From 754e8f214b940e05298cb360ed829f5c685d55a5 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 25 Jul 2024 11:07:33 -0500
Subject: Rename module: qc_app --> uploader

---
 .../rqtl2/upload-rqtl2-bundle-step-01.html         | 276 ---------------------
 1 file changed, 276 deletions(-)
 delete mode 100644 qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html

(limited to 'qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html')

diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
deleted file mode 100644
index 07c240f..0000000
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
+++ /dev/null
@@ -1,276 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-{%from "upload_progress_indicator.html" import upload_progress_indicator%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-{%macro rqtl2_file_help()%}
-<span class="form-text text-muted">
-  <p>
-    Provide a valid R/qtl2 zip file here. In particular, ensure your zip bundle
-    contains exactly one control file and the corresponding files mentioned in
-    the control file.
-  </p>
-  <p>
-    The control file can be either a YAML or JSON file. <em>ALL</em> other data
-    files in the zip bundle should be CSV files.
-  </p>
-  <p>See the
-    <a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html"
-       target="_blank">
-      R/qtl2 file format specifications
-    </a>
-    for more details.
-  </p>
-</span>
-{%endmacro%}
-{{upload_progress_indicator()}}
-
-<div id="resumable-file-display-template"
-     class="panel panel-info"
-     style="display: none">
-  <div class="panel-heading"></div>
-  <div class="panel-body"></div>
-</div>
-
-
-<h2 class="heading">Upload R/qtl2 Bundle</h2>
-
-<div id="resumable-drop-area"
-     style="display:none;background:#eeeeee;min-height:12em;border-radius:0.5em;padding:1em;">
-  <p>
-    <a id="resumable-browse-button" href="#"
-       class="btn btn-info">Browse</a>
-  </p>
-  <p class="form-text text-muted">
-    You can drag and drop your file here, or click the browse button.
-    Click on the file to remove it.
-  </p>
-  {{rqtl2_file_help()}}
-  <div id="resumable-selected-files"
-       style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;"></div>
-  <div id="resumable-class-buttons" style="text-align: right;">
-    <button id="resumable-upload-button"
-            class="btn btn-primary"
-            style="display: none">start upload</button>
-    <button id="resumable-cancel-upload-button"
-            class="btn btn-danger"
-            style="display: none">cancel upload</button>
-  </div>
-  <div id="resumable-progress-bar" class="progress" style="display: none">
-    <div class="progress-bar"
-         role="progress-bar"
-         aria-valuenow="60"
-         aria-valuemin="0"
-         aria-valuemax="100"
-         style="width: 0%;">
-      Uploading: 60%
-    </div>
-  </div>
-</div>
-
-<form id="frm-upload-rqtl2-bundle"
-      action="{{url_for('upload.rqtl2.upload_rqtl2_bundle',
-	      species_id=species.SpeciesId,
-	      population_id=population.InbredSetId)}}"
-      method="POST"
-      enctype="multipart/form-data"
-      data-resumable-target="{{url_for(
-                             'upload.rqtl2.upload_rqtl2_bundle_chunked_post',
-                             species_id=species.SpeciesId,
-                             population_id=population.InbredSetId)}}">
-  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-  <input type="hidden" name="population_id"
-	 value="{{population.InbredSetId}}" />
-
-  {{flash_all_messages()}}
-
-  <div class="form-group">
-    <legend class="heading">file upload</legend>
-    <label for="file-rqtl2-bundle" class="form-label">R/qtl2 bundle</label>
-    <input type="file" id="file-rqtl2-bundle" name="rqtl2_bundle_file"
-	   accept="application/zip, .zip"
-	   required="required"
-           class="form-control" />
-    {{rqtl2_file_help()}}
-  </div>
-
-  <button type="submit"
-          class="btn btn-primary"
-          data-toggle="modal"
-          data-target="#upload-progress-indicator">upload R/qtl2 bundle</button>
-</form>
-
-{%endblock%}
-
-{%block javascript%}
-<script src="{{url_for('base.node_modules',
-             filename='resumablejs/resumable.js')}}"></script>
-<script type="text/javascript" src="/static/js/upload_progress.js"></script>
-<script type="text/javascript">
-  function readBinaryFile(file) {
-      return new Promise((resolve, reject) => {
-          var _reader = new FileReader();
-          _reader.onload = (event) => {resolve(_reader.result);};
-          _reader.readAsArrayBuffer(file);
-      });
-  }
-
-  function computeFileChecksum(file) {
-      return readBinaryFile(file)
-          .then((content) => {
-              return window.crypto.subtle.digest(
-                  "SHA-256", new Uint8Array(content));
-          }).then((digest) => {
-              return Uint8ArrayToHex(new Uint8Array(digest))
-          });
-  }
-
-  function Uint8ArrayToHex(arr) {
-      var toHex = (val) => {
-          _hex = val.toString(16);
-          if(_hex.length < 2) {
-              return "0" + val;
-          }
-          return _hex;
-      };
-      _hexstr = ""
-      arr.forEach((val) => {_hexstr += toHex(val)});
-      return _hexstr
-  }
-
-  var r = Resumable({
-      target: $("#frm-upload-rqtl2-bundle").attr("data-resumable-target"),
-      fileType: ["zip"],
-      maxFiles: 1,
-      forceChunkSize: true,
-      generateUniqueIdentifier: (file, event) => {
-          return computeFileChecksum(file).then((checksum) => {
-              var _relativePath = (file.webkitRelativePath
-                                   || file.relativePath
-                                   || file.fileName
-                                   || file.name);
-              return checksum + "-" + _relativePath.replace(
-                  /[^a-zA-Z0-9_-]/img, "");
-          });
-      }
-  });
-
-  if(r.support) {
-      //Hide form and display drag&drop UI
-      $("#frm-upload-rqtl2-bundle").css("display", "none");
-      $("#resumable-drop-area").css("display", "block");
-
-      // Define UI elements for browse and drag&drop
-      r.assignDrop(document.getElementById("resumable-drop-area"));
-      r.assignBrowse(document.getElementById("resumable-browse-button"));
-
-      // Event handlers
-
-      function display_files(files) {
-          displayArea = $("#resumable-selected-files")
-          displayArea.empty();
-          files.forEach((file) => {
-              var displayElement = $(
-                  "#resumable-file-display-template").clone();
-              displayElement.removeAttr("id");
-              displayElement.css("display", "");
-              displayElement.find(".panel-heading").text(file.fileName);
-              list = $("<ul></ul>");
-              list.append($("<li><strong>Name</strong>: "
-                            + (file.name
-                               || file.fileName
-                               || file.relativePath
-                               || file.webkitRelativePath)
-                            + "</li>"));
-              list.append($("<li><strong>Size</strong>: "
-                            + (file.size / (1024*1024)).toFixed(2)
-                            + " MB</li>"));
-              list.append($("<li><strong>Unique Identifier</strong>: "
-                            + file.uniqueIdentifier + "</li>"));
-              list.append($("<li><strong>Mime</strong>: "
-                            + file.file.type
-                            + "</li>"));
-              displayElement.find(".panel-body").append(list);
-              displayElement.appendTo("#resumable-selected-files");
-          });
-      }
-
-      r.on("filesAdded", function(files) {
-          display_files(files);
-          $("#resumable-upload-button").css("display", "");
-          $("#resumable-upload-button").on("click", (event) => {
-              r.upload();
-          });
-      });
-
-      r.on("uploadStart", (event) => {
-          $("#resumable-upload-button").css("display", "none");
-          $("#resumable-cancel-upload-button").css("display", "");
-          $("#resumable-cancel-upload-button").on("click", (event) => {
-              r.files.forEach((file) => {
-                  if(file.isUploading()) {
-                      file.abort();
-                  }
-              });
-              $("#resumable-cancel-upload-button").css("display", "none");
-              $("#resumable-upload-button").on("click", (event) => {
-                  r.files.forEach((file) => {file.retry();});
-              });
-              $("#resumable-upload-button").css("display", "");
-          });
-      });
-
-      r.on("progress", () => {
-          var progress = (r.progress() * 100).toFixed(2);
-          var pbar = $("#resumable-progress-bar > .progress-bar");
-          $("#resumable-progress-bar").css("display", "");
-          pbar.css("width", progress+"%");
-          pbar.attr("aria-valuenow", progress);
-          pbar.text("Uploading: " + progress + "%");
-      })
-
-      r.on("fileSuccess", (file, message) => {
-          if(message != "OK") {
-              var uri = (window.location.protocol
-                         + "//"
-                         + window.location.host
-                         + message);
-              window.location.replace(uri);
-          }
-      });
-
-      r.on("error", (message, file) => {
-          filename = (file.webkitRelativePath
-                      || file.relativePath
-                      || file.fileName
-                      || file.name);
-          jsonmsg = JSON.parse(message);
-          alert("There was an error while uploading your file '"
-                + filename
-                + "'. The error message was:\n\n\t"
-                + jsonmsg.error
-                + " ("
-                + jsonmsg.statuscode
-                + "): " + jsonmsg.message);
-      })
-  } else {
-      setup_upload_handlers(
-          "frm-upload-rqtl2-bundle", make_data_uploader(
-	      function (form) {
-	          var formdata = new FormData();
-	          formdata.append(
-		      "species_id",
-		      form.querySelector('input[name="species_id"]').value);
-	          formdata.append(
-		      "population_id",
-		      form.querySelector('input[name="population_id"]').value);
-	          formdata.append(
-		      "rqtl2_bundle_file",
-		      form.querySelector("#file-rqtl2-bundle").files[0]);
-	          return formdata;
-	      }));
-  }
-</script>
-{%endblock%}
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