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Merge pull request #2 from ENCODE-DCC/dev
v0.3.3
2 parents 8a5a7a5 + bfe5a97 commit 97e5901

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‎README.md‎

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## ENCODE metadata submitter
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Metadata manager based on Google Sheet + Google Apps Script
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https://docs.google.com/spreadsheets/d/1mmTsrT4tnD4fRAf7nkdduq810nZvMQxZy0ga4Z_zK74/edit?usp=sharing
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## Google Sheet
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## Grant permission first
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Make a copy of this document.
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Grant permissions for the script to access your data on the sheet/account.
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https://docs.google.com/spreadsheets/d/1mmTsrT4tnD4fRAf7nkdduq810nZvMQxZy0ga4Z_zK74/edit?usp=sharing
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## Authorization (username/password)
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Go to portail's Profile page and get credentials pair (username/password).
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Go to `ENCODE` - `Authorize`. Credentials entered here will be shared for all sheets in the whole spreadsheet, but **NOT SHARED WITH OTHERS EVEN WHEN THEY MAKE A COPY OF YOUR SPREADSHEET**.
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## Set a profile name
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Go to `ENCODE` - `Set profile name` and enter a valid profile name. A profile name in snakecase or capitalized CamelCase are allowed. For example, `experiment`, `Expertiment`, `biosample_type` and `BiosampleType`. Such profile name should be set for each sheet.
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## Check your current profile
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Go to `ENCODE` - `Show sheet/header info`.
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## Special commented headers
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Data values under commented headers will be ignored and not be sent to the portal.
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- `#skip`: For all REST actions (GET/PUT/POST). You can additionally make `#skip` header and set row's data cell as 1 to skip REST actions for that specific row.
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- `#error`: For debugging purposese. This is filled with `HTTP ERROR CODE` + `HELP TEXT MESSAGE` for any recent REST action.
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## Make a POST template based on profile
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Once you set a valid profile name, go to `ENCODE` - `Make new template row`. This will make a new row with empty/default values for each property. This templatre include ALL editable properties for a given profile. Some of them are shown but not editable (e.g. `schema_version` and `accession`).
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## GET metadata from portal
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Make a new header with a proper identifying property (`accession` or `uuid` according to the given profile). And then define accession/uuids you want to retrieve from the portal under the header. Go to `ENCODE` - `Get metadata for all raws`.
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## PUT metadata to portal
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GET metadata from portal first and then edit it. Set `#skip` as `0` if it is present and then go to `ENCODE` - `PUT all rows to the portal` .
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## POST metadata to portal
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Starting from a template or existing metadata (retrieved from GET), set `#skip` as `0` if it is present and then go to `ENCODE` - `POST all rows to the portal` .
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## How to debug?
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Any REST (GET/PUT/POST) action will return `HTTP ERROR CODE` + `HELP TEXT MESSAGE` in the `#error` column. Fix your problem with the help message and resubmit.
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## How to search for items on portal
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Go to a data cell and hover your mouse on the header (1st row) of the column and check if it's shown as `SEARCH AVAILABLE` in its tooltop. On a data cell that you want to edit, go to `ENCODE` - `Search`. Then you will see a dialog box to edit your values.

‎src/Library.gs‎

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const DEBUG = false;
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const DEBUG_AUTO_YES = false;
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// const DEBUG = true;
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// const DEBUG_AUTO_YES = true;
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function getType(p) {
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if (Array.isArray(p)) return "array";
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else if (typeof p == "string") return "string";

‎src/Metadata.gs‎

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function makeMetadataUrl(method, profileName, endpoint, identifyingVal) {
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switch(method) {
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case "GET":
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return `${endpoint}/${profileName}/${identifyingVal}/?format=json&frame=edit`;
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return `${endpoint}/${profileName}/${identifyingVal}/?format=json&frame=object`;
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case "PUT":
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return `${endpoint}/${profileName}/${identifyingVal}`;
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case "POST":
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var responseJson = JSON.parse(response.getContentText());
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if (error === 200) {
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// if no error, merge parsed JSON to row object
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// automatically set #skip as 1 to prevent duplicate GET
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object[HEADER_COMMENTED_PROP_SKIP] = 1;
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object = {...object, ...responseJson};
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// filter out
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// - "nonSubmittable" properties
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// - properties that are not present in the profile
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var profile = getProfile(profileName, endpoint);
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var filteredResponseJson = Object.keys(responseJson)
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.filter((prop) => profile["properties"].hasOwnProperty(prop))
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.filter((prop) => !isNonSubmittableProp(profile, prop))
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.reduce((cur, prop) => { return Object.assign(cur, { [prop]: responseJson[prop] })}, {});
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// then merge it with commented properties
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object = {...object, ...filteredResponseJson};
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}
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else {
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// if error, write helpText to provide debugging information
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return sortedProps;
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}
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getIdentifyingPropForProfile
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function updateSheetWithMetadataFromPortal(sheet, profileName, endpointForGet, endpointForProfile) {
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var profile = getProfile(profileName, endpointForProfile);
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if (!profile) {
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switch(method) {
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case "PUT":
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var url = makeMetadataUrl(method, profileName, endpointForPut, json[identifyingProp]);
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var response = restPut(url, payloadJson=json);
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break;

‎src/UserInterface.gs‎

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const KEY_ENDPOINT_READ = "endpointRead";
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const KEY_ENDPOINT_WRITE = "endpointWrite";
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const KEY_PROFILE_NAME = "profileName";
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const URL_GITHUB = "https://github.com/encode-DCC/google-sheet-metadata-submitter";
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function onOpen() {
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menu.addItem("Set endpoint for WRITE actions", "setEndpointWrite");
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menu.addItem("Set profile name", "setProfileName");
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menu.addItem("Open profile page", "openProfilePage");
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menu.addSeparator();
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menu.addItem("Open tool's github page for README", "openToolGithubPage");
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menu.addToUi();
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}
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);
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}
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function openToolGithubPage() {
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openUrl(URL_GITHUB);
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}
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function showSheetAndHeaderInfo() {
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alertBox(
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"* Sheet information\n" +

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