Allow independent transposition of each file

* Rework UI to provide independent selection of whether or not each
  file is transposed
* Update the backend code to individually set the transposition status
  for each file independently.

1 files changed, 203 insertions, 127 deletions

diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
index 5c6aaab..67b56e3 100644
--- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html
+++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
@@ -103,139 +103,215 @@
       <a href="#docs-file-na" title="Documentation for no-value fields">
         documentation for more information</a>.</span>
   </div>
-
-  <div class="form-check form-group">
-    <div class="">
-      <input id="chk-file-transposed"
-             name="file-transposed"
-             type="checkbox"
-             class="form-check-input"
-             style="border: solid #8EABF0" />
-      <label for="chk-file-transposed" class="form-check-label">
-        File transposed</label>
-    </div>
-    <span class="form-text text-muted">
-      We expect the data in the file as a matrix of
-      <strong>samples × phenotypes</strong>, but it could be your file is
-      transposed, (i.e. it is a matrix of
-      &ldquo;<em>phenotypes × samples</em>&rdquo;, rather than the expected
-      form).
-      <br />
-      If that is the case for your files, mark your files as trasposed by
-      ensuring that this checkbox is checked.
-    </span>
-  </div>
 </fieldset>
 
-<fieldset id="fldset-data-files">
+<fieldset id="fldset-files">
   <legend>Data File(s)</legend>
 
-  <div class="form-group non-resumable-elements">
-    <label for="finput-phenotype-descriptions" class="form-label">
-      Phenotype Descriptions</label>
-    <input id="finput-phenotype-descriptions"
-           name="phenotype-descriptions"
-           class="form-control"
-           type="file"
-           data-preview-table="tbl-preview-pheno-desc"
-           required="required"  />
-    <span class="form-text text-muted">
-      Provide a file that contains only the phenotype descriptions,
-      <a href="#docs-file-phenotype-description"
-         title="Documentation of the phenotype data file format.">
-        the documentation for the expected format of the file</a>.</span>
-  </div>
-
-  {{display_resumable_elements(
-  "resumable-phenotype-descriptions",
-  "phenotype descriptions",
-  '<p>You can drop a CSV file that contains the phenotype descriptions here,
-    or you can click the "Browse" button (below and to the right) to select it
-    from your computer.</p>
-  <p>The CSV file must conform to some standards, as documented in the
-    <a href="#docs-file-phenotype-description"
-       title="Documentation of the phenotype data file format.">
-      "Phenotypes Descriptions" documentation</a> section below.</p>')}}
-  {{display_preview_table("tbl-preview-pheno-desc", "phenotype descriptions")}}
-
-
-  <div class="form-group non-resumable-elements">
-    <label for="finput-phenotype-data" class="form-label">Phenotype Data</label>
-    <input id="finput-phenotype-data"
-           name="phenotype-data"
-           class="form-control"
-           type="file"
-           data-preview-table="tbl-preview-pheno-data"
-           required="required"  />
-    <span class="form-text text-muted">
-      Provide a file that contains only the phenotype data. See
-      <a href="#docs-file-phenotype-data"
-         title="Documentation of the phenotype data file format.">
-        the documentation for the expected format of the file</a>.</span>
-  </div>
-
-  {{display_resumable_elements(
-  "resumable-phenotype-data",
-  "phenotype data",
-  '<p>You can drop a CSV file that contains the phenotype data here,
-    or you can click the "Browse" button (below and to the right) to select it
-    from your computer.</p>
-  <p>The CSV file must conform to some standards, as documented in the
-    <a href="#docs-file-phenotype-data"
-       title="Documentation of the phenotype data file format.">
-      "Phenotypes Data" documentation</a> section below.</p>')}}
-  {{display_preview_table("tbl-preview-pheno-data", "phenotype data")}}
-
-  {%if population.Family in families_with_se_and_n%}
-  <div class="form-group non-resumable-elements">
-    <label for="finput-phenotype-se" class="form-label">Phenotype: Standard Errors</label>
-    <input id="finput-phenotype-se"
-           name="phenotype-se"
-           class="form-control"
-           type="file"
-           data-preview-table="tbl-preview-pheno-se"
-           required="required"  />
-    <span class="form-text text-muted">
-      Provide a file that contains only the standard errors for the phenotypes,
-      computed from the data above.</span>
-  </div>
-  {{display_resumable_elements(
-  "resumable-phenotype-se",
-  "standard errors",
-  '<p>You can drop a CSV file that contains the computed standard-errors data
-    here, or you can click the "Browse" button (below and to the right) to
-    select it from your computer.</p>
-  <p>The CSV file must conform to some standards, as documented in the
-    <a href="#docs-file-phenotype-se"
-       title="Documentation of the phenotype data file format.">
-      "Phenotypes Data" documentation</a> section below.</p>')}}
-  {{display_preview_table("tbl-preview-pheno-se", "standard errors")}}
+  <fieldset id="fldset-descriptions-file">
+    <div class="form-group">
+      <div class="form-check">
+        <input id="chk-phenotype-descriptions-transposed"
+               name="phenotype-descriptions-transposed"
+               type="checkbox"
+               class="form-check-input"
+               style="border: solid #8EABF0" />
+        <label for="chk-phenotype-descriptions-transposed"
+               class="form-check-label">
+          Description file transposed?</label>
+      </div>
+
+      <div class="non-resumable-elements">
+        <label for="finput-phenotype-descriptions" class="form-label">
+          Phenotype Descriptions</label>
+        <input id="finput-phenotype-descriptions"
+               name="phenotype-descriptions"
+               class="form-control"
+               type="file"
+               data-preview-table="tbl-preview-pheno-desc"
+               required="required"  />
+        <span class="form-text text-muted">
+          Provide a file that contains only the phenotype descriptions,
+          <a href="#docs-file-phenotype-description"
+             title="Documentation of the phenotype data file format.">
+            the documentation for the expected format of the file</a>.</span>
+      </div>
+      {{display_resumable_elements(
+      "resumable-phenotype-descriptions",
+      "phenotype descriptions",
+      '<p>Drag and drop the CSV file that contains the descriptions of your
+        phenotypes here.</p>
+
+      <p>The CSV file should be a matrix of
+        <strong>phenotypes × descriptions</strong> i.e. The first column
+        contains the phenotype names/identifiers whereas the first row is a list
+        of metadata fields like, "description", "units", etc.</p>
+
+      <p>If the format is transposed (i.e.
+        <strong>descriptions × phenotypes</strong>) select the checkbox above.
+      </p>
+
+      <p>Please see the
+        <a href="#docs-file-phenotype-description"
+           title="Documentation of the phenotype data file format.">
+          "Phenotypes Descriptions" documentation</a> section below for more
+        information on the expected format of the file provided here.</p>')}}
+      {{display_preview_table(
+      "tbl-preview-pheno-desc", "phenotype descriptions")}}
+    </div>
+  </fieldset>
+
+
+  <fieldset id="fldset-data-file">
+    <div class="form-group">
+      <div class="form-check">
+        <input id="chk-phenotype-data-transposed"
+               name="phenotype-data-transposed"
+               type="checkbox"
+               class="form-check-input"
+               style="border: solid #8EABF0" />
+        <label for="chk-phenotype-data-transposed" class="form-check-label">
+          Data file transposed?</label>
+      </div>
+
+      <div class="non-resumable-elements">
+        <label for="finput-phenotype-data" class="form-label">Phenotype Data</label>
+        <input id="finput-phenotype-data"
+               name="phenotype-data"
+               class="form-control"
+               type="file"
+               data-preview-table="tbl-preview-pheno-data"
+               required="required"  />
+        <span class="form-text text-muted">
+          Provide a file that contains only the phenotype data. See
+          <a href="#docs-file-phenotype-data"
+             title="Documentation of the phenotype data file format.">
+            the documentation for the expected format of the file</a>.</span>
+      </div>
+
+      {{display_resumable_elements(
+      "resumable-phenotype-data",
+      "phenotype data",
+      '<p>Drag and drop a CSV file that contains the phenotypes numerical data
+        here. You can click the "Browse" button (below and to the right) to
+        select the file from your computer.</p>
+
+      <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>,
+        i.e. The first column contains the samples identifiers while the first
+        row is the list of phenotypes identifiers occurring in the phenotypes
+        descriptions file.</p>
+
+      <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>)
+        select the checkbox above.</p>
+      <p>Please see the
+        <a href="#docs-file-phenotype-data"
+           title="Documentation of the phenotype data file format.">
+          "Phenotypes Data" documentation</a> section below for more information
+        on the expected format for the file provided here.</p>')}}
+      {{display_preview_table("tbl-preview-pheno-data", "phenotype data")}}
+    </div>
+  </fieldset>
 
   
-  <div class="form-group non-resumable-elements">
-    <label for="finput-phenotype-n" class="form-label">Phenotype: Number of Samples/Individuals</label>
-    <input id="finput-phenotype-n"
-           name="phenotype-n"
-           class="form-control"
-           type="file"
-           data-preview-table="tbl-preview-pheno-n"
-           required="required"  />
-    <span class="form-text text-muted">
-      Provide a file that contains only the number of samples/individuals used in
-      the computation of the standard errors above.</span>
-  </div>
-  {{display_resumable_elements(
-  "resumable-phenotype-n",
-  "number of samples/individuals",
-  '<p>You can drop a CSV file that contains the number of samples/individuals
-    used in computation of the standard-errors here, or you can click the
-    "Browse" button (below and to the right) to select it from your computer.
-  </p>
-  <p>The CSV file must conform to some standards, as documented in the
-    <a href="#docs-file-phenotype-n"
-       title="Documentation of the phenotype data file format.">
-      "Phenotypes Data" documentation</a> section below.</p>')}}
-  {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}}
+  {%if population.Family in families_with_se_and_n%}
+  <fieldset id="fldset-se-file">
+    <div class="form-group">
+      <div class="form-check">
+        <input id="chk-phenotype-se-transposed"
+               name="phenotype-se-transposed"
+               type="checkbox"
+               class="form-check-input"
+               style="border: solid #8EABF0" />
+        <label for="chk-phenotype-se-transposed" class="form-check-label">
+          Standard-Errors file transposed?</label>
+      </div>
+      <div class="group non-resumable-elements">
+        <label for="finput-phenotype-se" class="form-label">Phenotype: Standard Errors</label>
+        <input id="finput-phenotype-se"
+               name="phenotype-se"
+               class="form-control"
+               type="file"
+               data-preview-table="tbl-preview-pheno-se"
+               required="required"  />
+        <span class="form-text text-muted">
+          Provide a file that contains only the standard errors for the phenotypes,
+          computed from the data above.</span>
+      </div>
+
+      {{display_resumable_elements(
+      "resumable-phenotype-se",
+      "standard errors",
+      '<p>Drag and drop a CSV file that contains the phenotypes standard-errors
+        data here. You can click the "Browse" button (below and to the right) to
+        select the file from your computer.</p>
+
+      <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>,
+        i.e. The first column contains the samples identifiers while the first
+        row is the list of phenotypes identifiers occurring in the phenotypes
+        descriptions file.</p>
+
+      <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>)
+        select the checkbox above.</p>
+
+      <p>Please see the
+        <a href="#docs-file-phenotype-se"
+           title="Documentation of the phenotype data file format.">
+          "Phenotypes Data" documentation</a> section below for more information
+        on the expected format of the file provided here.</p>')}}
+
+      {{display_preview_table("tbl-preview-pheno-se", "standard errors")}}
+    </div>
+  </fieldset>
+
+
+  <fieldset id="fldset-n-file">
+    <div class="form-group">
+      <div class="form-check">
+        <input id="chk-phenotype-n-transposed"
+               name="phenotype-n-transposed"
+               type="checkbox"
+               class="form-check-input"
+               style="border: solid #8EABF0" />
+        <label for="chk-phenotype-n-transposed" class="form-check-label">
+          Counts file transposed?</label>
+      </div>
+      <div class="non-resumable-elements">
+        <label for="finput-phenotype-n" class="form-label">Phenotype: Number of Samples/Individuals</label>
+        <input id="finput-phenotype-n"
+               name="phenotype-n"
+               class="form-control"
+               type="file"
+               data-preview-table="tbl-preview-pheno-n"
+               required="required"  />
+        <span class="form-text text-muted">
+          Provide a file that contains only the number of samples/individuals used in
+          the computation of the standard errors above.</span>
+      </div>
+
+      {{display_resumable_elements(
+      "resumable-phenotype-n",
+      "number of samples/individuals",
+      '<p>Drag and drop a CSV file that contains the samples\' phenotypes counts
+        data here. You can click the "Browse" button (below and to the right) to
+        select the file from your computer.</p>
+
+      <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>,
+        i.e. The first column contains the samples identifiers while the first
+        row is the list of phenotypes identifiers occurring in the phenotypes
+        descriptions file.</p>
+
+      <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>)
+        select the checkbox above.</p>
+
+      <p>Please see the
+        <a href="#docs-file-phenotype-se"
+           title="Documentation of the phenotype data file format.">
+          "Phenotypes Data" documentation</a> section below for more information
+        on the expected format of the file provided here.</p>')}}
+
+      {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}}
+    </div>
+  </fieldset>
 </fieldset>
 {%endif%}
 {%endblock%}