Commit 234ff625 authored by Vermaat's avatar Vermaat
Browse files

Rename GenBank Uploader to Reference File Loader

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@370 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
parent f8d9bab7
......@@ -76,7 +76,7 @@
well-annotated genomic reference sequence. (See
<a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=16944057">AL449423.14</a> or NCBI's new
<a href="http://www.ncbi.nlm.nih.gov/RefSeq/RSG/">RefSeqGene</a>
records for example). Alternatively, you can use the GenBank Uploader
records for example). Alternatively, you can use the Reference File Loader
options described below to obtain a suitable genomic reference
sequence. If the annotation of this record contains information about
the transcript specified by the NM_ number, Mutalyzer can use the
......@@ -219,7 +219,7 @@
</p>
<p>&nbsp;</p>
<p>
4) The Mutalyzer reference sequence uploader
4) The Mutalyzer reference file loader
</p>
<p>
<span style="font-size: 12.0pt; font-family: Times New Roman">Users can
......@@ -248,7 +248,7 @@
</p>
<p>
<i>
<span style="font-family: Times New Roman">Click the GenBank Uploader
<span style="font-family: Times New Roman">Click the Reference File Loader
link in
</span> the list on the left side of any Mutalyzer window to see its
options.
......@@ -257,7 +257,7 @@
<p>
<span style="font-family: Times New Roman">
If you already have a well-annotated GenBank file on your computer or
stored on a web server, the first two GenBank uploader options
stored on a web server, the first two Reference File Loader options
facilitate easy uploading and will return the
</span>
<span style="font-size: 12.0pt; font-family: Times New Roman">
......
......@@ -67,7 +67,7 @@
try to retrieve the underlying sequences to check the sequence variant,
but it may lose track of the corresponding positions due to the
different levels of assembly and return errors. Users are advised
circumvent this problem by using the Genbank uploader when (part of)
circumvent this problem by using the Reference File Loader when (part of)
these NC_ or NT references are used. The
<a href="http://www.humgen.nl/mutalyzer_exercise.html">
Mutalyzer exercise</a> provides more detailed information.
......@@ -116,7 +116,7 @@
</p>
<p>
If you are the curator of an LSDB in need of an appropriate genomic
reference sequence, you can use the options on the GenBank uploader
reference sequence, you can use the options on the Reference File Loader
page to select a genomic reference sequence. More information about the
selection and modification of reference sequences can be found in the
<a href="http://www.humgen.nl/mutalyzer_exercise.html">
......@@ -161,7 +161,7 @@
</p>
<h3>
Why does the Genbank uploader not work with my local file or the URL
Why does the Reference File Loader not work with my local file or the URL
provided?
</h3>
<p>
......
......@@ -11,8 +11,8 @@
updateVisibility();
}
</script>
<center><h3>Reference Sequence Uploader</h3></center>
The Reference Sequence Uploader allows you to use your own reference
<center><h3>Reference File Loader</h3></center>
The Reference File Loader allows you to use your own reference
sequence when no appropriate RefSeq, GenBank or LRG file is available.
<br>
Please select one of the options below to upload or retrieve your reference
......@@ -126,7 +126,7 @@
<div tal:condition = "UD">
<b>Output:</b><br>
<br>
Your reference sequence was uploaded successfully.<br>
Your reference sequence was loaded successfully.<br>
You now can use mutalyzer with the following accession number as
reference: <b tal:content = "UD"></b><br>
<a tal:attributes = "href string:Reference/${UD}.gb">
......
......@@ -63,7 +63,7 @@
with the Name checker
</p>
<p>
- <a href="#GenBankUploader">GenBank Uploader</a>: allows you to
- <a href="#GenBankUploader">Refrence File Loader</a>: allows you to
upload and use your own reference sequence.
</p>
<p>
......@@ -112,7 +112,7 @@
user-defined files in GenBank format, including slices of chromosomal
reference sequences. These files are specified by unique
<i><a href="#UD">UD identifiers</a></i>, which are returned by Mutalyzer
after upload (See the <a href="#GenBankUploader">GenBank Uploader</a>
after upload (See the <a href="#GenBankUploader">Reference File Loader</a>
section for more information).<br>
</p>
<p>
......@@ -132,7 +132,7 @@
LRG_1). The <a href="http://www.lrg-sequence.org/"> LRG website</a>
lists existing LRG sequences and has an
<a href="ftp://ftp.ebi.ac.uk/pub/databases/lrgex/">FTP site</a> for
downloading LRGs. To maintain LRG stability, Mutalyzer's uploader does
downloading LRGs. To maintain LRG stability, Mutalyzer's Reference File Loader does
not accept user-defined LRG files.
</p>
......@@ -734,7 +734,7 @@
<hr>
<h3>GenBank Uploader Help<a name="GenBankUploader"></a></h3>
<h3>Reference File Loader Help<a name="GenBankUploader"></a></h3>
<p>
Users can upload their own reference sequence file in
<a href="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html"
......@@ -754,7 +754,7 @@
>these instructions</a>.
</p>
<p>
Uploader options:
Loader options:
</p>
<p>
<b>The reference sequence file is a local file</b>
......@@ -857,14 +857,14 @@
</p>
<div style="padding-left:20px; width:400px">
<p>
Your reference sequence was uploaded successfully. You now can use
Your reference sequence was loaded successfully. You now can use
mutalyzer with the following accession number as reference:
UD_127955523176 <br>
Download this reference sequence.
</p>
</div>
<p>
The GenBank uploader uses JavaScript to change the form depending on
The Reference File Loader uses JavaScript to change the form depending on
the selected option. In Internet Explorer, forms may not be displayed
correctly. Adding Mutalyzer to your trusted sites is one option to
solve this.
......@@ -895,7 +895,7 @@
<a href="http://www.hgvs.org/mutnomen/"
>standard human sequence variation nomenclature</a>. When trying to
retrieve genomic reference sequences using gene symbols with the
Genbank uploader or when specifying a particular gene in a genomic
Reference File Loader or when specifying a particular gene in a genomic
reference sequence, the gene symbol should be similar to that used in
the (genome) sequence annotation.
</p>
......
......@@ -32,7 +32,7 @@
versa.
</li>
<li>
The <a href = "upload">GenBank Uploader</a> allows you to upload and
The <a href = "upload">Reference File Loader</a> allows you to load and
use your own reference sequence.
</li>
<li>
......
......@@ -298,7 +298,7 @@
'upload');"
onmouseout="navDeAct('base/images/bullitdonker.gif',
'upload');"
class="vertnavsub">GenBank Uploader</a>
class="vertnavsub">Reference File Loader</a>
</td>
</tr>
......
......@@ -605,7 +605,7 @@ facilisi."""
form.set('bestandsveld', ('test_upload.gb',
open(test_genbank_file, 'r').read()))
r = form.submit()
r.mustcontain('Your reference sequence was uploaded successfully.')
r.mustcontain('Your reference sequence was loaded successfully.')
def test_upload_local_file_invalid(self):
"""
......
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