console.log("Data is", data) // let xmlSerializer = new XMLSerializer(); diff --git a/src/preload/index.js b/src/preload/index.js index a499a2e0b..57e79a873 100644 --- a/src/preload/index.js +++ b/src/preload/index.js @@ -17,9 +17,7 @@ fixPath(); import "v8-compile-cache"; -console.log(log); -console.log(log.transports); -console.log(log.transports.file); + log.initialize(); // Custom APIs for renderer diff --git a/src/preload/update-path-darwin.js b/src/preload/update-path-darwin.js index e40047c9a..73ffbf0d2 100644 --- a/src/preload/update-path-darwin.js +++ b/src/preload/update-path-darwin.js @@ -16,7 +16,6 @@ const fixPath = () => { window.process.env.PATH, ].join(":"); - console.log("PATH updated to: " + window.process.env.PATH) } }; diff --git a/src/renderer/src/assets/imports.js b/src/renderer/src/assets/imports.js index 7bf9d733a..7ce2f624e 100644 --- a/src/renderer/src/assets/imports.js +++ b/src/renderer/src/assets/imports.js @@ -42,7 +42,6 @@ document.addEventListener('DOMContentLoaded', async function () { } if (allPresentInDom) { clearInterval(interval) - console.log("Finished loading html") resolve() } else { console.log('Nothing in DOM yet, waiting 100ms') diff --git a/src/renderer/src/assets/nav.js b/src/renderer/src/assets/nav.js index ce0d7a2a6..4af7c1b0b 100644 --- a/src/renderer/src/assets/nav.js +++ b/src/renderer/src/assets/nav.js @@ -3,7 +3,6 @@ import Swal from "sweetalert2"; while (!window.htmlPagesAdded) { await new Promise((resolve) => setTimeout(resolve, 100)) } -console.log("Going for it") // this variable is here to keep track of when the Organize datasets/Continue button is enabled or disabled @@ -81,7 +80,6 @@ const handleSectionTrigger = async (event) => { } if (sectionId === "guided_mode-section") { - console.log("IN this section") // Disallow the transition if an upload is in progress if (document.getElementById("returnButton") !== null) { Swal.fire({ @@ -225,10 +223,8 @@ const handleSectionTrigger = async (event) => { ]; if (showSidebarSections.includes(sectionId)) { - console.log("Here?") forceActionSidebar("show"); } else { - console.log("In elese statement") forceActionSidebar("hide"); } @@ -253,7 +249,6 @@ const handleSectionTrigger = async (event) => { }; function showMainContent() { - console.log(document.querySelector(".js-nav").classList) document.querySelector(".js-nav").classList.add("is-shown"); document.querySelector(".js-content").classList.add("is-shown"); } diff --git a/src/renderer/src/scripts/globals.js b/src/renderer/src/scripts/globals.js index fe79b47ee..8f87ccb5c 100644 --- a/src/renderer/src/scripts/globals.js +++ b/src/renderer/src/scripts/globals.js @@ -1365,7 +1365,6 @@ window.openDropdownPrompt = async (ev, dropdown, show_timer = true) => { } let result = responseObject.data.datasets; - console.log("Dataset results: ", result) window.datasetList = []; window.datasetList = result; window.refreshDatasetList(); @@ -1701,7 +1700,6 @@ window.openDropdownPrompt = async (ev, dropdown, show_timer = true) => { }, }); - console.log(result) if (result) { await window.openDropdownPrompt(this, "bf"); diff --git a/src/renderer/src/scripts/guided-mode/guided-curate-dataset.js b/src/renderer/src/scripts/guided-mode/guided-curate-dataset.js index 51b3209e9..8f5beb052 100644 --- a/src/renderer/src/scripts/guided-mode/guided-curate-dataset.js +++ b/src/renderer/src/scripts/guided-mode/guided-curate-dataset.js @@ -3259,7 +3259,6 @@ const generateProgressCardElement = (progressFileJSONObj) => { }; const guidedRenderProgressCards = async () => { - console.log("Loading the render progress cards func"); const progressCardsContainer = document.getElementById("guided-container-progress-cards"); const progressCardLoadingDiv = document.getElementById("guided-section-loading-progress-cards"); @@ -3429,7 +3428,6 @@ window.guidedOpenManifestEditSwal = async (highLevelFolderName) => { //upon receiving a reply of the spreadsheet, handle accordingly window.electron.ipcRenderer.on("spreadsheet-reply", async (event, result) => { - console.log("Spreadsheet reply from guided curate"); if (!result || result === "") { window.electron.ipcRenderer.removeAllListeners("spreadsheet-reply"); return; @@ -3936,7 +3934,6 @@ const setActiveProgressionTab = (targetPageID) => { let targetProgressionTab = $(`#${targetProgressionTabID}`); targetProgressionTab.addClass("selected-tab"); }; -console.log(window.api); let homeDir = await window.electron.ipcRenderer.invoke("get-app-path", "home"); let guidedProgressFilePath = window.path.join(homeDir, "SODA", "Guided-Progress"); @@ -4834,17 +4831,14 @@ const updateGuidedRadioButtonsFromJSON = (parentPageID) => { }; const guidedAddUsersAndTeamsToDropdown = (usersArray, teamsArray) => { - console.log("HERE?"); const guidedUsersAndTeamsDropdown = document.getElementById("guided_bf_list_users_and_teams"); // Reset the dropdown guidedUsersAndTeamsDropdown.innerHTML = ""; - console.log(usersArray); // Loop through the users and add them to the dropdown for (const userString of usersArray) { - console.log(userString); const userNameAndEmail = userString.split("!|**|!")[0].trim(); const userID = userString.split("!|**|!")[1].trim(); const userOption = ` @@ -5037,7 +5031,6 @@ const handleNextButtonVisibility = (targetPageID) => { // //If the keys exist, extract the data from the window.sodaJSONObj and populate the page // //If the keys do not exist, reset the page (inputs, tables etc.) to the default state window.openPage = async (targetPageID) => { - console.log("TargetPageID is: ", targetPageID); //NOTE: 2 Bottom back buttons (one handles sub pages, and the other handles main pages) //Back buttons should be disabled and the function setLoading should be (set as false?) @@ -6076,10 +6069,8 @@ window.openPage = async (targetPageID) => { //Banner is returned as an s3 bucket url but image needs to be converted as //base64 to save and write to users local system - console.log(res); let img_base64 = await window.getBase64(res); // encode image to base64 - console.log("Not failing hehjasfhjk"); let guided_img_url = res; let imageType = ""; let fullBase64Image = ""; @@ -6152,7 +6143,6 @@ window.openPage = async (targetPageID) => { } window.sodaJSONObj["pages-fetched-from-pennsieve"].push("guided-banner-image-tab"); } catch (error) { - console.log("Failure is here"); clientError(error); const emessage = userErrorMessage(error); await guidedShowOptionalRetrySwal(emessage, "guided-banner-image-tab"); @@ -9425,7 +9415,6 @@ window.openGuidedAddContributorSwal = async () => { confirmButtonText: "Add contributor", confirmButtonColor: "#3085d6 !important", willOpen: () => { - console.log("Loading up the add contributor modal. ON wil open"); //Create Affiliation(s) tagify for each contributor const contributorAffiliationInput = document.getElementById( "guided-contributor-affiliation-input" @@ -9740,7 +9729,6 @@ const renderDatasetDescriptionContributorsTable = () => { }; const addContributorField = () => { - console.log("Adding contributor"); const contributorsContainer = document.getElementById("contributors-container"); //create a new div to hold contributor fields const newContributorField = document.createElement("div"); @@ -10839,7 +10827,6 @@ window.specifyPool = (event, poolNameInput) => { setActiveSubPage("guided-organize-subjects-into-pools-page"); return; } else { - console.log("Pools here?"); //Add left border back to subject dropdown cell to separate pool name and subject dropdown poolSubjectsDropdownCell.removeClass("remove-left-border"); @@ -12229,7 +12216,6 @@ const createPennsievePermissionsTableRowElement = (entityType, name, permission, } }; const renderPermissionsTable = () => { - console.log("Rendering permissions table?"); // when rendering permissions we will need to check if the permission was fetched from pennsieve // we will then create a different table element that will behave differently // visually showing user that the permission will be deleted upon upload @@ -12500,7 +12486,6 @@ const setGuidedDatasetPiOwner = (newPiOwnerObj) => { }; const guidedAddUserPermission = (newUserPermissionObj) => { - console.log("Adding user permissions"); //If an existing user with the same ID already exists, update the existing user's position for (userPermission of window.sodaJSONObj["digital-metadata"]["user-permissions"]) { if ( @@ -13076,7 +13061,6 @@ document.getElementById("button-homepage-guided-mode").addEventListener("click", attachGuidedMethodsToSodaJSONObj(); guidedTransitionFromHome(); - console.log("About to unlock sidebar"); guidedUnLockSideBar(); guidedUnSkipPage("guided-select-starting-point-tab"); @@ -13094,7 +13078,6 @@ document.querySelector("#button-homepage-freeform-mode").addEventListener("click }); $("#guided-button-add-permission-user-or-team").on("click", function () { - console.log("Here finally"); try { //get the selected permission element const newPermissionElement = $("#guided_bf_list_users_and_teams option:selected"); @@ -13681,7 +13664,6 @@ $("#guided-input-destination-getting-started-locally").on("click", () => { }); const guidedCreateOrRenameDataset = async (bfAccount, datasetName) => { - console.log("That is the dataset name: ", datasetName); document.getElementById("guided-dataset-name-upload-tr").classList.remove("hidden"); const datasetNameUploadText = document.getElementById("guided-dataset-name-upload-text"); @@ -14574,7 +14556,6 @@ window.electron.ipcRenderer.on( // Remove unnecessary key from sodaJSONObjCopy since we don't need to // check if the account details are valid during local generation delete sodaJSONObjCopy["bf-account-selected"]; - console.log("making post request to /curate_datasets/curation"); updateDatasetUploadProgressTable("local", { "Current action": `Preparing dataset for local generation`, @@ -14601,7 +14582,6 @@ window.electron.ipcRenderer.on( const { data } = response; const main_curate_progress_message = data["main_curate_progress_message"]; if (main_curate_progress_message === "Success: COMPLETED!") { - console.log("Done with generation"); break; // Exit the loop when generation is done } const elapsed_time_formatted = data["elapsed_time_formatted"]; @@ -14646,10 +14626,7 @@ window.electron.ipcRenderer.on( updateDatasetUploadProgressTable("local", { "Current action": `Generating metadata files`, }); - console.log( - "Subjects path: ", - window.path.join(filePath, guidedDatasetName, "subjects.xlsx") - ); + // Generate all dataset metadata files await guidedGenerateSubjectsMetadata( window.path.join(filePath, guidedDatasetName, "subjects.xlsx") @@ -14992,10 +14969,7 @@ const guidedGenerateDatasetDescriptionMetadata = async (destination) => { ); } - console.log("guidedDatasetInformation", guidedDatasetInformation); - console.log("guidedStudyInformation", guidedStudyInformation); - console.log("guidedContributorInformation", guidedContributorInformation); - console.log("datasetLinks", datasetLinks); + try { await client.post( `/prepare_metadata/dataset_description_file`, @@ -16128,7 +16102,6 @@ $("#guided-generate-changes-file").on("click", () => { }); $("#guided-generate-dataset-button").on("click", async function () { - console.log("Generating for GM"); // Ensure that the current workspace is the workspace the user confirmed const currentWorkspace = guidedGetCurrentUserWorkSpace(); const datasetWorkspace = window.sodaJSONObj["digital-metadata"]["dataset-workspace"]; @@ -16217,7 +16190,6 @@ $("#guided-generate-dataset-button").on("click", async function () { }); const guidedSaveBannerImage = async () => { - console.log("Wowawhoo"); $("#guided-para-dataset-banner-image-status").html("Please wait..."); //Save cropped image locally and check size let imageFolder = path.join(homeDirectory, "SODA", "guided-banner-images"); diff --git a/src/renderer/src/scripts/manage-dataset/manage-dataset.js b/src/renderer/src/scripts/manage-dataset/manage-dataset.js index ccff67f19..282ce8328 100644 --- a/src/renderer/src/scripts/manage-dataset/manage-dataset.js +++ b/src/renderer/src/scripts/manage-dataset/manage-dataset.js @@ -1656,7 +1656,6 @@ const showDatasetDescription = async () => { }; window.getBase64 = async (url) => { - console.log("THe url passed down will be: ", url) return await window.electron.ipcRenderer.invoke("get-string-representation-of-buffer", url, "binary") }; @@ -2034,7 +2033,6 @@ const uploadBannerImage = async () => { } else { //final size is greater than 5mb so compress image here (image already created and stored in temp file) let scaledImagePath = await window.scaleBannerImage(imagePath); //scaled image will be in temp folder - console.log("Scaled image path value: ", scaledImagePath) let image_file_size = window.fs.fileSizeSync(scaledImagePath); //update size for analytics try { let uploadBannerImage = await client.put( diff --git a/src/renderer/src/scripts/metadata-files/datasetDescription.js b/src/renderer/src/scripts/metadata-files/datasetDescription.js index b840c65e8..98879af74 100644 --- a/src/renderer/src/scripts/metadata-files/datasetDescription.js +++ b/src/renderer/src/scripts/metadata-files/datasetDescription.js @@ -1283,7 +1283,6 @@ window.edit_current_con_id = (ev) => { const memorizeAffiliationInfo = (values) => { window.createMetadataDir(); - console.log("affiliationConfigPath", window.affiliationConfigPath) var content = window.parseJson(window.affiliationConfigPath); content["affiliation"] = values; window.fs.writeFileSync(window.affiliationConfigPath, JSON.stringify(content)); diff --git a/src/renderer/src/scripts/metadata-files/downloadTemplates.js b/src/renderer/src/scripts/metadata-files/downloadTemplates.js index c6486d9f1..907c3d776 100644 --- a/src/renderer/src/scripts/metadata-files/downloadTemplates.js +++ b/src/renderer/src/scripts/metadata-files/downloadTemplates.js @@ -26,9 +26,7 @@ let templateArray = [ const downloadTemplates = async (templateItem, destinationFolder) => { let currentDirectory = await window.electron.ipcRenderer.invoke("get-current-directory"); let templatePath = window.path.join(currentDirectory, "..", "renderer", "file_templates", templateItem); - console.log(templatePath) let destinationPath = window.path.join(destinationFolder, templateItem); - console.log(destinationPath) if (window.fs.existsSync(destinationPath)) { let emessage = "File '" + templateItem + "' already exists in " + destinationFolder; diff --git a/src/renderer/src/scripts/metadata-files/manifest.js b/src/renderer/src/scripts/metadata-files/manifest.js index 67986687a..3d6d81f90 100644 --- a/src/renderer/src/scripts/metadata-files/manifest.js +++ b/src/renderer/src/scripts/metadata-files/manifest.js @@ -268,7 +268,6 @@ $(document).ready(async function () { //Event listener for the jstree to open manifest files $(jstreePreviewManifest).on("select_node.jstree", async function (evt, data) { - console.log("Doing this?") // Check if pennsieve option was selected to reset localDataSetImport if (document.getElementById("pennsieve-option-create-manifest").classList.contains("checked")) { localDataSetImport = false; @@ -529,7 +528,6 @@ $(document).ready(async function () { //upon receiving a reply of the spreadsheet, handle accordingly window.electron.ipcRenderer.on("spreadsheet-reply", async (event, result) => { - console.log("Spreadsheet reply") openedEdit = false; if (!result || result === "") { window.electron.ipcRenderer.removeAllListeners("spreadsheet-reply"); @@ -558,8 +556,7 @@ $(document).ready(async function () { window.fs.closeSync(window.fs.openSync(selectedManifestFilePath, "w")); } - console.log("Creating the stuff here") - console.log(selectedManifestFilePath) + jsonManifest = await window.electron.ipcRenderer.invoke("excelToJsonSheet1Options",{ sourceFile: selectedManifestFilePath, columnToKey: { @@ -679,7 +676,6 @@ $(document).ready(async function () { window.sodaJSONObj["digital-metadata"]["name"], parentFolderName ); - console.log("Failing here?") var selectedManifestFilePath = window.path.join(localFolderPath, "manifest.xlsx"); jsonManifest = await window.electron.ipcRenderer.invoke("excelToJsonSheet1Options",{ sourceFile: selectedManifestFilePath, @@ -756,7 +752,6 @@ window.generateManifestPrecheck = async (manifestEditBoolean, ev) => { ).placeholder; pennsievePreview = false; const type = determineStandaloneManifestGeneratorOrigin(); - console.log("Type is: ", type) window.exitCurate(); window.sodaJSONObj["starting-point"] = {}; @@ -767,7 +762,6 @@ window.generateManifestPrecheck = async (manifestEditBoolean, ev) => { if (type === "bf") { titleTerm = "on Pennsieve"; } else if (type != "bf" && !pennsievePreview) { - console.log("Validating?") continueProgressValidateDataset = validateSPARCdataset(); if (!continueProgressValidateDataset) { @@ -780,8 +774,7 @@ window.generateManifestPrecheck = async (manifestEditBoolean, ev) => { localGenerationDifferentDestination = true; } - console.log("Local generation different destination: ", localGenerationDifferentDestination) - console.log("Local dataset path: ", localDatasetPath) + await window.wait(500); if (!localGenerationDifferentDestination) { @@ -904,11 +897,9 @@ const generateManifest = async (action, type, manifestEditBoolean, ev) => { localDatasetFolderPath = $("#input-manifest-local-folder-dataset").attr("placeholder"); } await window.create_json_object(action, window.sodaJSONObj, localDatasetFolderPath); - console.log("FInished create json object") window.datasetStructureJSONObj = window.sodaJSONObj["dataset-structure"]; window.populate_existing_folders(window.datasetStructureJSONObj); window.populate_existing_metadata(window.sodaJSONObj); - console.log("FInished populate methods") window.sodaJSONObj["manifest-files"] = { destination: "generate-dataset" }; window.sodaJSONObj["bf-account-selected"] = {}; window.sodaJSONObj["bf-dataset-selected"] = {}; @@ -917,7 +908,6 @@ const generateManifest = async (action, type, manifestEditBoolean, ev) => { let continueProgressEmptyFolder = await checkEmptySubFolders( window.sodaJSONObj["dataset-structure"] ); - console.log("FInished check empty sub folders") if (continueProgressEmptyFolder === false) { Swal.fire({ title: "Failed to generate the manifest files.", @@ -947,7 +937,6 @@ const generateManifest = async (action, type, manifestEditBoolean, ev) => { let continueProgressNoSPARCFolders = await checkNoSparcFolders( window.sodaJSONObj["dataset-structure"] ); - console.log("FInished check no sparc folders") if (continueProgressNoSPARCFolders === true) { Swal.fire({ title: "Failed to generate the manifest files.", @@ -976,7 +965,6 @@ const generateManifest = async (action, type, manifestEditBoolean, ev) => { let continueProgressInvalidFolders = await checkInvalidHighLevelFolders( window.sodaJSONObj["dataset-structure"] ); - console.log("FInished check invalid high level folders") if (continueProgressInvalidFolders === true) { Swal.fire({ title: "Failed to generate the manifest files.", @@ -1001,9 +989,7 @@ const generateManifest = async (action, type, manifestEditBoolean, ev) => { return; } await generateManifestHelper(); - console.log("FInished generate manifest helper") await initiate_generate_manifest_local(manifestEditBoolean, localDatasetFolderPath); - console.log("FInished initiate generate manifest local") } } else { // Case 2: bf dataset @@ -1187,21 +1173,16 @@ const updateJSONStructureManifestGenerate = () => { const initiate_generate_manifest_local = async (manifestEditBoolean, originalDataset) => { if (manifestEditBoolean === false) { - console.log("Creating manifest file locally yes") createManifestLocally("local", false, originalDataset); } else { - console.log("Editing not creating? ") // SODA Manifest Files folder let dir = window.path.join(homeDirectory, "SODA", "manifest_files"); // Move manifest files to the local dataset let moveFinishedBool; let generationLocation; if (window.finalManifestGenerationPath == originalDataset) { - console.log("Generating over the existing dataset and will move ") moveFinishedBool = await moveManifestFiles(dir, originalDataset); - console.log("After movefunction") } else { - console.log("Move manifest preview flow") [moveFinishedBool, generationLocation] = await moveManifestFilesPreview( dir, window.finalManifestGenerationPath @@ -1215,7 +1196,6 @@ const initiate_generate_manifest_local = async (manifestEditBoolean, originalDat ); if (moveFinishedBool) { - console.log("Move finished") window.resetManifest(false); // reset window.sodaJSONObj window.sodaJSONObj = { @@ -2124,7 +2104,6 @@ const createManifestLocally = async (type, editBoolean, originalDataset) => { // create the manifest files based off the user's edits to the manifest files try { - console.log("IN the server at curate_datasets/manifest_files") let generate_local_manifest = await client.post( `/curate_datasets/manifest_files`, { @@ -2134,7 +2113,6 @@ const createManifestLocally = async (type, editBoolean, originalDataset) => { { timeout: 0 } ); - console.log("After the server at curate_datasets/manifest_files") let res = generate_local_manifest.data.success_message_or_manifest_destination; diff --git a/src/renderer/src/scripts/metadata-files/subjects-samples.js b/src/renderer/src/scripts/metadata-files/subjects-samples.js index d260cb771..85a95c22d 100644 --- a/src/renderer/src/scripts/metadata-files/subjects-samples.js +++ b/src/renderer/src/scripts/metadata-files/subjects-samples.js @@ -423,7 +423,6 @@ const addNewIDToTable = (newID, secondaryID, type) => { keyword + "_id(this)'>"); } else if (type === "samples") { - console.log("In samples ttypes"); var row = (table.insertRow(rowIndex).outerHTML = "