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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,77 +1,159 @@ | ||
| <!DOCTYPE html> | ||
| <html> | ||
| <h1>Redirecting...</h1> | ||
| <script> | ||
| // config vars, these are DEFAULTS | ||
| var audience = "wolf.cci.emory.edu/camic_uat" | ||
| var scope = "openid%20email" | ||
| var client_id = "YLRDUmEs5Jivi6FX3XtNNAt97X3a0epD" | ||
| // handle urls automatically | ||
| var base_deployment_url = window.location.toString().split("/").slice(0,-1).join("/") | ||
| var redirect_uri = base_deployment_url + "/login.html" | ||
| var default_redirect = base_deployment_url + "/apps/table.html" | ||
| var response_type = "id_token" | ||
| var base_auth_url = "https://birmstuff.auth0.com/authorize?" | ||
| var cookie_name = "token" // "token" is expected by elevate router | ||
| // make the url | ||
| var auth_url = base_auth_url | ||
| auth_url += "&audience=" + audience | ||
| auth_url += "&scope=" + scope | ||
| auth_url += "&response_type=" + response_type | ||
| auth_url += "&client_id=" + client_id | ||
| auth_url += "&redirect_uri=" + redirect_uri | ||
| <head> | ||
| <title>CaMicroscope</title> | ||
| <meta charset="utf-8" /> | ||
| <meta name="google-signin-client_id" content="539699277901-buh78f048405grejogqbrskj233rt0d0.apps.googleusercontent.com"> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1" /> | ||
| <link rel="stylesheet" href="./apps/landing/main.css" /> | ||
| <script type="text/javascript" src="./common/util.js"></script> | ||
| </head> | ||
| <body> | ||
| <header id="header"> | ||
| <label style="color:white;padding:0 15px;font-size:20px;">CaMicroscope</label> | ||
| <nav id="nav"> | ||
| <ul> | ||
| <li><a target="_blank" href="https://docs.google.com/forms/d/e/1FAIpQLScL91LxrpAZjU88GBZP9gmcdgdf8__uNUwhws2lzU6Lr4qNwA/viewform">Feedback</a></li> | ||
| <!-- <li><a href="./login.html?logout=true">Sign Out</a></li> --> | ||
| </ul> | ||
| </nav> | ||
| </header> | ||
| <section id="main" class="wrapper" style="padding:3em;"> | ||
| <div class="inner"> | ||
| <header class="major"> | ||
| <h2 style="margin:0;">caMicroscope</h2> | ||
| </header> | ||
| <!-- Content --> | ||
|
|
||
| function randomString(length) { | ||
| var bytes = new Uint8Array(length); | ||
| var random = window.crypto.getRandomValues(bytes); | ||
| var result = []; | ||
| var charset = '0123456789ABCDEFGHIJKLMNOPQRSTUVXYZabcdefghijklmnopqrstuvwxyz-._~' | ||
| random.forEach(function (c) { | ||
| <div class="content"> | ||
| <p><strong>caMicroscope</strong> is a tool to view, label, and annotate biomedical images.</p> | ||
| <a href="#" class="image fit"><img src="./apps/landing/banner1.jpg" alt="" /></a> | ||
|
|
||
| </div> | ||
|
|
||
| <div class="posts" style="justify-content: center;"> | ||
| <!-- Organizer --> | ||
| <section class="post"> | ||
| <a href="../table.html" class="image"><img src="./apps/landing/camic.jpg" alt=""/></a> | ||
| <div class="content"> | ||
| <h3>Please Sign In With Your Google Account</h3> | ||
| <div id="google-signin2"></div> | ||
| </div> | ||
| </section> | ||
| </div> | ||
| </section> | ||
|
|
||
| <script> | ||
| function onSuccess(googleUser) { | ||
| // don't if we're logging out | ||
| if (getUrlParam("logout")) { | ||
| removeUserConsentAcceptance(getUserId()); | ||
| signOut(); | ||
| deleteCookies(); | ||
| console.log("logging out"); | ||
| window.location.href = "./login.html"; | ||
| } else { | ||
| var id_token = googleUser.getAuthResponse().id_token; | ||
| // console.info(id_token); | ||
| // trade for camic token | ||
| var cookie_name = "token"; // "token" is expected by elevate router | ||
| var base_deployment_url = window.location | ||
| .toString() | ||
| .split("/") | ||
| .slice(0, -1) | ||
| .join("/"); | ||
| var redirect_uri = base_deployment_url + "/login.html"; | ||
| var default_redirect = base_deployment_url + "/apps/table.html"; | ||
| var state; | ||
| if (getUrlParam("state")) { | ||
| state = decodeURIComponent(getUrlParam("state")); | ||
| } | ||
| if (!state) { | ||
| state = default_redirect; | ||
| } | ||
| if (id_token) { | ||
| document.cookie = cookie_name + "=" + id_token; | ||
| fetch("./auth/Token/check", { | ||
| headers: { | ||
| Authorization: "Bearer " + id_token | ||
| } | ||
| }) | ||
| .then(x => x.json()) | ||
| .then(x => { | ||
| if (x.hasOwnProperty("token")) { | ||
| document.cookie = cookie_name + "=" + x.token; | ||
| let token_data = parseJwt(x.token); | ||
| window.location = "./apps/landing/landing.html"; | ||
| } else { | ||
| window.alert("User not added"); | ||
| window.location = "./apps/signup/signup"; | ||
| } | ||
| }); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| function onFailure(error) { | ||
| console.error(error); | ||
| } | ||
|
|
||
| function renderButton() { | ||
| gapi.signin2.render('google-signin2', { | ||
| 'scope': 'profile email', | ||
| 'width': 240, | ||
| 'height': 50, | ||
| 'longtitle': true, | ||
| 'theme': 'dark', | ||
| 'onsuccess': onSuccess, | ||
| 'onfailure': onFailure | ||
| }); | ||
| } | ||
|
|
||
| function signOut() { | ||
| var auth2 = gapi.auth2.getAuthInstance(); | ||
| auth2.signOut().then(function() { | ||
| console.log("User signed out."); | ||
| }); | ||
| } | ||
|
|
||
| function deleteCookies() { | ||
| var allcookies = document.cookie.split(";"); | ||
| for (var i = 0; i < allcookies.length; i++) { | ||
| var cookie = allcookies[i]; | ||
| var eqPos = cookie.indexOf("="); | ||
| var name = eqPos > -1 ? cookie.substr(0, eqPos) : cookie; | ||
| document.cookie = name + "=;expires=Thu, 01 Jan 1970 00:00:00 GMT;"; | ||
| } | ||
| } | ||
|
|
||
| // google's jwk is here: https://www.googleapis.com/oauth2/v3/certs | ||
| function randomString(length) { | ||
| var bytes = new Uint8Array(length); | ||
| var random = window.crypto.getRandomValues(bytes); | ||
| var result = []; | ||
| var charset = | ||
| "0123456789ABCDEFGHIJKLMNOPQRSTUVXYZabcdefghijklmnopqrstuvwxyz-._~"; | ||
| random.forEach(function(c) { | ||
| result.push(charset[c % charset.length]); | ||
| }); | ||
| return result.join(''); | ||
| } | ||
| }); | ||
| return result.join(""); | ||
| } | ||
|
|
||
| function getUrlParam(name, url) { | ||
| if (!url) url = window.location.href; | ||
| name = name.replace(/[\[\]]/g, '\\$&'); | ||
| var regex = new RegExp('[?&#]' + name + '(=([^&#]*)|&|#|$)'), | ||
| function getUrlParam(name, url) { | ||
| if (!url) url = window.location.href; | ||
| name = name.replace(/[\[\]]/g, "\\$&"); | ||
| var regex = new RegExp("[?&#]" + name + "(=([^&#]*)|&|#|$)"), | ||
| results = regex.exec(url); | ||
| if (!results) return null; | ||
| if (!results[2]) return ''; | ||
| return decodeURIComponent(results[2].replace(/\+/g, ' ')); | ||
| } | ||
|
|
||
| // get variables | ||
| let id_token = getUrlParam("id_token") | ||
| let state = getUrlParam("state") | ||
| if (!state){ | ||
| state = default_redirect | ||
| } | ||
| // is this a login pre or post? | ||
| if (id_token){ | ||
| document.cookie = cookie_name + "=" + id_token; | ||
| fetch("./auth/Token/check", | ||
| {headers: { | ||
| 'Authorization': "Bearer " + id_token | ||
| }} | ||
| ).then(x=>x.json()).then(x=>{ | ||
| console.log("{id provider", id_token) | ||
| console.log("{auth service}", x) | ||
| if (x.hasOwnProperty('token')){ | ||
| document.cookie = cookie_name + "=" + x.token; | ||
| window.location = state | ||
| } else { | ||
| console.error("please give me a better failure message/response") | ||
| window.alert("User not added") | ||
| window.location = "./apps/signup/signup" | ||
| if (!results) return null; | ||
| if (!results[2]) return ""; | ||
| return decodeURIComponent(results[2].replace(/\+/g, " ")); | ||
| } | ||
| </script> | ||
|
|
||
| }) | ||
| } else { | ||
| window.localStorage.setItem('nonce', randomString(16)); | ||
| auth_url += "&state=" + state | ||
| auth_url += "&nonce=" + window.localStorage.getItem('nonce') | ||
| window.location = auth_url | ||
| } | ||
| </script> | ||
| <html> | ||
| <script src="https://apis.google.com/js/platform.js?onload=renderButton" async defer></script> | ||
|
|
||
| <script> | ||
|
|
||
| </script> | ||
| </body> | ||
| </html> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| # caMicroscope Data Types | ||
| A description of data types for use with caMicroscope | ||
|
|
||
| ## Files | ||
|
|
||
| ### Slides | ||
| All slides should be openslide compatible, but not all formats seem to work consistently. SVS and TIF file extensions seem to work most reliably. | ||
|
|
||
| ### TFJS Models and Weights | ||
| The prediction and segmentation applications can use a suitable tensorflow.js formatted model and weights to operate. [This guide](https://www.tensorflow.org/js/guide/save_load) may be useful for the generation of these files. | ||
|
|
||
| ### Data Associated with Mongo | ||
| Segmentations, Heatmaps, annotations, and Templates are all primarily mongo documents, and are described in the next section. Use mongoexport or mongoimport in a `docker exec -it ca-mongo` context. | ||
|
|
||
| ## Mongo Data and Metadata | ||
|
|
||
| ### Slide Metadata | ||
| Slides are identified by their uuid, which is automatically generated. Slides have a display name `name`, a file location in context `location`, a measurement scale conversion factor in micrometers per pixel `mpp`, and `study` and `specimen` fields. | ||
|
|
||
| ### Marks/Annotations | ||
| Marks are extended [geoJson](https://geojson.org/) formatted items with [viewport coordinates](https://openseadragon.github.io/examples/viewport-coordinates/). The geojson component is contained within `geometries`. `provenance` describes the source `provenance.analysis.source` and associated slide uuid `provenance.image.slide` of the mark, as well as the mark's execution id `provenance.analysis.execution_id`, and the mark's display name `provenance.analysis.name`. `properties` has any filled out information associated with an active template. | ||
|
|
||
| ### Heatmaps | ||
| Heatmaps are data on a grid. `data` is a list of grid elements, in the format `[x position, y position, variable 1 value, *any additional values, if any*]`. The associated fields are stored `provenance.analysis.fields` in a list of items of format `{"name":"FIELDNAME", "range":[min,max]}`. The x and y positions are translated according to `provenance.analysis.coordinateSystem`. The associated slide, as with marks, is `provenance.image.slide`. The heatmap relative id is `provenance.image.execution_id`. | ||
|
|
||
| ## Sample Data | ||
|
|
||
| ### Mongo Data | ||
| See https://github.com/camicroscope/Distro/blob/master/config/test_seed.js |
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