Move code handling expression data upload into new module.

24 files changed, 126 insertions, 30 deletions

diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 40a1255..58227f4 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -44,13 +44,14 @@
     <aside id="nav-sidebar" class="container-fluid">
       <ul class="nav flex-column">
         <li><a href="/" >Home</a></li>
+        <li><a href="{{url_for('expression-data.index.index')}}" >Expression Data</a></li>
       </ul>
     </aside>
 
     <main id="main" class="main container-fluid">
 
       <div class="pagetitle row">
-        <h1>GN Uploader: {%block pagetitle%}%{%endblock%}</h1>
+        <h1>GN Uploader: {%block pagetitle%}{%endblock%}</h1>
         <nav>
           <ol class="breadcrumb">
             {%block breadcrumb%}{%endblock%}
diff --git a/uploader/templates/data_review.html b/uploader/templates/data_review.html
index b7528fd..4e5c586 100644
--- a/uploader/templates/data_review.html
+++ b/uploader/templates/data_review.html
@@ -26,7 +26,7 @@
           <small class="text-muted">
             If you encounter an error saying your sample(s)/case(s) do not exist
             in the GeneNetwork database, then you will have to use the
-            <a href="{{url_for('samples.select_species')}}"
+            <a href="{{url_for('expression-data.samples.select_species')}}"
                title="Upload samples/cases feature">Upload Samples/Cases</a>
             option on this system to upload them.
           </small>
diff --git a/uploader/templates/expression-data/index.html b/uploader/templates/expression-data/index.html
new file mode 100644
index 0000000..ed5d8dd
--- /dev/null
+++ b/uploader/templates/expression-data/index.html
@@ -0,0 +1,95 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Expression Data{%endblock%}
+
+{%block pagetitle%}Expression Data{%endblock%}
+
+{%block breadcrumb%}
+<li class="breadcrumb-item">
+  <a href="{{url_for('base.index')}}">Home</a>
+</li>
+<li class="breadcrumb-item active">
+  <a href="{{url_for('expression-data.index.index')}}">Expression Data</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+<div class="row">
+  {{flash_all_messages()}}
+
+  <h1 class="heading">data upload</h1>
+
+  <div class="explainer">
+    <p>Each of the sections below gives you a different option for data expression-data.
+      Please read the documentation for each section carefully to understand what
+      each section is about.</p>
+  </div>
+</div>
+
+<div class="row">
+  <h2 class="heading">R/qtl2 Bundles</h2>
+
+  <div class="explainer">
+    <p>This feature combines and extends the two upload methods below. Instead of
+      uploading one item at a time, the R/qtl2 bundle you upload can contain both
+      the genotypes data (samples/individuals/cases and their data) and the
+      expression data.</p>
+    <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither
+      of the methods below can handle.</p>
+
+    <a href="{{url_for('expression-data.rqtl2.select_species')}}"
+       title="Upload a zip bundle of R/qtl2 files">
+      <button class="btn btn-primary">upload R/qtl2 bundle</button></a>
+  </div>
+</div>
+
+
+<div class="row">
+  <h2 class="heading">Expression Data</h2>
+
+  <div class="explainer">
+    <p>This feature enables you to upload expression data. It expects the data to
+      be in <strong>tab-separated values (TSV)</strong> files. The data should be
+      a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a
+      list of the <em>phenotypes</em> and the first row is a list of
+      <em>samples/cases</em>.</p>
+
+    <p>If you haven't done so please go to this page to learn the requirements for
+      file formats and helpful suggestions to enter your data in a fast and easy
+      way.</p>
+
+    <ol>
+      <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies
+        with our system requirements. (
+        <a href="{{url_for('expression-data.index.data_review')}}#data-concerns"
+	   title="Details for the data expectations.">Help</a>
+        )</li>
+      <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept
+        <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong>
+        files (<a href="{{url_for('expression-data.index.data_review')}}#file-types"
+	          title="Details for the data expectations.">Help</a>)</li>
+    </ol>
+  </div>
+
+  <a href="{{url_for('expression-data.index.upload_file')}}"
+     title="Upload your expression data"
+     class="btn btn-primary">upload expression data</a>
+</div>
+
+<div class="row">
+  <h2 class="heading">samples/cases</h2>
+
+  <div class="explainer">
+    <p>For the expression data above, you need the samples/cases in your file to
+      already exist in the GeneNetwork database. If there are any samples that do
+      not already exist the upload of the expression data will fail.</p>
+    <p>This section gives you the opportunity to upload any missing samples</p>
+  </div>
+
+  <a href="{{url_for('expression-data.samples.select_species')}}"
+     title="Upload samples/cases/individuals for your data"
+     class="btn btn-primary">upload Samples/Cases</a>
+</div>
+
+{%endblock%}
diff --git a/uploader/templates/index.html b/uploader/templates/index.html
index e99b031..75d7dec 100644
--- a/uploader/templates/index.html
+++ b/uploader/templates/index.html
@@ -7,7 +7,7 @@
 
 {%block breadcrumb%}
 <li class="breadcrumb-item active">
-  <a href="{{url_for('entry.index')}}">Home</a>
+  <a href="{{url_for('base.index')}}">Home</a>
 </li>
 {%endblock%}
 
diff --git a/uploader/templates/job_progress.html b/uploader/templates/job_progress.html
index 1af0763..2feaa89 100644
--- a/uploader/templates/job_progress.html
+++ b/uploader/templates/job_progress.html
@@ -11,7 +11,7 @@
 <h1 class="heading">{{job_name}}</h2>
 
 <div class="row">
-  <form action="{{url_for('parse.abort')}}" method="POST">
+  <form action="{{url_for('expression-data.parse.abort')}}" method="POST">
     <legend class="heading">Status</legend>
     <div class="form-group">
       <label for="job_status" class="form-label">status:</label>
diff --git a/uploader/templates/no_such_job.html b/uploader/templates/no_such_job.html
index 42a2d48..874d047 100644
--- a/uploader/templates/no_such_job.html
+++ b/uploader/templates/no_such_job.html
@@ -1,7 +1,7 @@
 {%extends "base.html"%}
 
 {%block extrameta%}
-<meta http-equiv="refresh" content="5;url={{url_for('entry.upload_file')}}">
+<meta http-equiv="refresh" content="5;url={{url_for('expression-data.index.upload_file')}}">
 {%endblock%}
 
 {%block title%}No Such Job{%endblock%}
diff --git a/uploader/templates/parse_results.html b/uploader/templates/parse_results.html
index e2bf7f0..46fbaaf 100644
--- a/uploader/templates/parse_results.html
+++ b/uploader/templates/parse_results.html
@@ -21,7 +21,7 @@
 
 {%if errors | length > 0 or user_aborted %}
 <br />
-<a href="{{url_for('entry.upload_file')}}" title="Back to index page."
+<a href="{{url_for('expression-data.index.upload_file')}}" title="Back to index page."
    class="btn btn-primary">
   Go back
 </a>
diff --git a/uploader/templates/rqtl2/create-geno-dataset-success.html b/uploader/templates/rqtl2/create-geno-dataset-success.html
index 1b50221..bb6d63d 100644
--- a/uploader/templates/rqtl2/create-geno-dataset-success.html
+++ b/uploader/templates/rqtl2/create-geno-dataset-success.html
@@ -33,7 +33,7 @@
 
 <div class="row">
   <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('upload.rqtl2.select_dataset_info',
+        action="{{url_for('expression-data.rqtl2.select_dataset_info',
 	        species_id=species.SpeciesId,
 	        population_id=population.InbredSetId)}}"
         method="POST"
diff --git a/uploader/templates/rqtl2/create-probe-dataset-success.html b/uploader/templates/rqtl2/create-probe-dataset-success.html
index 790d174..03b75c7 100644
--- a/uploader/templates/rqtl2/create-probe-dataset-success.html
+++ b/uploader/templates/rqtl2/create-probe-dataset-success.html
@@ -36,7 +36,7 @@
 
 <div class="row">
   <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('upload.rqtl2.select_dataset_info',
+        action="{{url_for('expression-data.rqtl2.select_dataset_info',
 	        species_id=species.SpeciesId,
 	        population_id=population.InbredSetId)}}"
         method="POST"
diff --git a/uploader/templates/rqtl2/create-probe-study-success.html b/uploader/templates/rqtl2/create-probe-study-success.html
index d0ee508..e293f6f 100644
--- a/uploader/templates/rqtl2/create-probe-study-success.html
+++ b/uploader/templates/rqtl2/create-probe-study-success.html
@@ -28,7 +28,7 @@
   </p>
 
   <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('upload.rqtl2.select_dataset_info',
+        action="{{url_for('expression-data.rqtl2.select_dataset_info',
 	        species_id=species.SpeciesId,
 	        population_id=population.InbredSetId)}}"
         method="POST"
diff --git a/uploader/templates/rqtl2/create-tissue-success.html b/uploader/templates/rqtl2/create-tissue-success.html
index 5f2c5a0..d6fe154 100644
--- a/uploader/templates/rqtl2/create-tissue-success.html
+++ b/uploader/templates/rqtl2/create-tissue-success.html
@@ -56,7 +56,7 @@
 
     <form id="frm-create-tissue-success-continue"
           method="POST"
-          action="{{url_for('upload.rqtl2.select_dataset_info',
+          action="{{url_for('expression-data.rqtl2.select_dataset_info',
 	          species_id=species.SpeciesId,
 	          population_id=population.InbredSetId)}}"
           style="display: inline; width: 100%; grid-column: 1 / 2;
@@ -85,7 +85,7 @@
 <div class="row">
   <form id="frm-create-tissue-success-select-existing"
         method="POST"
-        action="{{url_for('upload.rqtl2.select_tissue',
+        action="{{url_for('expression-data.rqtl2.select_tissue',
 	        species_id=species.SpeciesId,
 	        population_id=population.InbredSetId)}}"
         style="display: inline; width: 100%; grid-column: 3 / 4;
diff --git a/uploader/templates/rqtl2/index.html b/uploader/templates/rqtl2/index.html
index f3329c2..8ce13bf 100644
--- a/uploader/templates/rqtl2/index.html
+++ b/uploader/templates/rqtl2/index.html
@@ -8,7 +8,7 @@
 
 <h2>R/qtl2 Upload</h2>
 
-<form method="POST" action="{{url_for('upload.rqtl2.select_species')}}"
+<form method="POST" action="{{url_for('expression-data.rqtl2.select_species')}}"
       id="frm-rqtl2-upload">
   <legend class="heading">upload R/qtl2 bundle</legend>
   {{flash_messages("error-rqtl2")}}
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-results.html b/uploader/templates/rqtl2/rqtl2-qc-job-results.html
index 59bc8cd..b3c3a8f 100644
--- a/uploader/templates/rqtl2/rqtl2-qc-job-results.html
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-results.html
@@ -15,7 +15,7 @@
 
 <div class="row">
   <form id="form-qc-job-results"
-        action="{{url_for('upload.rqtl2.select_dataset_info',
+        action="{{url_for('expression-data.rqtl2.select_dataset_info',
 	        species_id=species.SpeciesId,
 	        population_id=population.Id)}}"
         method="POST">
diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-success.html b/uploader/templates/rqtl2/rqtl2-qc-job-success.html
index 2861a04..f126835 100644
--- a/uploader/templates/rqtl2/rqtl2-qc-job-success.html
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-success.html
@@ -18,7 +18,7 @@
   -->
 <div class="row">
   <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('upload.rqtl2.select_dataset_info',
+        action="{{url_for('expression-data.rqtl2.select_dataset_info',
 	        species_id=species.SpeciesId,
 	        population_id=population.InbredSetId)}}"
         method="POST"
diff --git a/uploader/templates/rqtl2/select-geno-dataset.html b/uploader/templates/rqtl2/select-geno-dataset.html
index 873f9c3..1db51e0 100644
--- a/uploader/templates/rqtl2/select-geno-dataset.html
+++ b/uploader/templates/rqtl2/select-geno-dataset.html
@@ -15,7 +15,7 @@
 
 <div class="row">
   <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('upload.rqtl2.select_geno_dataset',
+        action="{{url_for('expression-data.rqtl2.select_geno_dataset',
 	        species_id=species.SpeciesId,
 	        population_id=population.InbredSetId)}}"
         method="POST"
@@ -62,7 +62,7 @@
 
 <div class="row">
   <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('upload.rqtl2.create_geno_dataset',
+        action="{{url_for('expression-data.rqtl2.create_geno_dataset',
 	        species_id=species.SpeciesId,
 	        population_id=population.InbredSetId)}}"
         method="POST"
diff --git a/uploader/templates/rqtl2/select-population.html b/uploader/templates/rqtl2/select-population.html
index 37731f0..7d27303 100644
--- a/uploader/templates/rqtl2/select-population.html
+++ b/uploader/templates/rqtl2/select-population.html
@@ -17,7 +17,7 @@
 </div>
 
 <form method="POST"
-      action="{{url_for('upload.rqtl2.select_population', species_id=species.SpeciesId)}}">
+      action="{{url_for('expression-data.rqtl2.select_population', species_id=species.SpeciesId)}}">
   <legend class="heading">select grouping/population</legend>
   {{flash_messages("error-select-population")}}
 
@@ -47,7 +47,7 @@
 <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
 
 <form method="POST"
-      action="{{url_for('upload.rqtl2.create_population', species_id=species.SpeciesId)}}">
+      action="{{url_for('expression-data.rqtl2.create_population', species_id=species.SpeciesId)}}">
   <legend class="heading">create new grouping/population</legend>
   {{flash_messages("error-create-population")}}
 
diff --git a/uploader/templates/rqtl2/select-probeset-dataset.html b/uploader/templates/rqtl2/select-probeset-dataset.html
index 26f52ed..74f8f69 100644
--- a/uploader/templates/rqtl2/select-probeset-dataset.html
+++ b/uploader/templates/rqtl2/select-probeset-dataset.html
@@ -15,7 +15,7 @@
 {%if datasets | length > 0%}
 <div class="row">
   <form method="POST"
-        action="{{url_for('upload.rqtl2.select_probeset_dataset',
+        action="{{url_for('expression-data.rqtl2.select_probeset_dataset',
 	        species_id=species.SpeciesId, population_id=population.Id)}}"
         id="frm:select-probeset-dataset">
     <legend class="heading">Select from existing ProbeSet datasets</legend>
@@ -68,7 +68,7 @@
 
 <div class="row">
   <form method="POST"
-        action="{{url_for('upload.rqtl2.create_probeset_dataset',
+        action="{{url_for('expression-data.rqtl2.create_probeset_dataset',
 	        species_id=species.SpeciesId, population_id=population.Id)}}"
         id="frm:create-probeset-dataset">
     <legend class="heading">Create a new ProbeSet dataset</legend>
diff --git a/uploader/templates/rqtl2/select-probeset-study-id.html b/uploader/templates/rqtl2/select-probeset-study-id.html
index b9bf52e..e3fd9cc 100644
--- a/uploader/templates/rqtl2/select-probeset-study-id.html
+++ b/uploader/templates/rqtl2/select-probeset-study-id.html
@@ -12,7 +12,7 @@
   <p>In this page, you can either select from a existing dataset:</p>
 
   <form method="POST"
-        action="{{url_for('upload.rqtl2.select_probeset_study',
+        action="{{url_for('expression-data.rqtl2.select_probeset_study',
 	        species_id=species.SpeciesId, population_id=population.Id)}}"
         id="frm:select-probeset-study">
     <legend class="heading">Select from existing ProbeSet studies</legend>
@@ -62,7 +62,7 @@
   <p>Create a new ProbeSet dataset below:</p>
 
   <form method="POST"
-        action="{{url_for('upload.rqtl2.create_probeset_study',
+        action="{{url_for('expression-data.rqtl2.create_probeset_study',
 	        species_id=species.SpeciesId, population_id=population.Id)}}"
         id="frm:create-probeset-study">
     <legend class="heading">Create new ProbeSet study</legend>
diff --git a/uploader/templates/rqtl2/select-tissue.html b/uploader/templates/rqtl2/select-tissue.html
index 34e1758..fe3080a 100644
--- a/uploader/templates/rqtl2/select-tissue.html
+++ b/uploader/templates/rqtl2/select-tissue.html
@@ -15,7 +15,7 @@
 {%if tissues | length > 0%}
 <div class="row">
   <form method="POST"
-        action="{{url_for('upload.rqtl2.select_tissue',
+        action="{{url_for('expression-data.rqtl2.select_tissue',
 	        species_id=species.SpeciesId, population_id=population.Id)}}"
         id="frm:select-probeset-dataset">
     <legend class="heading">Select from existing ProbeSet datasets</legend>
@@ -65,7 +65,7 @@
     to the system below.</p>
 
   <form method="POST"
-        action="{{url_for('upload.rqtl2.create_tissue',
+        action="{{url_for('expression-data.rqtl2.create_tissue',
 	        species_id=species.SpeciesId, population_id=population.Id)}}"
         id="frm:create-probeset-dataset">
     <legend class="heading">Add new tissue, organ or biological material</legend>
diff --git a/uploader/templates/rqtl2/summary-info.html b/uploader/templates/rqtl2/summary-info.html
index 1be87fa..0adba2e 100644
--- a/uploader/templates/rqtl2/summary-info.html
+++ b/uploader/templates/rqtl2/summary-info.html
@@ -44,7 +44,7 @@
 
 <div class="row">
   <form id="frm:confirm-rqtl2bundle-details"
-        action="{{url_for('upload.rqtl2.confirm_bundle_details',
+        action="{{url_for('expression-data.rqtl2.confirm_bundle_details',
 	        species_id=species.SpeciesId,
 	        population_id=population.InbredSetId)}}"
         method="POST"
diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
index 07c240f..9d45c5f 100644
--- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
+++ b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-01.html
@@ -71,13 +71,13 @@
 </div>
 
 <form id="frm-upload-rqtl2-bundle"
-      action="{{url_for('upload.rqtl2.upload_rqtl2_bundle',
+      action="{{url_for('expression-data.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',
+                             'expression-data.rqtl2.upload_rqtl2_bundle_chunked_post',
                              species_id=species.SpeciesId,
                              population_id=population.InbredSetId)}}">
   <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
diff --git a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
index 93b1dc9..8210ed0 100644
--- a/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
+++ b/uploader/templates/rqtl2/upload-rqtl2-bundle-step-02.html
@@ -14,7 +14,7 @@
   <p>Click "Continue" below to proceed.</p>
 
   <form id="frm-upload-rqtl2-bundle"
-        action="{{url_for('upload.rqtl2.select_dataset_info',
+        action="{{url_for('expression-data.rqtl2.select_dataset_info',
 	        species_id=species.SpeciesId,
 	        population_id=population.InbredSetId)}}"
         method="POST"
diff --git a/uploader/templates/samples/select-species.html b/uploader/templates/samples/select-species.html
index edadc61..aa64ecf 100644
--- a/uploader/templates/samples/select-species.html
+++ b/uploader/templates/samples/select-species.html
@@ -10,7 +10,7 @@
 
 {{flash_all_messages()}}
 
-<form method="POST" action="{{url_for('samples.select_species')}}">
+<form method="POST" action="{{url_for('expression-data.samples.select_species')}}">
   <legend class="heading">upload samples</legend>
   <div class="form-group">
     <label for="select_species02" class="form-label">Species</label>
diff --git a/uploader/templates/select_species.html b/uploader/templates/select_species.html
index 3b1a8a9..1642401 100644
--- a/uploader/templates/select_species.html
+++ b/uploader/templates/select_species.html
@@ -10,7 +10,7 @@
 <h2 class="heading">expression data: select species</h2>
 
 <div class="row">
-  <form action="{{url_for('entry.upload_file')}}"
+  <form action="{{url_for('expression-data.index.upload_file')}}"
         method="POST"
         enctype="multipart/form-data"
         id="frm-upload-expression-data">