From 028f66b707532a99e08548640a4dd14addfa9765 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 21 Aug 2012 13:25:32 +0000
Subject: [PATCH] Rename 'webservice' to 'web service' (for Peter)
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@601 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
README | 6 +-
bin/mutalyzer-json-service.wsgi | 2 +-
bin/mutalyzer-soap-service.wsgi | 2 +-
extras/apache/mutalyzer.conf | 4 +-
.../007-apache-json-webservice.migration | 2 +-
extras/soap-tools/checkSyntax.py | 4 +-
extras/soap-tools/chromAccession.py | 2 +-
extras/soap-tools/descriptionExtract.py | 4 +-
extras/soap-tools/getCache.py | 4 +-
extras/soap-tools/getGeneAndTranscript.py | 2 +-
extras/soap-tools/getTranscripts.py | 2 +-
extras/soap-tools/getTranscriptsAndInfo.py | 4 +-
extras/soap-tools/getTranscriptsByGeneName.py | 2 +-
extras/soap-tools/getTranscriptsMapping.py | 4 +-
extras/soap-tools/getdbSNPDescriptions.py | 2 +-
extras/soap-tools/info.py | 2 +-
extras/soap-tools/mappingInfo.py | 2 +-
extras/soap-tools/numberConversion.py | 2 +-
extras/soap-tools/runMutalyzer.py | 2 +-
extras/soap-tools/sliceChromosomeByGene.py | 2 +-
extras/soap-tools/sp.py | 2 +-
extras/soap-tools/transcriptInfo.py | 4 +-
mutalyzer/models.py | 2 +-
mutalyzer/services/json.py | 2 +-
mutalyzer/services/rpc.py | 2 +-
mutalyzer/services/soap.py | 2 +-
mutalyzer/templates/about.html | 2 +-
mutalyzer/templates/client-mono.cs | 2 +-
mutalyzer/templates/client-php.php | 2 +-
mutalyzer/templates/client-savon.rb | 2 +-
mutalyzer/templates/client-soappy.py | 2 +-
mutalyzer/templates/client-suds.py | 2 +-
mutalyzer/templates/help.html | 136 +++++++++---------
mutalyzer/templates/index.html | 18 +--
mutalyzer/templates/menu.html | 4 +-
mutalyzer/templates/textmining.py | 2 +-
mutalyzer/templates/webservices.html | 16 +--
mutalyzer/website.py | 14 +-
tests/test_services_soap.py | 2 +-
tests/test_website.py | 8 +-
40 files changed, 141 insertions(+), 141 deletions(-)
diff --git a/README b/README
index a735a0db..9020a995 100644
--- a/README
+++ b/README
@@ -20,7 +20,7 @@ Unit tests
----------
The unit tests depend on a running batch daemon, webserver, and SOAP
-webservice:
+web service:
sudo /etc/init.d/mutalyzer-batchd start
sudo /etc/init.d/apache2 start
@@ -135,8 +135,8 @@ Todo list:
for example jinja.
- Develop a large test suite.
- Create a web interface url to watch the progress of a batch job.
-- Create webservices for the batch jobs (steal ideas from Jeroen's DVD
- webservice).
+- Create web services for the batch jobs (steal ideas from Jeroen's DVD
+ web service).
- Use virtualenv?
- Use SQLAlchemy?
- Password for MySQL user.
diff --git a/bin/mutalyzer-json-service.wsgi b/bin/mutalyzer-json-service.wsgi
index 4e2f9802..bb7dc7d9 100755
--- a/bin/mutalyzer-json-service.wsgi
+++ b/bin/mutalyzer-json-service.wsgi
@@ -1,6 +1,6 @@
#!/usr/bin/env python
"""
-WSGI interface to the Mutalyzer HTTP/RPC+JSON webservice.
+WSGI interface to the Mutalyzer HTTP/RPC+JSON web service.
The WSGI interface is exposed through the module variable 'application'.
diff --git a/bin/mutalyzer-soap-service.wsgi b/bin/mutalyzer-soap-service.wsgi
index 79fe02e1..5467bb91 100755
--- a/bin/mutalyzer-soap-service.wsgi
+++ b/bin/mutalyzer-soap-service.wsgi
@@ -1,6 +1,6 @@
#!/usr/bin/env python
"""
-WSGI interface to the Mutalyzer SOAP webservice.
+WSGI interface to the Mutalyzer SOAP web service.
The WSGI interface is exposed through the module variable 'application'.
diff --git a/extras/apache/mutalyzer.conf b/extras/apache/mutalyzer.conf
index 0142a576..69b816ad 100644
--- a/extras/apache/mutalyzer.conf
+++ b/extras/apache/mutalyzer.conf
@@ -11,7 +11,7 @@ Alias /mutalyzer/base /var/www/mutalyzer/base
WSGIDaemonProcess mutalyzer processes=2 threads=15 maximum-requests=10000
WSGIProcessGroup mutalyzer
-# SOAP/1.1 webservice
+# SOAP/1.1 web service
WSGIScriptAlias /mutalyzer/services <MUTALYZER_BIN_SOAP_SERVICE>
<Directory /mutalyzer/services>
Order deny,allow
@@ -19,7 +19,7 @@ WSGIScriptAlias /mutalyzer/services <MUTALYZER_BIN_SOAP_SERVICE>
Options -Indexes
</Directory>
-# HTTP/RPC+JSON webservice
+# HTTP/RPC+JSON web service
WSGIScriptAlias /mutalyzer/json <MUTALYZER_BIN_JSON_SERVICE>
<Directory /mutalyzer/json>
Order deny,allow
diff --git a/extras/migrations/007-apache-json-webservice.migration b/extras/migrations/007-apache-json-webservice.migration
index cd9b8278..e4bf006b 100755
--- a/extras/migrations/007-apache-json-webservice.migration
+++ b/extras/migrations/007-apache-json-webservice.migration
@@ -1,6 +1,6 @@
#!/bin/bash
-# Add HTTP/RPC+JSON webservice entry to Apache configuration.
+# Add HTTP/RPC+JSON web service entry to Apache configuration.
#
# Usage:
# ./007-apache-json-webservice.migration [migrate]
diff --git a/extras/soap-tools/checkSyntax.py b/extras/soap-tools/checkSyntax.py
index decfbc13..78c63e5c 100755
--- a/extras/soap-tools/checkSyntax.py
+++ b/extras/soap-tools/checkSyntax.py
@@ -7,8 +7,8 @@ Usage:
description: Variant description to check.
-The syntaxchecker results are retrieved from the Mutalyzer SOAP webservice and
-printed to standard output.
+The syntaxchecker results are retrieved from the Mutalyzer SOAP web service
+and printed to standard output.
"""
diff --git a/extras/soap-tools/chromAccession.py b/extras/soap-tools/chromAccession.py
index 61494754..4fb6e04f 100755
--- a/extras/soap-tools/chromAccession.py
+++ b/extras/soap-tools/chromAccession.py
@@ -8,7 +8,7 @@ Usage:
chromosome: Chromosome to get accession number for, e.g. 'chr2'.
build: Human genome build, 'hg18' or 'hg19' (default: 'hg19').
-The accession number is retrieved from the Mutalyzer SOAP webservice and
+The accession number is retrieved from the Mutalyzer SOAP web service and
printed to standard output.
"""
diff --git a/extras/soap-tools/descriptionExtract.py b/extras/soap-tools/descriptionExtract.py
index d1ff2b90..7ca3b2ec 100755
--- a/extras/soap-tools/descriptionExtract.py
+++ b/extras/soap-tools/descriptionExtract.py
@@ -9,8 +9,8 @@ Usage:
reference: Reference DNA sequence.
observed: Observed DNA sequence.
-The extracted HGVS description is retrieved from the Mutalyzer SOAP webservice
-and printed to standard output.
+The extracted HGVS description is retrieved from the Mutalyzer SOAP web
+service and printed to standard output.
"""
diff --git a/extras/soap-tools/getCache.py b/extras/soap-tools/getCache.py
index cc8ecc18..2f9c7df2 100755
--- a/extras/soap-tools/getCache.py
+++ b/extras/soap-tools/getCache.py
@@ -7,8 +7,8 @@ Usage:
days: Retrieve entries of at most this number of days old.
-The cache entries are retrieved from the Mutalyzer SOAP webservice and printed
-to standard output.
+The cache entries are retrieved from the Mutalyzer SOAP web service and
+printed to standard output.
"""
diff --git a/extras/soap-tools/getGeneAndTranscript.py b/extras/soap-tools/getGeneAndTranscript.py
index 979e52d9..8946d59e 100755
--- a/extras/soap-tools/getGeneAndTranscript.py
+++ b/extras/soap-tools/getGeneAndTranscript.py
@@ -9,7 +9,7 @@ Usage:
transcript_reference: Reference of the transcript to lookup.
The transcript and product name are retrieved from the Mutalyzer SOAP
-webservice and printed to standard output.
+web service and printed to standard output.
"""
diff --git a/extras/soap-tools/getTranscripts.py b/extras/soap-tools/getTranscripts.py
index 310fb3fa..51052fca 100755
--- a/extras/soap-tools/getTranscripts.py
+++ b/extras/soap-tools/getTranscripts.py
@@ -9,7 +9,7 @@ Usage:
position: Position to lookup overlapping transcripts for.
The transcript accession numbers are retrieved from the Mutalyzer SOAP
-webservice and printed to standard output.
+web service and printed to standard output.
"""
diff --git a/extras/soap-tools/getTranscriptsAndInfo.py b/extras/soap-tools/getTranscriptsAndInfo.py
index ee5a9e72..86dc3ff4 100755
--- a/extras/soap-tools/getTranscriptsAndInfo.py
+++ b/extras/soap-tools/getTranscriptsAndInfo.py
@@ -9,8 +9,8 @@ Usage:
example 'AL449423.14'.
gene: Optionally restrict results to transcripts for this gene.
-The transcript information is retrieved from the Mutalyzer SOAP webservice and
-printed to standard output.
+The transcript information is retrieved from the Mutalyzer SOAP web service
+and printed to standard output.
"""
diff --git a/extras/soap-tools/getTranscriptsByGeneName.py b/extras/soap-tools/getTranscriptsByGeneName.py
index d757dcf1..d7789a0a 100755
--- a/extras/soap-tools/getTranscriptsByGeneName.py
+++ b/extras/soap-tools/getTranscriptsByGeneName.py
@@ -8,7 +8,7 @@ Usage:
gene: Gene name to lookup transcripts for.
The transcript accession numbers are retrieved from the Mutalyzer SOAP
-webservice and printed to standard output.
+web service and printed to standard output.
"""
diff --git a/extras/soap-tools/getTranscriptsMapping.py b/extras/soap-tools/getTranscriptsMapping.py
index 3aacfab6..79683369 100755
--- a/extras/soap-tools/getTranscriptsMapping.py
+++ b/extras/soap-tools/getTranscriptsMapping.py
@@ -11,8 +11,8 @@ Usage:
pos2: End of chromosomal region, e.g. 230938269.
tolerant: Optionally set region matching to be tolerant, e.g. 1.
-The transcript information is retrieved from the Mutalyzer SOAP webservice and
-printed to standard output.
+The transcript information is retrieved from the Mutalyzer SOAP web service
+and printed to standard output.
"""
diff --git a/extras/soap-tools/getdbSNPDescriptions.py b/extras/soap-tools/getdbSNPDescriptions.py
index 11cc54a8..f5745533 100755
--- a/extras/soap-tools/getdbSNPDescriptions.py
+++ b/extras/soap-tools/getdbSNPDescriptions.py
@@ -7,7 +7,7 @@ Usage:
rs_number: A valid dbSNP rs number, e.g. 'rs9919552'.
-The HGVS descriptions are retrieved from the Mutalyzer SOAP webservice and
+The HGVS descriptions are retrieved from the Mutalyzer SOAP web service and
printed to standard output.
"""
diff --git a/extras/soap-tools/info.py b/extras/soap-tools/info.py
index e7f80ef3..eb3cd058 100755
--- a/extras/soap-tools/info.py
+++ b/extras/soap-tools/info.py
@@ -5,7 +5,7 @@ Get static version information from a Mutalyzer installation.
Usage:
{command}
-The version information is retrieved from the Mutalyzer SOAP webservice and
+The version information is retrieved from the Mutalyzer SOAP web service and
printed to standard output.
"""
diff --git a/extras/soap-tools/mappingInfo.py b/extras/soap-tools/mappingInfo.py
index 3fc0dda3..49fb4ac4 100755
--- a/extras/soap-tools/mappingInfo.py
+++ b/extras/soap-tools/mappingInfo.py
@@ -9,7 +9,7 @@ Usage:
variant: Variant to map, e.g. 'g.112039014G>T'.
build: Human genome build, 'hg18' or 'hg19' (default: 'hg19').
-The mapping information is retrieved from the Mutalyzer SOAP webservice and
+The mapping information is retrieved from the Mutalyzer SOAP web service and
printed to standard output.
"""
diff --git a/extras/soap-tools/numberConversion.py b/extras/soap-tools/numberConversion.py
index f72fb532..977bbc71 100755
--- a/extras/soap-tools/numberConversion.py
+++ b/extras/soap-tools/numberConversion.py
@@ -9,7 +9,7 @@ Usage:
description: Variant description to convert.
The converted HGVS description(s) is (are) retrieved from the Mutalyzer SOAP
-webservice and printed to standard output.
+web service and printed to standard output.
"""
diff --git a/extras/soap-tools/runMutalyzer.py b/extras/soap-tools/runMutalyzer.py
index 6cdc4697..852e467b 100755
--- a/extras/soap-tools/runMutalyzer.py
+++ b/extras/soap-tools/runMutalyzer.py
@@ -8,7 +8,7 @@ Usage:
description: Variant description to check.
verbosity: If 'verbose', also output full original and variant sequences.
-The namechecker results are retrieved from the Mutalyzer SOAP webservice and
+The namechecker results are retrieved from the Mutalyzer SOAP web service and
printed to standard output.
"""
diff --git a/extras/soap-tools/sliceChromosomeByGene.py b/extras/soap-tools/sliceChromosomeByGene.py
index 698a927c..8e24c54d 100755
--- a/extras/soap-tools/sliceChromosomeByGene.py
+++ b/extras/soap-tools/sliceChromosomeByGene.py
@@ -8,7 +8,7 @@ Usage:
gene: Gene symbol of the gene to slice.
A slice containing the gene with 5000 upstream bases and 2000 downstream bases
-is created with the Mutalyzer SOAP webservice. The resulting UD number is
+is created with the Mutalyzer SOAP web service. The resulting UD number is
printed to standard output.
"""
diff --git a/extras/soap-tools/sp.py b/extras/soap-tools/sp.py
index 29fa9019..d395d199 100755
--- a/extras/soap-tools/sp.py
+++ b/extras/soap-tools/sp.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python
-# Example SOAP client for the Mutalyzer webservice in Python using the
+# Example SOAP client for the Mutalyzer web service in Python using the
# SOAPpy library.
#
# See http://www.mutalyzer.nl/2.0/webservices
diff --git a/extras/soap-tools/transcriptInfo.py b/extras/soap-tools/transcriptInfo.py
index eaeb5792..d25d361a 100755
--- a/extras/soap-tools/transcriptInfo.py
+++ b/extras/soap-tools/transcriptInfo.py
@@ -7,8 +7,8 @@ Usage:
transcript: Transcript accession number, e.g. 'NM_002001.2'.
-The transcript information is retrieved from the Mutalyzer SOAP webservice and
-printed to standard output.
+The transcript information is retrieved from the Mutalyzer SOAP web service
+and printed to standard output.
"""
diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index 9f5622a6..dcb530ed 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -1,5 +1,5 @@
"""
-Collection of serilizable objects used by the SOAP webservice. They extend
+Collection of serilizable objects used by the SOAP web service. They extend
from the spyne ClassModel.
Default attributes for the spyne ClassModel:
diff --git a/mutalyzer/services/json.py b/mutalyzer/services/json.py
index ae94a503..bcf35ec6 100644
--- a/mutalyzer/services/json.py
+++ b/mutalyzer/services/json.py
@@ -1,5 +1,5 @@
"""
-Mutalyzer webservice HTTP/RPC with JSON response payloads.
+Mutalyzer web service HTTP/RPC with JSON response payloads.
"""
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 0270a194..a655b2fd 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -118,7 +118,7 @@ def _checkVariant(L, variant) :
class MutalyzerService(ServiceBase):
"""
- Mutalyzer webservices.
+ Mutalyzer web services.
These methods are made public via a SOAP interface.
"""
diff --git a/mutalyzer/services/soap.py b/mutalyzer/services/soap.py
index e442b9d0..278841d0 100644
--- a/mutalyzer/services/soap.py
+++ b/mutalyzer/services/soap.py
@@ -1,5 +1,5 @@
"""
-Mutalyzer SOAP/1.1 webservice.
+Mutalyzer SOAP/1.1 web service.
"""
diff --git a/mutalyzer/templates/about.html b/mutalyzer/templates/about.html
index c2377125..a0ec8312 100644
--- a/mutalyzer/templates/about.html
+++ b/mutalyzer/templates/about.html
@@ -13,7 +13,7 @@
<ul>
<li>The LRG parser, as well as the Batch interfaces are written
by Gerben R. Stouten.</li>
- <li>The position converter interfaces (webservice and WWW) are
+ <li>The position converter interfaces (web service and WWW) are
written by Gerard C.P. Schaafsma.</li>
<li>Current development and maintenance is done by Martijn
Vermaat.</li>
diff --git a/mutalyzer/templates/client-mono.cs b/mutalyzer/templates/client-mono.cs
index 0168ec39..b3baac66 100644
--- a/mutalyzer/templates/client-mono.cs
+++ b/mutalyzer/templates/client-mono.cs
@@ -1,5 +1,5 @@
/*
- Example SOAP client for the Mutalyzer webservice in C# for the Mono
+ Example SOAP client for the Mutalyzer web service in C# for the Mono
platform.
See {path}/webservices
diff --git a/mutalyzer/templates/client-php.php b/mutalyzer/templates/client-php.php
index 975eaad3..ccf52c85 100644
--- a/mutalyzer/templates/client-php.php
+++ b/mutalyzer/templates/client-php.php
@@ -1,7 +1,7 @@
<?php
/*
- Example SOAP client for the Mutalyzer webservice in PHP.
+ Example SOAP client for the Mutalyzer web service in PHP.
See {path}/webservices
diff --git a/mutalyzer/templates/client-savon.rb b/mutalyzer/templates/client-savon.rb
index a411ebeb..5404fba5 100644
--- a/mutalyzer/templates/client-savon.rb
+++ b/mutalyzer/templates/client-savon.rb
@@ -1,6 +1,6 @@
#!/usr/bin/env ruby
-# Example SOAP client for the Mutalyzer webservice in Ruby using the savon
+# Example SOAP client for the Mutalyzer web service in Ruby using the savon
# library.
#
# See {path}/webservices
diff --git a/mutalyzer/templates/client-soappy.py b/mutalyzer/templates/client-soappy.py
index 1d74d9c9..4b503dda 100644
--- a/mutalyzer/templates/client-soappy.py
+++ b/mutalyzer/templates/client-soappy.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python
-# Example SOAP client for the Mutalyzer webservice in Python using the
+# Example SOAP client for the Mutalyzer web service in Python using the
# SOAPpy library.
#
# See {path}/webservices
diff --git a/mutalyzer/templates/client-suds.py b/mutalyzer/templates/client-suds.py
index dc97fab4..46ea68f9 100644
--- a/mutalyzer/templates/client-suds.py
+++ b/mutalyzer/templates/client-suds.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python
-# Example SOAP client for the Mutalyzer webservice in Python using the
+# Example SOAP client for the Mutalyzer web service in Python using the
# suds library.
#
# See {path}/webservices
diff --git a/mutalyzer/templates/help.html b/mutalyzer/templates/help.html
index c6c7f4fd..448d0824 100644
--- a/mutalyzer/templates/help.html
+++ b/mutalyzer/templates/help.html
@@ -11,20 +11,20 @@
Mutalyzer is a tool primarily designed to check descriptions of
sequence variants according to the standard human sequence variant
nomenclature of the Human Genome Sequence Variation Society
- (<a href="http://www.hgvs.org/">HGVS</a>) (For an overview, visit
+ (<a href="http://www.hgvs.org/">HGVS</a>) (For an overview, visit
<a href="http://www.hgvs.org/mutnomen/"
>http://www.hgvs.org/mutnomen/</a>).
Mutalyzer aims to encourage the proper use of nomenclature in
publications and reduce redundancy in sequence variation databases. In
principle, Mutalyzer can check descriptions of sequence variants
detected in other organisms, provided that the standard HGVS
- nomenclature is applied.
+ nomenclature is applied.
</p>
<h3>Mutalyzer 2 flow</h3>
<p>
The user specifies a reference sequence (file) and a variant using the
- <a href="#NameGenerator">Name Generator</a> or the
+ <a href="#NameGenerator">Name Generator</a> or the
<a href="#NameChecker">Name checker</a> interface. The Name Generator
builds the complete variant description for the Name Checker (e.g.,
Mutalyzer uses this input to perform the nomenclature check in the
@@ -32,8 +32,8 @@
</p>
<p>
1) Retriever: retrieves
- <a href="#Ref">reference sequence records</a> from the
- <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a> or
+ <a href="#Ref">reference sequence records</a> from the
+ <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a> or
<a href="http://www.lrg-sequence.org/">LRG</a> websites.
</p>
<p>
@@ -76,7 +76,7 @@
different checkers that accept a large list of descriptions as input.
</p>
<p>
- - <a href="#Webservices">Webservices</a>: programmatic access to
+ - <a href="#Webservices">Web services</a>: programmatic access to
Mutalyzer's functionality.
</p>
<p> </p>
@@ -99,18 +99,18 @@
1) GenBank files
</p>
<p>
- GenBank records (e.g., NG_007400.1) are specified by a
+ GenBank records (e.g., NG_007400.1) are specified by a
<i>GenBank accession number</i> (NG_007400) and a version number (.1).
Omission of the version number automatically results in selection of
the most recent version of that record. In case of outdated versions,
- Mutalyzer will issue a warning. Alternatively, the unique
+ Mutalyzer will issue a warning. Alternatively, the unique
<i>GenInfo identifier</i> (gi) of the reference sequence (e.g.,
4506864) can be used with or without the letters ''gi'';.
Mutalyzer does not accept GenBank records containing no sequence (e.g.
chromosomal reference sequence identifiers referring to contig
accession numbers) or files larger than 10 MB. Mutalyzer also accepts
user-defined files in GenBank format, including slices of chromosomal
- reference sequences. These files are specified by unique
+ 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">Reference File Loader</a>
section for more information).<br>
@@ -121,16 +121,16 @@
<p>
Locus Reference Genomic (LRG) files containing uniquely and stable
reference DNA sequences along with all relevant transcript and protein
- sequences essential to the description of gene variants (see the
+ sequences essential to the description of gene variants (see the
<a href="http://www.lrg-sequence.org/"> LRG website</a> for more
- information). LRG files are based on
- <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>'s
+ information). LRG files are based on
+ <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>'s
<a href="http://www.ncbi.nlm.nih.gov/RefSeq/RSG/">RefSeqGene project</a>
and created in collaboration with the community of research and
diagnostic labs, LSDB curators and mutation consortia. LRG files are
specified by the prefix "LRG_" followed by a number (e.g.,
LRG_1). The <a href="http://www.lrg-sequence.org/"> LRG website</a>
- lists existing LRG sequences and has an
+ 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 Reference File Loader does
not accept user-defined LRG files.
@@ -140,7 +140,7 @@
<p>
The Mutalyzer nomenclature checker accepts variant descriptions in
standard human sequence variant nomenclature format. For users, who are
- not familiar with the nomenclature syntax, Mutalyzer's
+ not familiar with the nomenclature syntax, Mutalyzer's
<a href="#NameGenerator">Name Generator</a> provides a form to acquire
the separate components necessary to construct variant descriptions.
</p>
@@ -207,7 +207,7 @@
</p>
<p>
The <i>Non-coding DNA</i> or <i>ncDNA</i> position numbering scheme can
- be used with:<br>
+ be used with:<br>
a) <i> GenBank</i> records containing genomic sequences with annotated
transcripts without a corresponding coding sequence.<br>
b) LRG records<br>
@@ -247,10 +247,10 @@
The value 1 is assigned to the A of the ATG start codon and all the
exonic bases between start and stop are counted normally.<br>
5' untranslated region: Exonic bases upstream of (i.e. before) the ATG
- are numbered -1, -2, -3 and so on.<br>
+ are numbered -1, -2, -3 and so on.<br>
3' untranslated region: Exonic bases downstream of (i.e. behind) the
stop codon are numbered *1, *2, *3 and so on.<br>
- Intronic bases in the Coding sequence are numbered x+1, x+2, x+3, ...
+ Intronic bases in the Coding sequence are numbered x+1, x+2, x+3, ...
y-3, y-2, y-1 where x is the value of the last exonic base
upstream of the intron, y is the value of the first exonic base
downstream of the intron and x and y are consecutive numbers. Intronic
@@ -485,7 +485,7 @@
</p>
<hr>
-
+
<h3>Mutalyzer Name Checker Help<a name="NameChecker"></a></h3>
<p>
Users can check the correctness of a variant description. The Name
@@ -494,15 +494,15 @@
</p>
<p>
Examples: <br>
- AB026906.1:c.3_4insG<br>
- AB026906.1:c.[1del;4G>T]<br>
- AL449423.14(CDKN2A_v1):c.1_10del<br>
+ AB026906.1:c.3_4insG<br>
+ AB026906.1:c.[1del;4G>T]<br>
+ AL449423.14(CDKN2A_v1):c.1_10del<br>
UD_127955523176(DMD_v002):c.136G>T<br>
LRG_1t1:c.266G>T
</p>
<hr>
-
+
<h3>Mutalyzer Syntax Checker Help<a name="SyntaxChecker"></a></h3>
<p>
Users can check the correctness of the standard nomenclature syntax.
@@ -517,9 +517,9 @@
AB026906.1:c.35_36ins<br>
LRG_1t1:c.266G>T
</p>
-
+
<hr>
-
+
<h3>
Mutalyzer Position Converter Help<a name="PositionConverter"></a>
</h3>
@@ -528,23 +528,23 @@
description from the chromosomal position for a specific human genome
build to a position relative to RefSeq transcript reference sequences.
The Position Converter uses a local database containing the mapping
- information from the
+ information from the
<a href="http://genome.ucsc.edu/index.html?org=Human"
>UCSC genome browser</a> for human genome builds hg18 (NCBI 36) and
hg19 (GRCh37). The specified version of the RefSeq transcript Accession
number has to be present in the database. The sequence variation
- description has <u>not</u> been checked by Mutalyzer's
+ description has <u>not</u> been checked by Mutalyzer's
<a href="#NameChecker">Name Checker</a>.
</p>
<p>
Examples:<br>
- NM_003002.2:c.274G>T<br>
- chr11:g.111959693G>T<br>
+ NM_003002.2:c.274G>T<br>
+ chr11:g.111959693G>T<br>
NC_000011.9:g.111959693G>T
</p>
<hr>
-
+
<h3>Mutalyzer SNP Converter Help<a name="SNPConverter"></a></h3>
<p>
The SNP Converter will submit a <a
@@ -560,7 +560,7 @@
</p>
<hr>
-
+
<h3>Mutalyzer Name Generator Help<a name="NameGenerator"></a></h3>
<p>
The Name Generator aims to assist users, who are not familiar with all
@@ -573,28 +573,28 @@
</p>
<p>
Example: <br>
- Reference: AL449423.14<br>
- Sequence Type: Coding DNA<br>
- Gene symbol: CDKN2A<br>
+ Reference: AL449423.14<br>
+ Sequence Type: Coding DNA<br>
+ Gene symbol: CDKN2A<br>
Transcript: v_1
</p>
<p>
- Variant 1<br>
- Mutation Type: Substitution<br>
- Start Position: 112<br> End Position: 112<br>
- Deleted Sequence: C<br>
+ Variant 1<br>
+ Mutation Type: Substitution<br>
+ Start Position: 112<br> End Position: 112<br>
+ Deleted Sequence: C<br>
Inserted Sequence: T
</p>
<hr>
-
+
<h3>Mutalyzer Batch Checker Help<a name="BatchChecker"></a></h3>
<p>
<br>
The Batch checkers support submission of files containing large
- datasets to the <a href="#NameChecker">Name Checker</a>,
- <a href="#SyntaxChecker">Syntax Checker</a>, and
- <a href="#PositionConverter">Position Converter</a> tools.
+ datasets to the <a href="#NameChecker">Name Checker</a>,
+ <a href="#SyntaxChecker">Syntax Checker</a>, and
+ <a href="#PositionConverter">Position Converter</a> tools.
</p>
<p>The Mutalyzer batch checker accepts the following file formats
<ul>
@@ -603,7 +603,7 @@
<li>OpenOffice .odt File</li>
</ul>
</p>
-
+
<h5>
We accept two types of input files, you can download examples below
</h5>
@@ -627,7 +627,7 @@
</div>
<h5>
- Old Style:
+ Old Style:
<a href="downloads/batchtestold.txt">Download Example File</a>
</h5>
<div style="padding-left:20px; width:400px">
@@ -658,7 +658,7 @@
Users can upload a tab-delimited text file with the sequence
variations to be checked. Files for the Name Checker and the Syntax
Checker may contain any combination of reference sequences and sequence
- types for different genes. Mutalyzer's
+ types for different genes. Mutalyzer's
<i><a href="#UD">UD identifiers</a></i> can also be used, but we
strongly suggest to update any GenBank record following
<a href="http://www.ncbi.nlm.nih.gov/Genbank/update.html"
@@ -677,9 +677,9 @@
Internet Explorer, progress may not be reported correctly. Adding
Mutalyzer to your trusted sites is one option to solve this.
</p>
-
+
<hr>
-
+
<h2>Mutalyzer Output</h2>
<p>
Mutalyzer has been designed to issue warnings, when correcting entries,
@@ -692,7 +692,7 @@
</p>
<p>
<<i>Accession Number</i>>.<<i>version number></i>:<i><sequence type</i>>.<<i >mutation</i>><br>
-
+
(Examples: NM_003002.1:c.5delC or AL449423.14:g.61866_85191del)<br>
or<br>
<<i>Accession Number</i>>.<<i>version number><(Gene Symbol)></i>:<i ><sequence type</i>>.<<i >mutation</i>><br>
@@ -717,7 +717,7 @@
arginine substituted for a proline at position 2).
</p>
<p>
- Please note the following:
+ Please note the following:
</p>
<p>
- Sequence variation descriptions using genomic references in
@@ -731,12 +731,12 @@
on the selected Sequence Type. Example: 4506864:c.5del will be
converted into NM_003002.1:c.5delC
</p>
-
+
<hr>
-
+
<h3>Reference File Loader Help<a name="GenBankUploader"></a></h3>
<p>
- Users can upload their own reference sequence file in
+ Users can upload their own reference sequence file in
<a href="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html"
>GenBank Flat file format</a>, retrieve the genomic sequence of a
gene with its flanking regions, or specify a chromosomal range for use
@@ -770,11 +770,11 @@
<p>
Enter the URL of the website, where the Genbank Flat file with a .gb
extension can be found and press the submit button.
- </p>
+ </p>
<p> </p>
<p>
<b>
- Retrieve part of the reference genome for a
+ Retrieve part of the reference genome for a
(<a href="http://www.genenames.org">HGNC</a>) gene symbol
</b>
</p>
@@ -809,7 +809,7 @@
<tr>
<td>Number of 3' flanking nucleotides</td>
<td><input type="text" name="3utr" value="2000"></td>
- </tr>
+ </tr>
</table>
</div>
<p>
@@ -860,7 +860,7 @@
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.
+ Download this reference sequence.
</p>
</div>
<p>
@@ -872,20 +872,20 @@
<hr>
- <h3>Mutalyzer Webservices <a name="Webservices"></a></h3>
+ <h3>Mutalyzer Web services <a name="Webservices"></a></h3>
<p>
- Mutalyzer's webservices provide programmatic access to different parts
- of Mutalyzer's functionality. In the future, these will be used by
+ Mutalyzer's web services provide programmatic access to different parts
+ of Mutalyzer's functionality. In the future, these will be used by
<a href="http://www.LOVD.nl">LOVD</a> to convert coding DNA positions
to chromosomal positions for mapping and display purposes. A full
- description of available webservices can be found at the
- <a href="documentation">Webservice documentation page</a>.
- Example scripts and requirements can be found at the
- <a href="webservices">Webservice page</a>.
+ description of available web services can be found at the
+ <a href="documentation">Web service documentation page</a>.
+ Example scripts and requirements can be found at the
+ <a href="webservices">Web service page</a>.
</p>
<hr>
-
+
<h3>Using Mutalyzer with sequences from other organisms</h3>
<p>
Mutalyzer can process Genbank reference files from other organisms than
@@ -906,13 +906,13 @@
replicates the input of the user. Most errors occurring after mistyping
should be easy to understand and can be corrected immediately by
altering the data in the field specified. In other cases, Mutalyzer
- should advise you to contact
+ should advise you to contact
<a href="mailto:Mutalyzer@humgen.nl">us</a> when the error persists.
Please specify your input and which tool you used.
</p>
<p>
Occasionally, Mutalyzer will display an Internal Server Error message
- due to unexpected behavior. You can use Mutalyzer's
+ due to unexpected behavior. You can use Mutalyzer's
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer"
>bugtracking system</a> to report errors and send in feature requests.
</p>
@@ -923,7 +923,7 @@
Ophuizen E, den Dunnen JT, Taschner PE. Improving sequence variant
descriptions in mutation databases and literature using the MUTALYZER
sequence variation nomenclature checker.
- <a href="http://www.ncbi.nlm.nih.gov/entrez/utils/fref.fcgi?PrId=3058&itool=AbstractPlus-def&uid=18000842&db=pubmed&url=http://dx.doi.org/10.1002/humu.20654">Hum Mutat 29:6-13 (2008)</a>
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/utils/fref.fcgi?PrId=3058&itool=AbstractPlus-def&uid=18000842&db=pubmed&url=http://dx.doi.org/10.1002/humu.20654">Hum Mutat 29:6-13 (2008)</a>
[<a href="http://www.ncbi.nlm.nih.gov/pubmed/18000842?"
>PMID: 18000842</a>].
</p>
@@ -933,7 +933,7 @@
specifications provided by Peter E. M. Taschner and Johan T. den
Dunnen. The different parts of the nomenclature checker functionality
have been separated into modules, which can be used as independent
- webservices and undergo further development and extension in the
+ web services and undergo further development and extension in the
future.
</p>
@@ -942,7 +942,7 @@
<p>
If you have any comments or suggestions be sure to let us know!
</p>
-
+
<p>
Last modified: November 5, 2010
</p>
diff --git a/mutalyzer/templates/index.html b/mutalyzer/templates/index.html
index 87760fa2..e248df27 100644
--- a/mutalyzer/templates/index.html
+++ b/mutalyzer/templates/index.html
@@ -6,14 +6,14 @@
<div metal:define-macro="content">
<center><h3>Welcome to the Mutalyzer web site</h3></center>
<br>
-
+
The aim of this program suite is to support checks of sequence variant
- nomenclature according to the
- <a href="http://www.hgvs.org/mutnomen/">guidelines</a> of the
+ nomenclature according to the
+ <a href="http://www.hgvs.org/mutnomen/">guidelines</a> of the
<a href="http://www.hgvs.org">Human Genome Variation Society</a>.<br>
<br>
<br>
-
+
Different interfaces are provided to collect the information necessary
for the checks:
<ul>
@@ -54,8 +54,8 @@
checks.
</li>
<li>
- The <a href = "webservices">Webservices</a> page provides instructions
- for the webservices.
+ The <a href = "webservices">Web services</a> page provides instructions
+ for the web services.
</li>
</ul>
<br>
@@ -65,11 +65,11 @@
Python Scripting Language was chosen for good readability and therefore
easy maintenance.<br>
-->
- GenBank sequences are retrieved from the
- <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>
+ GenBank sequences are retrieved from the
+ <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>
(<a href="http://eutils.ncbi.nlm.nih.gov/About/disclaimer.html"
>Copyright and Disclaimers</a>).<br>
- This project is sponsored by
+ This project is sponsored by
<a href = "http://www.sun.com">SUN Microsystems</a> with server
hardware within the scope of the Academic Excellence Grant (AEG)
program (award EDUD-7832-080223-CNE).<br>
diff --git a/mutalyzer/templates/menu.html b/mutalyzer/templates/menu.html
index cd1665f3..b32ffeed 100644
--- a/mutalyzer/templates/menu.html
+++ b/mutalyzer/templates/menu.html
@@ -209,7 +209,7 @@
<tr tal:attributes="class active/webservices">
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a href="webservices">Webservices</a>
+ <a href="webservices">Web services</a>
</td>
</tr>
@@ -281,7 +281,7 @@
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
- <a href="http://www.hgvs.org/mutnomen/HGVS_extend_PT.doc"
+ <a href="http://dx.doi.org/10.1002/humu.21427"
>HGVS Nomenclature Extension Proposal</a>
</td>
</tr>
diff --git a/mutalyzer/templates/textmining.py b/mutalyzer/templates/textmining.py
index edf6d53a..e48fb350 100644
--- a/mutalyzer/templates/textmining.py
+++ b/mutalyzer/templates/textmining.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python
-# Example SOAP client for the Mutalyzer webservice in Python using the
+# Example SOAP client for the Mutalyzer web service in Python using the
# SOAPpy library.
#
# See {path}/webservices
diff --git a/mutalyzer/templates/webservices.html b/mutalyzer/templates/webservices.html
index c9dbd304..5ce11fdd 100644
--- a/mutalyzer/templates/webservices.html
+++ b/mutalyzer/templates/webservices.html
@@ -5,19 +5,19 @@
<body>
<div metal:define-macro="content">
<center>
- <h3>Webservices</h3>
+ <h3>Web services</h3>
</center>
<br>
- Most Mutalyzer functionality is programmatically available trough two
- interfaces: a SOAP webservice and a HTTP/RPC+JSON webservice.
+ Most Mutalyzer functionality is programmatically available through two
+ interfaces: a SOAP web service and a HTTP/RPC+JSON web service.
<br>
- <h3>SOAP webservice</h3>
+ <h3>SOAP web service</h3>
A <a href="services/?wsdl">WSDL description</a> is available
for easy generation of client programs in many languages. See the
<a href = "soap-api">annotated API</a> for detailed documentation.
<br>
<br>
- The following are some example client programs for SOAP webservice. They
+ The following are some example client programs for SOAP web service. They
use the <a href="documentation#op.checkSyntax">checkSyntax</a> method
to determine if a variant description adheres to the <span class="helper"
title="Human Genome Variation Society standard variant nomenclature">
@@ -37,8 +37,8 @@
Here is an example that could be used for
<a href="download/textmining.py">text mining</a> on a
<a href="downloads/textmining_sample.txt">sample</a> input file.
- <h3>HTTP/RPC+JSON webservice</h3>
- The HTTP/RPC+JSON webservice is experimental and currently undocumented.
+ <h3>HTTP/RPC+JSON web service</h3>
+ The HTTP/RPC+JSON web service is experimental and currently undocumented.
It can be called using HTTP GET requests on <code tal:content = "structure string:${location}${serviceJsonLocation}/method?param=value"></code> where <code>method</code> is the name of the method to be called and method parameters are expected as <code>param=value</code> query string parameters. Responses are JSON-encoded.
<br>
<br>
@@ -47,7 +47,7 @@
<br>
For now, you can work from this example using the above mentioned
<a href="soap-api">annotated SOAP API</a>, since the HTTP/RPC+JSON
- webservice mirrors the functionality of the SOAP webservice.
+ web service mirrors the functionality of the SOAP web service.
</div>
</body>
</html>
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 98700930..f7c9084d 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -318,10 +318,10 @@ class Reference:
This is used by LOVD to quickly check if a reference file is in the
cache. If it isn't, it will resubmit it.
- Of course a more proper solution here would be to have some webservice
- method which checks if the GenBank file is in the cache *or* can be
- reconstructed from the information in the database. Because if the
- latter is the case, Mutalyzer will add it to the cache on the fly.
+ Of course a more proper solution here would be to have some web
+ service method which checks if the GenBank file is in the cache *or*
+ can be reconstructed from the information in the database. Because if
+ the latter is the case, Mutalyzer will add it to the cache on the fly.
"""
file_path = os.path.join(config.get('cache'), '%s.bz2' % file)
@@ -1444,11 +1444,11 @@ class Uploader:
class SoapApi:
"""
- SOAP webservice documentation.
+ SOAP web service documentation.
"""
def GET(self):
"""
- HTML documentation for the webservice.
+ HTML documentation for the web service.
Generate the documentation by a XSL transform of the WSDL document.
The XSL transformation used is from Tomi Vanek:
@@ -1465,7 +1465,7 @@ class SoapApi:
.documentation { white-space: pre-line; }
@todo: Use some configuration setting for the location of the
- webservice.
+ web service.
@todo: Use configuration value for .xsl location.
@todo: Cache this transformation.
"""
diff --git a/tests/test_services_soap.py b/tests/test_services_soap.py
index 8f1ba62c..c3b40998 100644
--- a/tests/test_services_soap.py
+++ b/tests/test_services_soap.py
@@ -52,7 +52,7 @@ class TestServicesSoap():
"""
def setUp(self):
"""
- Initialize webservice entrypoint.
+ Initialize web service entrypoint.
@todo: Start the standalone server and stop it in self.tearDown
instead of depending on some running instance at a fixed address.
diff --git a/tests/test_website.py b/tests/test_website.py
index 97aed79e..0ebd3660 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -621,7 +621,7 @@ facilisi."""
def test_download_py(self):
"""
- Download a Python example client for the webservice.
+ Download a Python example client for the web service.
"""
r = self.app.get('/download/client-suds.py')
assert_equal(r.content_type, 'text/plain')
@@ -629,7 +629,7 @@ facilisi."""
def test_download_rb(self):
"""
- Download a Ruby example client for the webservice.
+ Download a Ruby example client for the web service.
"""
r = self.app.get('/download/client-savon.rb')
assert_equal(r.content_type, 'text/plain')
@@ -637,7 +637,7 @@ facilisi."""
def test_download_cs(self):
"""
- Download a C# example client for the webservice.
+ Download a C# example client for the web service.
"""
r = self.app.get('/download/client-mono.cs')
assert_equal(r.content_type, 'text/plain')
@@ -645,7 +645,7 @@ facilisi."""
def test_download_php(self):
"""
- Download a PHP example client for the webservice.
+ Download a PHP example client for the web service.
"""
r = self.app.get('/download/client-php.php')
assert_equal(r.content_type, 'text/plain')
--
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