From 0abce58301c368d2cea7210f8ffb0f7991f35f49 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Fri, 10 Jan 2014 16:11:19 +0100
Subject: [PATCH] Port website from web.py to Flask
This includes changing a lot of routes and parameter names to be more
consistent. We try to remain backwards compatible as much as possible
by providing redirects from old routes and parameter names.
---
MANIFEST.in | 2 +-
mutalyzer/File.py | 61 +-
mutalyzer/Scheduler.py | 52 +-
mutalyzer/config/__init__.py | 3 +
mutalyzer/config/default_settings.py | 13 +
mutalyzer/db/models.py | 10 +-
mutalyzer/entrypoints/mapping_update.py | 1 +
mutalyzer/entrypoints/website.py | 21 +-
mutalyzer/services/rpc.py | 5 +-
mutalyzer/templates/static/js/interface.js | 111 --
mutalyzer/templates/webservices.html | 69 -
mutalyzer/variantchecker.py | 3 +-
mutalyzer/website.py | 1478 -----------------
mutalyzer/website/__init__.py | 83 +
mutalyzer/{ => website}/templates/about.html | 4 +-
mutalyzer/{ => website}/templates/base.html | 69 +-
.../website/templates/batch-job-progress.html | 46 +
.../templates/batch-jobs.html} | 56 +-
.../templates/description-extractor.html} | 30 +-
.../templates/downloads/batchtestnew.txt | 0
.../templates/downloads/batchtestold.txt | 0
.../templates/downloads}/client-mono.cs | 18 +-
.../templates/downloads}/client-php.php | 16 +-
.../templates/downloads}/client-savon.rb | 8 +-
.../templates/downloads}/client-soappy.py | 4 +-
.../templates/downloads}/client-suds.py | 4 +-
.../templates/downloads}/textmining.py | 4 +-
.../templates/downloads/textmining_sample.txt | 0
.../templates/homepage.html} | 18 +-
.../templates/name-checker.html} | 70 +-
.../templates/name-generator.html} | 0
.../templates/position-converter.html} | 28 +-
.../templates/reference-loader.html} | 62 +-
.../templates/snp-converter.html} | 22 +-
.../templates/static/css/style.css | 0
.../templates/static/images/1x1b.gif | Bin
.../templates/static/images/1x1w.gif | Bin
.../templates/static/images/Eurogentest.png | Bin
.../templates/static/images/LUMC_24x24.png | Bin
.../templates/static/images/background.gif | Bin
.../static/images/background.gif.old | Bin
.../templates/static/images/banner.jpg | Bin
.../templates/static/images/bullit.gif | Bin
.../templates/static/images/bullitdonker.gif | Bin
.../templates/static/images/bullitlicht1.gif | Bin
.../templates/static/images/bullitlicht2.gif | Bin
.../templates/static/images/bullitmiddel.gif | Bin
.../static/images/bullitmiddel.gif.old | Bin
.../templates/static/images/commit_logo.png | Bin
.../templates/static/images/cubic4-17.gif | Bin
.../templates/static/images/cubic4-17c.gif | Bin
.../templates/static/images/debug.png | Bin
.../templates/static/images/detailkaart.jpg | Bin
.../templates/static/images/error.png | Bin
.../templates/static/images/favicon.ico | Bin
.../static/images/gen_2_phen_logo_print.png | Bin
.../templates/static/images/info.png | Bin
.../templates/static/images/logoULE.gif | Bin
.../static/images/mutalyzer_logo.png | Bin
.../static/images/mutalyzer_logo_bw.png | Bin
.../templates/static/images/nbic_logo.png | Bin
.../templates/static/images/project-1.jpg | Bin
.../templates/static/images/warning.png | Bin
.../templates/static/js/generator.js | 2 +-
.../website/templates/static/js/interface.js | 58 +
.../templates/static/js/jquery-1.10.2.min.js | 6 +
.../templates/syntax-checker.html} | 18 +-
mutalyzer/website/templates/webservices.html | 71 +
.../{ => website}/templates/wsdl-viewer.xsl | 0
mutalyzer/website/views.py | 1060 ++++++++++++
requirements.txt | 1 -
setup.py | 3 +-
72 files changed, 1598 insertions(+), 1992 deletions(-)
delete mode 100644 mutalyzer/templates/static/js/interface.js
delete mode 100644 mutalyzer/templates/webservices.html
delete mode 100644 mutalyzer/website.py
create mode 100644 mutalyzer/website/__init__.py
rename mutalyzer/{ => website}/templates/about.html (95%)
rename mutalyzer/{ => website}/templates/base.html (79%)
create mode 100644 mutalyzer/website/templates/batch-job-progress.html
rename mutalyzer/{templates/batch_jobs.html => website/templates/batch-jobs.html} (59%)
rename mutalyzer/{templates/description_extractor.html => website/templates/description-extractor.html} (72%)
rename mutalyzer/{ => website}/templates/downloads/batchtestnew.txt (100%)
rename mutalyzer/{ => website}/templates/downloads/batchtestold.txt (100%)
rename mutalyzer/{templates => website/templates/downloads}/client-mono.cs (80%)
rename mutalyzer/{templates => website/templates/downloads}/client-php.php (82%)
rename mutalyzer/{templates => website/templates/downloads}/client-savon.rb (85%)
rename mutalyzer/{templates => website/templates/downloads}/client-soappy.py (92%)
rename mutalyzer/{templates => website/templates/downloads}/client-suds.py (89%)
rename mutalyzer/{templates => website/templates/downloads}/textmining.py (85%)
rename mutalyzer/{ => website}/templates/downloads/textmining_sample.txt (100%)
rename mutalyzer/{templates/index.html => website/templates/homepage.html} (66%)
rename mutalyzer/{templates/name_checker.html => website/templates/name-checker.html} (76%)
rename mutalyzer/{templates/nameGenerator.html => website/templates/name-generator.html} (100%)
rename mutalyzer/{templates/position_converter.html => website/templates/position-converter.html} (61%)
rename mutalyzer/{templates/reference_loader.html => website/templates/reference-loader.html} (68%)
rename mutalyzer/{templates/snp_converter.html => website/templates/snp-converter.html} (65%)
rename mutalyzer/{ => website}/templates/static/css/style.css (100%)
rename mutalyzer/{ => website}/templates/static/images/1x1b.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/1x1w.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/Eurogentest.png (100%)
rename mutalyzer/{ => website}/templates/static/images/LUMC_24x24.png (100%)
rename mutalyzer/{ => website}/templates/static/images/background.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/background.gif.old (100%)
rename mutalyzer/{ => website}/templates/static/images/banner.jpg (100%)
rename mutalyzer/{ => website}/templates/static/images/bullit.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/bullitdonker.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/bullitlicht1.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/bullitlicht2.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/bullitmiddel.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/bullitmiddel.gif.old (100%)
rename mutalyzer/{ => website}/templates/static/images/commit_logo.png (100%)
rename mutalyzer/{ => website}/templates/static/images/cubic4-17.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/cubic4-17c.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/debug.png (100%)
rename mutalyzer/{ => website}/templates/static/images/detailkaart.jpg (100%)
rename mutalyzer/{ => website}/templates/static/images/error.png (100%)
rename mutalyzer/{ => website}/templates/static/images/favicon.ico (100%)
rename mutalyzer/{ => website}/templates/static/images/gen_2_phen_logo_print.png (100%)
rename mutalyzer/{ => website}/templates/static/images/info.png (100%)
rename mutalyzer/{ => website}/templates/static/images/logoULE.gif (100%)
rename mutalyzer/{ => website}/templates/static/images/mutalyzer_logo.png (100%)
rename mutalyzer/{ => website}/templates/static/images/mutalyzer_logo_bw.png (100%)
rename mutalyzer/{ => website}/templates/static/images/nbic_logo.png (100%)
rename mutalyzer/{ => website}/templates/static/images/project-1.jpg (100%)
rename mutalyzer/{ => website}/templates/static/images/warning.png (100%)
rename mutalyzer/{ => website}/templates/static/js/generator.js (99%)
create mode 100644 mutalyzer/website/templates/static/js/interface.js
create mode 100644 mutalyzer/website/templates/static/js/jquery-1.10.2.min.js
rename mutalyzer/{templates/syntax_checker.html => website/templates/syntax-checker.html} (69%)
create mode 100644 mutalyzer/website/templates/webservices.html
rename mutalyzer/{ => website}/templates/wsdl-viewer.xsl (100%)
create mode 100644 mutalyzer/website/views.py
diff --git a/MANIFEST.in b/MANIFEST.in
index 1d4a5396..8d1f660b 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,2 +1,2 @@
include AUTHORS README.md
-recursive-include mutalyzer/templates *
+recursive-include mutalyzer/website/templates *
diff --git a/mutalyzer/File.py b/mutalyzer/File.py
index cce718c3..118d6ca9 100644
--- a/mutalyzer/File.py
+++ b/mutalyzer/File.py
@@ -112,59 +112,8 @@ class File() :
@return: list of lists
@rtype: list
"""
-
- # If we naively assume the input file uses \n characters as
- # newlines, the CSV parser can trip over e.g. Windows style
- # newlines. It will probably complain with a message like:
- #
- # new-line character seen in unquoted field - do you need to open
- # the file in universal-newline mode?
- #
- # Here we try to support multiplatform newline modes in the input
- # file, so \n, \r, \r\n are all recognized as a newline.
- #
- # This can be done by opening the file in 'U' mode, but in this case
- # we already have an opened file (probably, if the call originated
- # from a web request, opened by the web.py input handler, which uses
- # the Python cgi module for opening uploaded files).
- #
- # A fix is to get the handle's file descriptor and create a new
- # handle for it, using 'U' mode.
- #
- # However, sometimes our handler has no .fileno(), for example when
- # the input file is quite small (< 1kb). In that case, the cgi
- # module seems to optimize things and use a StringIO for the file,
- # which of course has no .fileno().
- #
- # So our solution is:
- # - We have .fileno(): Create a new handle, using 'U' mode.
- # - We have no .fileno(): Replace all newlines by \n (in-memory)
- # and wrap the result in a new StringIO.
-
- if hasattr(handle, 'fileno'):
- # Todo: We get the following error in our logs (exact origin
- # unknown):
- #
- # close failed in file object destructor:
- # IOError: [Errno 9] Bad file descriptor
- #
- # I am unable to find the reason for this. Everything seems to
- # be working though.
- new_handle = os.fdopen(handle.fileno(), 'rU')
- elif hasattr(handle, 'getvalue'):
- data = handle.getvalue()
- data = data.replace('\r\n', '\n').replace('\r', '\n')
- new_handle = StringIO(data)
- else:
- self.__output.addMessage(__file__, 4, "EBPARSE",
- "Fatal error parsing input file, please"
- " report this as a bug including the"
- " input file.")
- return None
-
- # I don't think the .seek(0) is needed now we created a new handle
- new_handle.seek(0)
- buf = new_handle.read(BUFFER_SIZE)
+ handle.seek(0)
+ buf = handle.read(BUFFER_SIZE)
# Default dialect
dialect = 'excel'
@@ -186,14 +135,14 @@ class File() :
# if dialect.delimiter == ":":
# dialect.delimiter = "\t"
- new_handle.seek(0)
- reader = csv.reader(new_handle, dialect)
+ handle.seek(0)
+ reader = csv.reader(handle, dialect)
ret = []
for i in reader:
ret.append(i)
- new_handle.close()
+ handle.close()
return ret
#__parseCsvFile
diff --git a/mutalyzer/Scheduler.py b/mutalyzer/Scheduler.py
index 1547780a..ebec512a 100644
--- a/mutalyzer/Scheduler.py
+++ b/mutalyzer/Scheduler.py
@@ -374,9 +374,7 @@ Mutalyzer batch scheduler""" % url)
else:
print ('Job %s finished, email %s file %s'
% (batch_job.id, batch_job.email, batch_job.id))
- self.__sendMail(
- batch_job.email, '%sResults_%s.txt'
- % (batch_job.download_url_prefix, batch_job.result_id))
+ self.__sendMail(batch_job.email, batch_job.download_url)
session.delete(batch_job)
session.commit()
#process
@@ -430,7 +428,7 @@ Mutalyzer batch scheduler""" % url)
outputline += batchOutput[0]
#Output
- filename = "%s/Results_%s.txt" % (settings.CACHE_DIR, batch_job.result_id)
+ filename = "%s/batch-job-%s.txt" % (settings.CACHE_DIR, batch_job.result_id)
if not os.path.exists(filename) :
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
@@ -505,7 +503,7 @@ Mutalyzer batch scheduler""" % url)
result = "|".join(output.getBatchMessages(2))
#Output
- filename = "%s/Results_%s.txt" % (settings.CACHE_DIR, batch_job.result_id)
+ filename = "%s/batch-job-%s.txt" % (settings.CACHE_DIR, batch_job.result_id)
if not os.path.exists(filename) :
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
@@ -608,7 +606,7 @@ Mutalyzer batch scheduler""" % url)
error = "%s" % "|".join(O.getBatchMessages(2))
#Output
- filename = "%s/Results_%s.txt" % (settings.CACHE_DIR, batch_job.result_id)
+ filename = "%s/batch-job-%s.txt" % (settings.CACHE_DIR, batch_job.result_id)
if not os.path.exists(filename) :
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
@@ -671,7 +669,7 @@ Mutalyzer batch scheduler""" % url)
outputline += "%s\t" % "|".join(O.getBatchMessages(2))
#Output
- filename = "%s/Results_%s.txt" % (settings.CACHE_DIR, batch_job.result_id)
+ filename = "%s/batch-job-%s.txt" % (settings.CACHE_DIR, batch_job.result_id)
if not os.path.exists(filename) :
# If the file does not yet exist, create it with the correct
# header above it. The header is read from the config file as
@@ -696,30 +694,33 @@ Mutalyzer batch scheduler""" % url)
"Finished SNP converter batch rs%s" % cmd)
#_processSNP
-
- def addJob(self, eMail, queue, columns, fromHost, jobType,
- Arg1):
+ def addJob(self, email, queue, columns, job_type, argument=None,
+ create_download_url=None):
"""
Add a job to the Database and start the BatchChecker.
- @arg eMail: e-mail address of batch supplier
- @type eMail: string
+ @arg email: e-mail address of batch supplier
+ @type email: string
@arg queue: A list of jobs
@type queue: list
@arg columns: The number of columns.
@type columns: int
- @arg fromHost: From where is the request made
- @type fromHost:
- @arg jobType: The type of Batch Job that should be run
- @type jobType:
- @arg Arg1: Batch Arguments, for now only build info
- @type Arg1:
-
- @return: resultID
+ @arg job_type: The type of Batch Job that should be run
+ @type job_type:
+ @arg argument: Batch Arguments, for now only build info
+ @type argument:
+ @arg create_download_url: Function accepting a result_id and returning
+ the URL for downloading the batch job
+ result. Can be None.
+ @type create_download_url: function
+
+ @return: result_id
@rtype:
"""
# Add jobs to the database
- batch_job = BatchJob(jobType, email=eMail, download_url_prefix=fromHost, argument=Arg1)
+ batch_job = BatchJob(job_type, email=email, argument=argument)
+ if create_download_url:
+ batch_job.download_url = create_download_url(batch_job.result_id)
session.add(batch_job)
for i, inputl in enumerate(queue):
@@ -746,16 +747,7 @@ Mutalyzer batch scheduler""" % url)
item = BatchQueueItem(batch_job, inputl, flags=flag)
session.add(item)
- # Spawn child
- # Todo: Executable should be in bin/ directory.
- #p = subprocess.Popen(["MutalyzerBatch",
- # "bin/batch_daemon"], executable="python")
-
- #Wait for the BatchChecker to fork of the Daemon
- #p.communicate()
-
session.commit()
-
return batch_job.result_id
#addJob
#Scheduler
diff --git a/mutalyzer/config/__init__.py b/mutalyzer/config/__init__.py
index 0ca16a75..ffc40062 100644
--- a/mutalyzer/config/__init__.py
+++ b/mutalyzer/config/__init__.py
@@ -62,6 +62,9 @@ class LazySettings(util.LazyObject):
self._wrapped = Settings()
self._wrapped.from_object('mutalyzer.config.default_settings')
if from_environment:
+ # Todo: We crash if the environment variable is not set. Perhaps
+ # it is more user-friendly if we fall back on ./settings.py or
+ # ~/mutalyzer_settings.py or something if it exists.
self._wrapped.from_envvar(ENVIRONMENT_VARIABLE)
def configure(self, settings):
diff --git a/mutalyzer/config/default_settings.py b/mutalyzer/config/default_settings.py
index d7cd7457..3bcd94f9 100644
--- a/mutalyzer/config/default_settings.py
+++ b/mutalyzer/config/default_settings.py
@@ -4,6 +4,11 @@ pointed-to by the `MUTALYZER_SETTINGS` environment variable.
"""
+# Todo: Find an alternative to the temporary directories/files defined here,
+# since they are created even if the setting is reset from another
+# configuration file, and they are never removed.
+
+
# Use Mutalyzer in debug mode.
DEBUG = False
@@ -68,6 +73,14 @@ PROTEIN_LINK_EXPIRATION = 60 * 60 * 24 * 30
# seconds).
NEGATIVE_PROTEIN_LINK_EXPIRATION = 60 * 60 * 24 * 5
+# URL to the SOAP webservice WSDL document. Used for linking to it from the
+# documentation page on the website.
+SOAP_WSDL_URL = 'https://mutalyzer.nl/services/?wsdl'
+
+# URL to the HTTP/RPC+JSON webservice root (without trailing slash). Used for
+# linking to it from the documentation page on the website.
+JSON_ROOT_URL = 'https://mutalyzer.nl/json'
+
# Is Piwik enabled?
PIWIK = False
diff --git a/mutalyzer/db/models.py b/mutalyzer/db/models.py
index 81493251..a38ab2aa 100644
--- a/mutalyzer/db/models.py
+++ b/mutalyzer/db/models.py
@@ -72,9 +72,9 @@ class BatchJob(db.Base):
#: Email address of user who submitted the job.
email = Column(String(200))
- #: Prefix of URL for downloading the job result file. This would usually
- #: be the Mutalyzer website base URL.
- download_url_prefix = Column(String(200))
+ #: URL for downloading the job result file. This would usually be a view
+ #: on the Mutalyzer website.
+ download_url = Column(String(200))
#: Type of batch job.
job_type = Column(Enum(*BATCH_JOB_TYPES, name='job_type'), nullable=False)
@@ -91,11 +91,11 @@ class BatchJob(db.Base):
#: Date and time of creation.
added = Column(DateTime)
- def __init__(self, job_type, email=None, download_url_prefix=None,
+ def __init__(self, job_type, email=None, download_url=None,
argument=None):
self.job_type = job_type
self.email = email
- self.download_url_prefix = download_url_prefix
+ self.download_url = download_url
self.argument = argument
self.result_id = str(uuid.uuid4())
self.added = datetime.now()
diff --git a/mutalyzer/entrypoints/mapping_update.py b/mutalyzer/entrypoints/mapping_update.py
index a7848bda..e5610ea8 100644
--- a/mutalyzer/entrypoints/mapping_update.py
+++ b/mutalyzer/entrypoints/mapping_update.py
@@ -9,6 +9,7 @@ This program is intended to be run daily from cron. Example:
# Todo: Merge this script with mapping_import, the difference between the two
# makes no sense.
+# Todo: Check if the input file is sorted as required and abort if not.
import argparse
diff --git a/mutalyzer/entrypoints/website.py b/mutalyzer/entrypoints/website.py
index c55ae9ec..457422d7 100644
--- a/mutalyzer/entrypoints/website.py
+++ b/mutalyzer/entrypoints/website.py
@@ -36,39 +36,32 @@ also serve the static files.
import argparse
-import os
-import pkg_resources
from .. import website
-application = website.app.wsgifunc()
+application = website.create_app()
-def debugserver():
+def debugserver(port):
"""
Run the website with the Python built-in HTTP server.
"""
- # There's really no sane way to make web.py serve static files other than
- # providing it with a `static` directory, so we just jump to the template
- # directory where it can find this.
- os.chdir(pkg_resources.resource_filename('mutalyzer', 'templates'))
-
- website.app.run()
+ application.run(port=port, debug=True, use_reloader=False)
def main():
"""
- Command-line interface to the website.
+ Command-line interface to the website..
"""
parser = argparse.ArgumentParser(
description='Mutalyzer website.')
parser.add_argument(
- 'port', metavar='NUMBER', type=int, nargs='?', default=8080,
- help='port to run the website on (default: 8080)')
+ '-p', '--port', metavar='NUMBER', dest='port', type=int,
+ default=8089, help='port to run the website on (default: 8080)')
args = parser.parse_args()
- debugserver()
+ debugserver(args.port)
if __name__ == '__main__':
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index a8fe4c1a..362b6639 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -96,7 +96,6 @@ class MutalyzerService(ServiceBase):
# Todo: Set maximum request size by specifying the max_content_length
# argument for spyne.server.wsgi.WsgiApplication in all webservice
# instantiations.
-
max_size = settings.MAX_FILE_SIZE
batch_file = tempfile.TemporaryFile()
@@ -120,7 +119,7 @@ class MutalyzerService(ServiceBase):
raise Fault('EPARSE', 'Could not parse input file, please check your file format.')
result_id = scheduler.addJob('job@webservice', job, columns,
- 'webservice', batch_types[process], argument)
+ batch_types[process], argument)
return result_id
@srpc(Mandatory.String, _returns=Integer)
@@ -159,7 +158,7 @@ class MutalyzerService(ServiceBase):
if left > 0:
raise Fault('EBATCHNOTREADY', 'Batch job result is not yet ready.')
- filename = 'Results_%s.txt' % job_id
+ filename = 'batch-job-%s.txt' % job_id
handle = open(os.path.join(settings.CACHE_DIR, filename))
return handle
diff --git a/mutalyzer/templates/static/js/interface.js b/mutalyzer/templates/static/js/interface.js
deleted file mode 100644
index 90962d2a..00000000
--- a/mutalyzer/templates/static/js/interface.js
+++ /dev/null
@@ -1,111 +0,0 @@
-function updateVisibility() {
- document.getElementById('file_label').style.display = "none";
- document.getElementById('url_label').style.display = "none";
- document.getElementById('gene_label').style.display = "none";
- document.getElementById('range_label').style.display = "none";
- document.getElementById('chrname_label').style.display = "none";
-
- for (i = 0; i < document.invoer.invoermethode.length; i++) {
- if (document.invoer.invoermethode[i].checked) {
- if (document.invoer.invoermethode[i].value == 'file') {
- document.getElementById('file_label').style.display = "";
- }
- else if (document.invoer.invoermethode[i].value == 'url') {
- document.getElementById('url_label').style.display = "";
- }
- else if (document.invoer.invoermethode[i].value == 'gene') {
- document.getElementById('gene_label').style.display = "";
- }
- else if (document.invoer.invoermethode[i].value == 'chr') {
- document.getElementById('range_label').style.display = "";
- }
- else if (document.invoer.invoermethode[i].value == 'chrname') {
- document.getElementById('chrname_label').style.display = "";
- }
- }//if
- }//for
-}//updateVisibility
-
-//Toggle the build option in the batch.html page
-function changeBatch(sel) {
- var opt = sel.options[sel.selectedIndex].value;
- if(opt=='PositionConverter') {
- document.getElementById('build').style.display = "";
- } else {
- document.getElementById('build').style.display = "none";
- }
-}
-
-function toggle_visibility(id) {
- var e = document.getElementById(id);
- if (e.style.display == 'block') {
- e.style.display = 'none';
- } else {
- e.style.display = 'block';
- }
-}
-
-
-var doInterval;
-function onloadBatch() {
- changeBatch(document.getElementById('batchType'));
- doInterval = setInterval(updatePercentage, 3000);
-}
-
-// Get the HTTP Object
-function getHTTPObject(){
- if (window.ActiveXObject)
- return new ActiveXObject("Microsoft.XMLHTTP");
- else if (window.XMLHttpRequest)
- return new XMLHttpRequest();
- else {
- alert("Your browser does not support AJAX.");
- return null;
- }
-}
-
-function updatePercentage() {
- if (!document.getElementById('resultID')){ return; };
- var id = document.getElementById('resultID').value;
- var total = document.getElementById('totalJobs').value;
- var url = 'progress?resultID='+id+'&totalJobs='+total+'&ajax=1';
- var val = "";
-
- http = getHTTPObject();
- if (http == null){
- val = "Your browser does not support Ajax, swith to a different ";
- val +="or wait for the email to arrive."
- document.getElementById('percent').innerHTML = val;
- clearInterval(doInterval);
- return null;
- }
-
- http.open("GET", url, true);
- http.onreadystatechange=function() {
- if(http.readyState == 4) {
- if (http.responseText == "OK"){
- val = "Your job is finished, results can be downloaded from: ";
- val += "<a href='Results_"+id+".txt'>here</a>";
- clearInterval(doInterval);
- } else if (isNaN(http.responseText)){
- //Something went wrong
- val = "Updating went wrong please wait for your email";
- clearInterval(doInterval);
- } else {
- val = "Your job is in progress and currently at ";
- val += parseInt(http.responseText);
- val += "%.";
- }
- }
- document.getElementById('percent').innerHTML = val;
- }
- http.send(null);
-}
-
-function clearField(form, fieldName) {
- for (var i = 0; i < form.elements.length; i++) {
- if (form.elements[i].name == fieldName) {
- form.elements[i].value = '';
- }
- }
-}
diff --git a/mutalyzer/templates/webservices.html b/mutalyzer/templates/webservices.html
deleted file mode 100644
index 09607673..00000000
--- a/mutalyzer/templates/webservices.html
+++ /dev/null
@@ -1,69 +0,0 @@
-{% extends "base.html" %}
-
-{% set active_page = "webservices" %}
-{% set page_title = "Web Services" %}
-
-{% block content %}
-
-<p>
-Most Mutalyzer functionality is programmatically available through two
-interfaces: a SOAP web service and a HTTP/RPC+JSON web service.
-</p>
-
-<h3>SOAP web service</h3>
-
-<p>
-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.
-</p>
-
-<p>
-The following are some example client programs for SOAP web service. They
-use the <a href="soap-api#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">
-<a href="http://www.hgvs.org/mutnomen">HGVS</a> format</span>.
-</p>
-
-<ul>
- <li>Python client using the suds library:
- <a href="download/client-suds.py"><tt>client-suds.py</tt></a>
- <li>Python client using the soappy library:
- <a href="download/client-soappy.py"><tt>client-soappy.py</tt></a>
- <li>Ruby client using the Savon library:
- <a href="download/client-savon.rb"><tt>client-savon.rb</tt></a>
- <li>Mono client in C#:
- <a href="download/client-mono.cs"><tt>client-mono.cs</tt></a>
- <li>PHP client using the PHP5 SOAP extension:
- <a href="download/client-php.php"><tt>client-php.php</tt></a>
-</ul>
-
-<p>
-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.
-</p>
-
-<h3>HTTP/RPC+JSON web service</h3>
-
-<p>
-The HTTP/RPC+JSON web service is experimental and currently undocumented.
-It can be called using HTTP GET requests on
-<code>{{ location|e }}{{ serviceJsonLocation|e }}/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.
-</p>
-
-<p>
-Example: <a href="{{ location|urlencode }}{{ serviceJsonLocation|urlencode }}/checkSyntax?variant=AB026906.1:c.274del">checkSyntax?variant=AB026906.1:c.274del</a>
-</p>
-
-<p>
-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
-web service mirrors the functionality of the SOAP web service.
-</p>
-
-{% endblock content %}
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index f565d809..30bbbfc2 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1698,8 +1698,9 @@ def check_variant(description, output):
assembly = Assembly.query.filter_by(alias='hg19').first()
if assembly:
converter = Converter(assembly, output)
+ version = int(parsed_description.Version) if parsed_description.Version else None
chromosomal_positions = converter.chromosomal_positions(
- locations, parsed_description.RefSeqAcc, parsed_description.Version or None)
+ locations, parsed_description.RefSeqAcc, version)
if chromosomal_positions:
output.addOutput('rawVariantsChromosomal',
(chromosomal_positions[0], chromosomal_positions[1],
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
deleted file mode 100644
index 266185fd..00000000
--- a/mutalyzer/website.py
+++ /dev/null
@@ -1,1478 +0,0 @@
-"""
-General Mutalyzer website interface.
-"""
-
-
-SERVICE_SOAP_LOCATION = '/services'
-SERVICE_JSON_LOCATION = '/json'
-GENOME_BROWSER_URL = 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position={chromosome}:{start}-{stop}&hgt.customText={bed_file}'
-
-
-# WSGI applications should never print anything to stdout. We redirect to
-# stderr, but eventually Mutalyzer should be fixed to never just 'print'
-# anything.
-# http://code.google.com/p/modwsgi/wiki/DebuggingTechniques
-import sys
-sys.stdout = sys.stderr
-
-# Log exceptions to stdout
-import logging; logging.basicConfig()
-
-import re
-import os
-import bz2
-import web
-import urllib
-from collections import defaultdict
-from web.contrib.template import render_jinja
-
-from lxml import etree
-import pkg_resources
-from cStringIO import StringIO
-from spyne.server.http import HttpBase
-from sqlalchemy import and_, or_
-
-import mutalyzer
-from mutalyzer import stats, util
-from mutalyzer.config import settings
-from mutalyzer.db import session
-from mutalyzer.db.models import Assembly, BatchJob, BatchQueueItem
-from mutalyzer.grammar import Grammar
-from mutalyzer.services import soap
-from mutalyzer import variantchecker
-from mutalyzer.output import Output
-from mutalyzer.mapping import Converter
-from mutalyzer import Scheduler
-from mutalyzer import Retriever
-from mutalyzer import File
-from mutalyzer import describe
-
-
-# Show web.py debugging information.
-web.config.debug = settings.DEBUG
-
-
-# URL dispatch table
-urls = (
- '', 'RedirectHome',
- '/(index)?', 'Static',
- '/(about)', 'Static',
- '/(nameGenerator)', 'Static',
- '/(webservices)', 'Static',
- '/checkForward', 'CheckForward',
- '/check', 'Check',
- '/bed', 'Bed',
- '/syntaxCheck', 'SyntaxCheck',
- '/positionConverter', 'PositionConverter',
- '/snp', 'Snp',
- '/descriptionExtract', 'DescriptionExtractor',
- '/upload', 'Uploader',
- '/batch([a-zA-Z]+)?', 'BatchChecker',
- '/progress', 'BatchProgress',
- '/Results_([\da-z-]+)\.txt', 'BatchResult',
- '/soap-api', 'SoapApi',
- '/Variant_info', 'VariantInfo',
- '/getGS', 'GetGS',
- '/download/([a-zA-Z-]+\.(?:py|cs|php|rb))', 'Download',
- '/downloads/([a-zA-Z\._-]+)', 'Downloads',
- '/Reference/([\da-zA-Z\._-]+)', 'Reference'
-)
-
-
-# Jinja2 template render
-# Todo: We rely on Apache to add a Content-Type header, we should actually
-# set it ourselves.
-render = render_jinja(pkg_resources.resource_filename('mutalyzer', 'templates'),
- encoding='utf-8',
- globals = {
- 'version' : mutalyzer.__version__,
- 'nomenclatureVersion' : mutalyzer.NOMENCLATURE_VERSION,
- 'releaseDate' : mutalyzer.__date__,
- 'release' : mutalyzer.RELEASE,
- 'copyrightYears' : mutalyzer.COPYRIGHT_YEARS,
- 'contactEmail' : settings.EMAIL,
- 'serviceSoapLocation' : SERVICE_SOAP_LOCATION,
- 'serviceJsonLocation' : SERVICE_JSON_LOCATION,
- 'piwik' : settings.PIWIK,
- 'piwikBase' : settings.PIWIK_BASE_URL,
- 'piwikSite' : settings.PIWIK_SITE_ID})
-
-
-
-# web.py application
-app = web.application(urls, globals(), autoreload=False)
-
-
-# Close database session at end of each request.
-def _shutdown_session():
- session.remove()
-app.add_processor(web.unloadhook(_shutdown_session))
-
-
-class RedirectHome:
- """
- Permanent redirect to the homepage.
- """
- def GET(self):
- """
- Redirect to / and include the query string.
- """
- raise web.redirect('/' + web.ctx.query)
- #GET
-
- def POST(self):
- """
- Redirect to / and include the query string.
- """
- raise web.redirect('/' + web.ctx.query)
- #POST
-#RedirectHome
-
-
-class Download:
- """
- Download file from template directory, formatting it first.
- """
- def GET(self, file):
- """
- @arg file: Filename to download.
- @type file: string
-
- Be very careful to not call this with anything but an ordinary
- filename. A possible security issue is allowing this method to be
- called with file = '../mutalyzer.conf' for example.
-
- The url routing currently makes sure to only call this with filenames
- of the form [a-zA-Z-]+\.(?:py|cs).
- """
- file_path = os.path.join(
- pkg_resources.resource_filename('mutalyzer', 'templates'),
- file)
-
- if not os.path.isfile(file_path):
- raise web.notfound()
-
- content = open(file_path, 'r').read()
- # Force downloading
- web.header('Content-Type', 'text/plain')
- web.header('Content-Disposition', 'attachment; filename="%s"' % file)
- # We use new style string formatting (available from Python 2.6)
- # http://www.python.org/dev/peps/pep-3101/
- return content.format(path = web.ctx.homedomain + web.ctx.homepath)
- #GET
-#Download
-
-
-class Downloads:
- """
- Download plain text files from /templates/downloads directory.
- """
- def GET(self, file):
- """
- @arg file: Filename to download.
- @type file: string
-
- Be very careful to not call this with anything but an ordinary
- filename. A possible security issue is allowing this method to be
- called with file = '../../mutalyzer.conf' for example.
-
- The url routing currently makes sure to only call this with filenames
- of the form [a-zA-Z\._-]+.
- """
- file_path = os.path.join(
- pkg_resources.resource_filename('mutalyzer', 'templates'),
- 'downloads', file)
-
- if not os.path.isfile(file_path):
- raise web.notfound()
-
- handle = open(file_path)
- F = File.File(None)
- web.header('Content-Type', F.getMimeType(handle)[0])
- web.header('Content-Disposition', 'attachment; filename="%s"' % file)
-
- return handle.read()
- #GET
-#Downloads
-
-
-class Reference:
- """
- Download reference file from cache.
- """
- def GET(self, file):
- """
- @arg file: Filename to download from cache.
- @type file: string
-
- Be very careful to not call this with anything but an ordinary
- filename. A possible security issue is allowing this method to be
- called with file = '../../mutalyzer.conf' for example.
-
- The url routing currently makes sure to only call this with filenames
- of the form [a-zA-Z\._-]+.
- """
- file_path = os.path.join(settings.CACHE_DIR, '%s.bz2' % file)
-
- if not os.path.isfile(file_path):
- raise web.notfound()
-
- handle = bz2.BZ2File(file_path, 'r')
- web.header('Content-Type', 'text/plain')
- web.header('Content-Disposition', 'attachment; filename="%s"' % file)
-
- return handle.read()
- #GET
-
- def HEAD(self, file):
- """
- Do the same as in the GET case, but don't actually bunzip and send the
- file, just check if it exists.
-
- @arg file: Filename to download from cache.
- @type file: string
-
- 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 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(settings.CACHE_DIR, '%s.bz2' % file)
-
- if not os.path.isfile(file_path):
- # The following is a hack to return a 404 not found status with
- # empty body (as is checked by our unit test framework, WebTest).
- # Just passing nothing, or the empty string, causes web.py to
- # insert some default 'not found' message.
- class TrueEmptyString(object):
- def __str__(self):
- return ''
- def __nonzero__( self):
- return True
- #TrueEmptyString
-
- raise web.notfound(message = TrueEmptyString())
- #if
-
- web.header('Content-Type', 'text/plain')
- web.header('Content-Disposition', 'attachment; filename="%s"' % file)
-
- return ''
- #HEAD
-#Reference
-
-
-class GetGS:
- """
- LOVD bypass to get the correct GeneSymbol incl Transcript variant.
-
- Used by LOVD to get the correct transcript variant out of a genomic
- record. LOVD uses a genomic reference (NC_?) in combination with a gene
- symbol to pass variant info to mutalyzer. Mutalyzer 1.0 was only using
- the first transcript. LOVD supplies the NM of the transcript needed but
- this was ignored. This helper allows LOVD to get the requested
- transcript variant from a genomic reference.
- """
- def GET(self):
- """
- Parameters:
- - mutationName: The mutationname without gene symbol.
- - variantRecord: The NM reference of the variant.
- - forward: If set this forwards the request to the name checker.
-
- @return: Output of name checker if forward is set, otherwise the
- GeneSymbol with the variant notation as string.
- """
- output = Output(__file__)
- IP = web.ctx["ip"]
-
- i = web.input(mutationName=None, variantRecord=None, forward=None)
-
- output.addMessage(__file__, -1, 'INFO',
- 'Received request getGS(%s, %s, %s) from %s' % (i.mutationName,
- i.variantRecord, i.forward, IP))
-
- # Todo: The following is probably a problem elsewhere too.
- # We stringify the variant, because a unicode string crashes
- # Bio.Seq.reverse_complement in mapping.py:607.
-
- variantchecker.check_variant(str(i.mutationName), output)
-
- output.addMessage(__file__, -1, 'INFO',
- 'Finished request getGS(%s, %s, %s)' % (i.mutationName,
- i.variantRecord, i.forward))
-
- legends = output.getOutput("legends")
-
- # Filter the transcript from the legend
- legends = [l for l in legends if "_v" in l[0]]
- for l in legends:
- if l[1] == i.variantRecord:
- if i.forward:
- p, a = i.mutationName.split(':')
- return Check.check(p+'('+l[0]+'):'+a, standalone=True)
- else:
- web.header('Content-Type', 'text/plain')
- return l[0]
-
- web.header('Content-Type', 'text/plain')
-
- return "Transcript not found"#+`legends`
- #GET
-#GetGS
-
-
-class SyntaxCheck:
- """
- Syntax checker.
- """
- def GET(self):
- """
- Render syntax checker HTML form.
- """
- args = {
- "variant" : '',
- "messages" : [],
- "parseError" : None,
- "debug" : ""
- }
- return render.syntax_checker(args)
- #GET
-
- def POST(self):
- """
- Parse the given variant and render the syntax checker HTML form.
-
- Parameters:
- - variant: Variant name to check.
- """
- output = Output(__file__)
- IP = web.ctx["ip"]
- i = web.input()
-
- output.addMessage(__file__, -1, 'INFO',
- 'Received request syntaxCheck(%s) from %s' % (i.variant, IP))
-
- stats.increment_counter('syntax-checker/website')
-
- variant = i.variant or ''
- if variant.find(',') >= 0:
- output.addMessage(__file__, 2, "WCOMMASYNTAX",
- "Comma's are not allowed in the syntax, autofixed.")
- variant = variant.replace(',', '')
- #args["variant"]=variant
-
- grammar = Grammar(output)
- grammar.parse(variant)
-
- pe = output.getOutput("parseError")
- if pe:
- pe[0] = pe[0].replace('<', "<")
-
- args = {
- "variant" : variant,
- "messages" : map(util.message_info, output.getMessages()),
- "parseError" : pe,
- "debug" : ""
- }
-
- output.addMessage(__file__, -1, 'INFO',
- 'Finished request syntaxCheck(%s)' % i.variant)
-
- return render.syntax_checker(args)
- #POST
-#SyntaxCheck
-
-
-class Snp:
- """
- SNP converter.
-
- Convert a dbSNP rs number to HGVS description(s) of the SNP specified on
- the reference sequence(s) used by dbSNP.
- """
- def GET(self):
- """
- Render SNP converter HTML form.
- """
- return self.snp()
- #GET
-
- def POST(self):
- """
- Convert to HGVS description(s) and render SNP converter HTML form.
-
- Parameters:
- - rsId: The dbSNP rs number.
- """
- i = web.input(rsId=None)
- return self.snp(i.rsId)
- #POST
-
- def snp(self, rs_id=None):
- """
- Convert {rs_id} to HGVS description(s) and render SNP converter HTML
- form.
-
- @kwarg rs_id: The dbSNP rs number (including 'rs' prefix).
- @type rs_id: string
- """
- output = Output(__file__)
-
- IP = web.ctx["ip"]
-
- descriptions = []
-
- if rs_id:
- output.addMessage(__file__, -1, 'INFO',
- 'Received request snpConvert(%s) from %s' % (rs_id, IP))
-
- stats.increment_counter('snp-converter/website')
-
- retriever = Retriever.Retriever(output)
- descriptions = retriever.snpConvert(rs_id)
- output.addMessage(__file__, -1, 'INFO',
- 'Finished request snpConvert(%s)' % rs_id)
-
- args = {
- 'snp' : descriptions,
- 'messages' : map(util.message_info, output.getMessages()),
- 'summary' : output.Summary()[2],
- 'lastpost' : rs_id
- }
-
- return render.snp_converter(args)
- #snp
-#Snp
-
-
-class PositionConverter:
- """
- Convert a variant between genomic and coding positions.
- """
- def GET(self):
- """
- Render position converter HTML form.
- """
- return self.position_converter()
- #GET
-
- def POST(self):
- """
- Convert a variant and render position converter HTML form.
- """
- i = web.input(assembly_name_or_alias=None, variant='')
- # Todo: The following is probably a problem elsewhere too.
- # We stringify the variant, because a unicode string crashes
- # Bio.Seq.reverse_complement in mapping.py:607.
- return self.position_converter(i.assembly_name_or_alias,
- str(i.variant))
- #POST
-
- def position_converter(self, assembly_name_or_alias=None, variant=None):
- """
- Convert a variant and render position converter HTML form.
-
- :arg assembly_name_or_alias: Genome assembly.
- :type assembly_name_or_alias: string
- :arg variant: Variant to convert.
- :type variant: string
- """
- output = Output(__file__)
- IP = web.ctx["ip"]
-
- assemblies = Assembly.query \
- .order_by(Assembly.taxonomy_common_name.asc(),
- Assembly.name.asc()) \
- .all()
-
- assembly_name_or_alias = (assembly_name_or_alias or
- settings.DEFAULT_ASSEMBLY)
-
- attr = {
- "assemblies" : assemblies,
- "assembly_name_or_alias" : assembly_name_or_alias,
- "variant" : variant or '',
- "gName" : "",
- "cNames" : [],
- "messages" : [],
- }
-
- if variant:
- output.addMessage(__file__, -1, 'INFO',
- 'Received request positionConverter(%s, %s) from %s' % (
- assembly_name_or_alias, variant, IP))
-
- stats.increment_counter('position-converter/website')
-
- assembly = Assembly.query.filter(
- or_(Assembly.name == assembly_name_or_alias,
- Assembly.alias == assembly_name_or_alias)).first()
- if not assembly:
- output.addMessage(__file__, 3, "ENOASSEMBLY",
- "Not a valid assembly.")
-
- converter = Converter(assembly, output)
-
- #Convert chr accNo to NC number
- variant = converter.correctChrVariant(variant)
-
- if variant:
- if not(":c." in variant or ":n." in variant or ":g." in variant or ":m." in variant):
- #Bad name
- grammar = Grammar(output)
- grammar.parse(variant)
-
- if ":c." in variant or ":n." in variant:
- # Do the c2chrom dance
- variant = converter.c2chrom(variant)
-
- attr["gName"] = variant
-
- if variant and (":g." in variant or ":m." in variant):
- # Do the g2c dance
- variants = converter.chrom2c(variant, "dict")
- if variants is None:
- attr['gName'] = None
- elif variants:
- out = ["%-10s:\t%s" % (key[:10], "\n\t\t".join(value))
- for key, value in variants.items()]
- attr["cNames"].extend(out)
-
- attr['messages'] = map(util.message_info, output.getMessages())
-
- output.addMessage(__file__, -1, 'INFO',
- 'Finished request positionConverter(%s, %s)'
- % (assembly_name_or_alias, variant))
-
- return render.position_converter(attr)
- #position_converter
-#PositionConverter
-
-
-class VariantInfo:
- """
- The I{g.} to I{c.} and vice versa interface for LOVD.
-
- Search for an NM number in the MySQL database, if the version number
- matches, get the start and end positions in a variant and translate these
- positions to I{g.} notation if the variant is in I{c.} notation and vice
- versa.
- - If no end position is present, the start position is assumed to be the
- end position.
- - If the version number is not found in the database, an error message is
- generated and a suggestion for an other version is given.
- - If the reference sequence is not found at all, an error is returned.
- - If no variant is present, the transcription start and end and CDS end
- in I{c.} notation is returned.
- - If the variant is not accepted by the nomenclature parser, a parse error
- will be printed.
- """
- def GET(self):
- """
- Get variant info and return the result as plain text.
-
- Parameters:
- - LOVD_ver: The version of the calling LOVD.
- - build: The human genome build (hg19 assumed).
- - acc: The accession number (NM number).
- - var: A description of the variant.
-
- Returns:
- - start_main ; The main coordinate of the start position in I{c.}
- (non-star) notation.
- - start_offset ; The offset coordinate of the start position in I{c.}
- notation (intronic position).
- - end_main ; The main coordinate of the end position in I{c.}
- (non-star) notation.
- - end_offset ; The offset coordinate of the end position in I{c.}
- notation (intronic position).
- - start_g ; The I{g.} notation of the start position.
- - end_g ; The I{g.} notation of the end position.
- - type ; The mutation type.
-
- Returns (alternative):
- - trans_start ; Transcription start in I{c.} notation.
- - trans_stop ; Transcription stop in I{c.} notation.
- - CDS_stop ; CDS stop in I{c.} notation.
- """
- i = web.input(var = '')
- LOVD_ver = i.LOVD_ver
- build = i.build
- acc = i.acc
- var = i.var
-
- output = Output(__file__)
- IP = web.ctx["ip"]
-
- output.addMessage(__file__, -1, 'INFO',
- 'Received request variantInfo(%s:%s (LOVD_ver %s, build %s))'
- ' from %s' % (acc, var, LOVD_ver, build, IP))
-
- assembly = Assembly.query.filter(or_(Assembly.name == build,
- Assembly.alias == build)).first()
- if not assembly:
- return 'invalid build'
-
- converter = Converter(assembly, output)
-
- result = ''
-
- # If no variant is given, return transcription start, transcription
- # end and CDS stop in c. notation.
- if var:
- ret = converter.mainMapping(acc, var)
- else:
- ret = converter.giveInfo(acc)
- if ret:
- result = '%i\n%i\n%i' % ret
-
- if not result and not getattr(ret, 'startmain', None):
- out = output.getOutput('LOVDERR')
- if out:
- result = out[0]
- else:
- result = 'Unknown error occured'
-
- output.addMessage(__file__, -1, 'INFO',
- 'Finished request variantInfo(%s:%s (LOVD_ver %s, build %s))' % (
- acc, var, LOVD_ver, build))
-
- if not result and getattr(ret, 'startmain', None):
- result = '%i\n%i\n%i\n%i\n%i\n%i\n%s' % (ret.startmain,
- ret.startoffset, ret.endmain, ret.endoffset, ret.start_g,
- ret.end_g, ret.mutationType)
-
- web.header('Content-Type', 'text/plain')
-
- if LOVD_ver == "2.0-23": # Obsoleted error messages, remove soon.
- return re.sub("^Error \(.*\):", "Error:", result)
-
- return result
- #GET
-#VariantInfo
-
-
-class CheckForward:
- """
- Old entrypoint to the namechecker. We keep it to not break existing
- bookmarks (but this could also be done with an Apache rewrite rule).
- """
- def GET(self):
- """
- Permanently redirect to the name checker.
-
- Parameters:
- - mutationName: Variant to check.
- """
- i = web.input(mutationName=None)
- raise web.redirect('/check?name=' + urllib.quote(i.mutationName))
- #GET
-#CheckForward
-
-
-class Check:
- """
- The variant checker.
- """
- def GET(self):
- """
- Render the variant checker HTML form.
-
- For backwards compatibility with older LOVD versions, we support the
- 'mutationName' argument. If present, we redirect and add standalone=1.
-
- Parameters:
- - name: Variant to check.
- """
- i = web.input(name=None, mutationName=None, standalone=False)
-
- if i.mutationName:
- raise web.redirect('/check?name=%s&standalone=1'
- % urllib.quote(i.mutationName))
-
- return self.check(i.name, standalone=bool(i.standalone))
- #GET
-
- def POST(self):
- """
- For now we also accept POST requests with a permanent redirect.
- """
- i = web.input(name=None, mutationName=None, standalone=False)
- raise web.redirect('/check?name=%s'
- % urllib.quote(i.name or i.mutationName))
- #POST
-
- @staticmethod
- def check(name=None, standalone=False):
- """
- Render the variant checker HTML form. If the name argument is given,
- run the name checker.
-
- @kwarg name: Variant to check.
- @kwarg interactive: Run interactively, meaning we wrap the result in
- the site layout and include the HTML form.
- """
- if not name:
- return render.name_checker(dict(standalone=standalone))
-
- output = Output(__file__)
- output.addMessage(__file__, -1, 'INFO', 'Received variant %s from %s'
- % (name, web.ctx['ip']))
-
- stats.increment_counter('name-checker/website')
-
- # Todo: The following is probably a problem elsewhere too.
- # We stringify the variant, because a unicode string crashes
- # Bio.Seq.reverse_complement in mapping.py:607.
- variantchecker.check_variant(str(name), output)
-
- errors, warnings, summary = output.Summary()
- record_type = output.getIndexedOutput('recordType', 0, '')
- reference = output.getIndexedOutput('reference', 0, '')
-
- if reference:
- if record_type == 'LRG':
- reference = reference + '.xml'
- else :
- reference = reference + '.gb'
-
- # This is a tuple (variant, position) if we have a parse error
- parse_error = output.getOutput('parseError')
- if parse_error:
- parse_error[0] = parse_error[0].replace('<', '<')
-
- genomic_dna = output.getIndexedOutput('molType', 0) != 'n'
- genomic_description = output.getIndexedOutput('genomicDescription', 0, '')
-
- # Create a link to the UCSC Genome Browser
- browser_link = None
- raw_variants = output.getIndexedOutput('rawVariantsChromosomal', 0)
- if raw_variants:
- positions = [pos
- for descr, (first, last) in raw_variants[2]
- for pos in (first, last)]
- bed_url = web.ctx.homedomain + web.ctx.homepath + \
- '/bed?name=' + urllib.quote(name)
- browser_link = GENOME_BROWSER_URL.format(
- chromosome=raw_variants[0], start=min(positions) - 10,
- stop=max(positions) + 10, bed_file=urllib.quote(bed_url))
-
- if output.getIndexedOutput("original", 0) and output.getIndexedOutput("mutated", 0):
- allele = describe.describe(output.getIndexedOutput("original", 0),
- output.getIndexedOutput("mutated", 0))
- prot_allele = describe.describe(output.getIndexedOutput("oldprotein", 0),
- output.getIndexedOutput("newprotein", 0, default=""), DNA=False)
-
- extracted = extractedProt = '(skipped)'
-
- if allele:
- extracted = describe.alleleDescription(allele)
- if prot_allele:
- extractedProt = describe.alleleDescription(prot_allele)
-
- else:
- extracted = extractedProt = ''
-
- # Todo: Generate the fancy HTML views for the proteins here instead
- # of in mutalyzer/variantchecker.py.
- args = {
- 'name' : name,
- 'messages' : map(util.message_info, output.getMessages()),
- 'summary' : summary,
- 'parseError' : parse_error,
- 'errors' : errors,
- 'genomicDescription' : genomic_description,
- 'chromDescription' : output.getIndexedOutput('genomicChromDescription', 0),
- 'genomicDNA' : genomic_dna,
- 'visualisation' : output.getOutput('visualisation'),
- 'descriptions' : output.getOutput('descriptions'),
- 'protDescriptions' : output.getOutput('protDescriptions'),
- 'oldProtein' : output.getOutput('oldProteinFancy'),
- 'altStart' : output.getIndexedOutput('altStart', 0),
- 'altProtein' : output.getOutput('altProteinFancy'),
- 'newProtein' : output.getOutput('newProteinFancy'),
- 'transcriptInfo' : output.getIndexedOutput('hasTranscriptInfo', 0, False),
- 'transcriptCoding' : output.getIndexedOutput('transcriptCoding', 0, False),
- 'exonInfo' : output.getOutput('exonInfo'),
- 'cdsStart_g' : output.getIndexedOutput('cdsStart_g', 0),
- 'cdsStart_c' : output.getIndexedOutput('cdsStart_c', 0),
- 'cdsStop_g' : output.getIndexedOutput('cdsStop_g', 0),
- 'cdsStop_c' : output.getIndexedOutput('cdsStop_c', 0),
- 'restrictionSites' : output.getOutput('restrictionSites'),
- 'legends' : output.getOutput('legends'),
- 'reference' : reference,
- 'browserLink' : browser_link,
- 'extractedDescription' : extracted,
- 'extractedProtein' : extractedProt,
- 'standalone' : standalone
- }
-
- output.addMessage(__file__, -1, 'INFO', 'Finished variant %s' % name)
-
- web.header('Cache-Control', 'no-cache')
- web.header('Expires', '-1')
- return render.name_checker(args)
- #check
-#Check
-
-
-class DescriptionExtractor:
- """
- The Variant Description Extractor.
- """
- def GET(self):
- """
- Render the description extractor HTML form.
- """
- return self.descriptionExtract()
- #GET
-
- def POST(self):
- """
- Run the description extractor and render the description extractor HTML
- form.
-
- Parameters:
- - referenceSeq:
- - variantSeq:
- """
- i = web.input(referenceSeq=None, variantSeq=None)
- return self.descriptionExtract(i.referenceSeq, i.variantSeq)
- #POST
-
- @staticmethod
- def descriptionExtract(referenceSeq=None, variantSeq=None):
- """
- Render the description extractor HTML form. If the referenceSeq and
- variantSeq argument are given, run the description extractor.
-
- @kwarg referenceSeq: The reference sequence.
- @type referenceSeq: string
- @kwarg variantSeq: The observed sequence.
- @type variantSeq: string
- """
- output = Output(__file__)
- IP = web.ctx["ip"]
-
- if not (referenceSeq and variantSeq):
- return render.description_extractor()
-
- args = {
- 'lastReferenceSeq' : referenceSeq,
- 'lastVariantSeq' : variantSeq
- }
-
- output.addMessage(__file__, -1, 'INFO',
- "Received Description Extract request from %s" % IP)
-
- # Move this to the describe module.
- if not util.is_dna(referenceSeq):
- output.addMessage(__file__, 3, "ENODNA",
- "Reference sequence is not DNA.")
- if not util.is_dna(variantSeq):
- output.addMessage(__file__, 3, "ENODNA",
- "Variant sequence is not DNA.")
-
- result = describe.describe(referenceSeq, variantSeq)
- description = describe.alleleDescription(result)
-
- errors, warnings, summary = output.Summary()
-
- visualisation = []
- for i in result:
- visualisation.append([i.start, i.end, i.type, i.deleted,
- i.inserted, i.shift, i.hgvs])
-
- args = {
- 'lastReferenceSeq' : referenceSeq,
- 'lastVariantSeq' : variantSeq,
- 'description' : description,
- 'visualisation' : visualisation,
- 'errors' : errors,
- 'summary' : summary,
- 'messages' : map(util.message_info, output.getMessages())
- }
-
- output.addMessage(__file__, -1, 'INFO',
- "Finished Description Extract request")
-
- return render.description_extractor(args)
- #descriptionExtract
-#DescriptionExtract
-
-
-class Bed:
- """
- Create BED track.
- """
- def GET(self):
- """
- Create a BED track for the given variant, listing the positioning of
- its raw variants. E.g. for use in the UCSC Genome Browser.
-
- Parameters:
- - name: Variant to create BED track for.
-
- This basically just runs the variant checker and extracts the raw
- variants with positions.
- """
- web.header('Content-Type', 'text/plain')
-
- i = web.input(name=None)
- name = i.name
-
- if not name:
- web.ctx.status = '404 Not Found'
- return 'Sorry, we have not BED track for this variant.'
-
- output = Output(__file__)
-
- variantchecker.check_variant(str(name), output)
-
- raw_variants = output.getIndexedOutput('rawVariantsChromosomal', 0)
- if not raw_variants:
- web.ctx.status = '404 Not Found'
- return 'Sorry, we have no BED track for this variant.'
-
- fields = {
- 'name' : 'Mutalyzer',
- 'description': 'Mutalyzer track for ' + name,
- 'visibility' : 'pack',
- 'db' : 'hg19',
- 'url' : web.ctx.homedomain + web.ctx.homepath +
- '/check?name=' + urllib.quote(name),
- 'color': '255,0,0'}
-
- bed = ' '.join(['track'] + [
- '%s="%s"' % field for field in fields.items()]) + '\n'
-
- for description, positions in raw_variants[2]:
- bed += '\t'.join([raw_variants[0], str(min(positions) - 1),
- str(max(positions)), description, '0', raw_variants[1]]) + '\n'
-
- return bed
- #GET
-#Bed
-
-
-class BatchProgress:
- """
- Batch jobs progress viewer.
-
- Used from the 'batch' template by AJAX to get the progress of a batch
- job.
- """
- def GET(self):
- """
- Progress for a batch job.
-
- Parameters:
- - resultID: Result ID of the job to return progress for.
- - totalJobs: Total number of entries in this job.
-
- @todo: Actually, signaling 'OK' here only means the last entry was
- taken from the database queue. It might still be processing, in
- which case not all output is yet written to the result file.
- For the standard use case, this is no big deal, since any user
- will take more than a few milliseconds to actually click the
- download link.
- However, if we imagine some scripted batch uploader, it might get
- bitten by this bug. (This includes our unit tests, where we work
- around it by explicitely waiting a second.)
- """
- attr = {"percentage": 0}
-
- i = web.input(ajax=None)
- try:
- resultID = str(i.resultID)
- total = int(i.totalJobs)
- except ValueError:
- return
-
- left = BatchQueueItem.query.join(BatchJob).filter_by(result_id=resultID).count()
- percentage = int(100 - (100 * left / float(total)))
- if percentage < 0:
- percentage = 0
- elif percentage > 100:
- percentage = 100
-
- if percentage == 100:
- #download url, check if file still exists
- ret = "OK"
- else:
- ret = percentage
- web.header('Content-Type', 'text/plain')
- return ret
- #GET
-#BatchProgress
-
-
-class BatchChecker:
- """
- Run batch jobs.
- """
- def GET(self, batchType = None):
- """
- Render batch checker HTML form.
-
- @kwarg batchType: Type of batch job.
- """
- return self.batch(batchType=batchType)
- #GET
-
- def POST(self, bt=None):
- """
- Run batch jobs and render batch checker HTML form.
-
- @kwarg bt: Not used, batch type in URL.
-
- Parameters:
- - batchEmail: Email address to mail results to.
- - batchFile: Uploaded file with batch job entries.
- - arg1: Additional argument. Currently only used if batchType is
- 'PositionConverter', denoting the human genome build.
- - batchType: Type of batch job to run. One of 'NameChecker' (default),
- 'SyntaxChecker', 'PositionConverter', or 'SnpConverter'.
- """
- i = web.input(batchEmail=None, batchFile={}, arg1='', batchType=None)
-
- return self.batch(email=i.batchEmail, inFile=i.batchFile, arg1=i.arg1,
- batchType=i.batchType)
- #POST
-
- def batch(self, email=None, inFile=None, arg1='', batchType=None):
- """
- Run batch jobs and render batch checker HTML form. The batch jobs are
- added to the database by the scheduler and ran by the BatchChecker
- daemon.
-
- @kwarg email: Email address to mail results to.
- @kwarg inFile: Uploaded file with batch job entries.
- @kwarg arg1: Additional argument. Currently only used if batchType is
- 'PositionConverter', denoting the human genome build.
- @kwarg batchType: Type of batch job to run. One of 'NameChecker'
- (default), 'SyntaxChecker', 'PositionConverter', or
- 'SnpConverter'.
- """
- O = Output(__file__)
-
- maxUploadSize = settings.MAX_FILE_SIZE
-
- assemblies = Assembly.query \
- .order_by(Assembly.taxonomy_common_name.asc(),
- Assembly.name.asc()) \
- .all()
-
- attr = {
- "messages" : [],
- "errors" : [],
- "debug" : [],
- "maxSize" : float(maxUploadSize) / 1048576,
- "hideTypes" : batchType and 'none' or '',
- "selected" : "0",
- "batchType" : batchType or "",
- "assemblies" : assemblies,
- "default_assembly": settings.DEFAULT_ASSEMBLY,
- "jobID" : None,
- "totalJobs" : None
- }
-
- batch_types = ['NameChecker', 'SyntaxChecker', 'PositionConverter',
- 'SnpConverter']
-
- # Make sure the correct page is displayed for an entrypoint
- if not batchType:
- batchType = 'NameChecker'
-
- if batchType in batch_types:
- attr["selected"] = str(batch_types.index(batchType))
-
- # Todo: I think this test is kindof bogus
- def isEMail(a):
- return bool(
- re.match("^[a-zA-Z0-9._%-]+@[a-zA-Z0-9._%-]+.[a-zA-Z]{2,6}$",
- a))
-
- # Note: A FieldStorage instance (like inFile) seems to always test
- # to the truth value False, so 'if inFile: ...' is not useful.
-
- if email and isEMail(email) and not inFile == None and inFile.file:
- stats.increment_counter('batch-job/website')
-
- # Todo: These error messages could be delivered trough a template
- if not 'CONTENT_LENGTH' in web.ctx.environ.keys():
- web.header('Content-Type', 'text/plain')
- web.ctx.status = '411 Length required'
- return 'Content length required'
-
- if int(web.ctx.environ.get('CONTENT_LENGTH')) > maxUploadSize:
- web.header('Content-Type', 'text/plain')
- web.ctx.status = '413 Request entity too large'
- return 'Sorry, only files up to %s megabytes are accepted.' % (
- float(maxUploadSize) / 1048576)
-
- if batchType == 'PositionConverter':
- if not Assembly.query.filter(
- or_(Assembly.name == arg1,
- Assembly.alias == arg1)).first():
- output.addMessage(__file__, 4, "ENOASSEMBLY",
- "Not a valid assembly.")
- else:
- S = Scheduler.Scheduler()
- FileInstance = File.File(O)
-
- # Generate the fromhost URL from which the results can be fetched
- fromHost = web.ctx.homedomain + web.ctx.homepath + '/'
- #fromHost = "http://%s%s" % (
- # req.hostname, req.uri.rsplit("/", 1)[0]+"/")
-
- job, columns = FileInstance.parseBatchFile(inFile.file)
- if job is None:
- O.addMessage(__file__, 4, "PRSERR", "Could not parse input"
- " file, please check your file format.")
- else:
- attr["resultID"] = S.addJob(email, job, columns, fromHost,
- batchType, arg1)
- attr["totalJobs"] = len(job) or 1
- attr["messages"].append("Your file has been parsed and the job"
- " is scheduled, you will receive an email when the job is"
- " finished.")
-
- attr["errors"].extend(map(util.message_info, O.getMessages()))
-
- return render.batch_jobs(attr)
- #batch
-#BatchChecker
-
-
-class BatchResult:
- """
- Download result from the batch checker.
- """
- def GET(self, result):
- """
- Return raw content (for batch checker results).
-
- @arg result: Result identifier.
- @type result: string
-
- Be very careful to not call this with anything but an ordinary
- filename. A possible security issue is allowing this method to be
- called with result = '../../mutalyzer.conf' for example.
-
- The url routing currently makes sure to only call this with filenames
- of the form \d+.
- """
- # Todo: Check if batch job is ready (we have the job id).
- filename = 'Results_%s.txt' % result
- handle = open(os.path.join(settings.CACHE_DIR, filename))
- web.header('Content-Type', 'text/plain')
- web.header('Content-Disposition',
- 'attachment; filename="%s"' % filename)
-
- return handle.read()
- #GET
-#BatchResult
-
-
-def _checkInt(inpv, refname):
- """
- Remove [,.-] from inpv and try to convert the result to an integer value.
- Raise InputException if the conversion fails.
-
- This private function is used by Uploader.
-
- @arg inpv: Input value to convert.
- @arg refname: Name of input value.
-
- @return: Input value converted to an integer value.
-
- @raise InputException: If the converting to an integer value fails.
- """
- inpv = inpv.replace(',', '').replace('.', '').replace('-', '')
-
- try:
- return int(inpv)
- except ValueError:
- raise InputException("Expected an integer in field: %s" % refname)
-#_checkInt
-
-
-class InputException(Exception):
- """
- This exception is raised by Uploader.
- """
- pass
-#InputException
-
-
-class Uploader:
- """
- Reference sequence uploader.
-
- Upload or retrieve a reference sequence.
-
- @todo: Test this class.
- """
- def GET(self):
- """
- Render reference sequence uploader form.
- """
- maxUploadSize = settings.MAX_FILE_SIZE
-
- assemblies = Assembly.query \
- .order_by(Assembly.taxonomy_common_name.asc(),
- Assembly.name.asc()) \
- .all()
-
- assembly_name_or_alias = settings.DEFAULT_ASSEMBLY
-
- UD, errors = "", []
- args = {
- 'UD' : UD,
- 'assemblies' : assemblies,
- 'assembly_name_or_alias' : assembly_name_or_alias,
- 'maxSize' : float(maxUploadSize) / 1048576,
- 'errors' : errors
- }
- return render.reference_loader(args)
- #GET
-
- def POST(self):
- """
- Render reference sequence uploader form and handle a reference
- sequence upload or retrieval.
-
- This handler has four methods:
- 1. The reference sequence file is a local file.
- 2. The reference sequence file can be found at the following URL.
- 3. Retrieve part of the reference genome for a (HGNC) gene symbol.
- 4. Retrieve a range of a chromosome by accession number.
- 5. Retrieve a range of a chromosome by name.
-
- Parameters:
- - invoermethode: Input method. One of 'file', 'url', 'gene', 'chr',
- 'chrname'.
-
- Depending on the input method, additional parameters are expected.
-
- Parameters (method 'file'):
- - bestandsveld: Reference sequence file to upload.
-
- Parameters (method 'url'):
- - urlveld: URL of reference sequence file to upload.
-
- Parameters (method 'gene'):
- - genesymbol: Gene symbol.
- - organism: Organism.
- - fiveutr: Number of 5' flanking nucleotides.
- - threeutr: Number of 3' flanking nucleotides.
-
- Parameters (method 'chr'):
- - chracc: Chromosome Accession Number.
- - start: Start position.
- - stop: Stop position.
- - orientation: Orientation.
-
- Parameters (method 'chrname'):
- - chrnameassembly: Genome assembly (probably 'hg18' or 'hg19').
- - chrname: Chromosome name.
- - chrnamestart: Start position.
- - chrnamestop: Stop position.
- - chrnameorientation: Orientation.
- """
- maxUploadSize = settings.MAX_FILE_SIZE
-
- assemblies = Assembly.query \
- .order_by(Assembly.taxonomy_common_name.asc(),
- Assembly.name.asc()) \
- .all()
-
- O = Output(__file__)
- IP = web.ctx["ip"]
- R = Retriever.GenBankRetriever(O)
-
- UD, errors = "", []
-
- i = web.input(invoermethode='', bestandsveld={}, urlveld='',
- genesymbol='', organism='', fiveutr='', threeutr='',
- chracc='', start='', stop='', orientation='',
- chrnameassembly='', chrname='', chrnamestart='',
- chrnamestop='', chrnameorientation='')
-
- assembly_name_or_alias = i.chrnameassembly or settings.DEFAULT_ASSEMBLY
-
- O.addMessage(__file__, -1, 'INFO',
- 'Received request'
- ' upload(%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s) from %s' % (
- i.invoermethode, i.urlveld, i.genesymbol, i.organism, i.fiveutr,
- i.threeutr, i.chracc, i.start, i.stop, i.orientation, i.chrnameassembly,
- i.chrname, i.chrnamestart, i.chrnamestop, i.chrnameorientation, IP))
-
- try:
- if i.invoermethode == "file":
- if not 'CONTENT_LENGTH' in web.ctx.environ.keys():
- web.header('Content-Type', 'text/plain')
- web.ctx.status = '411 Length required'
- return 'Content length required.'
-
- if int(web.ctx.environ.get('CONTENT_LENGTH')) > maxUploadSize:
- web.header('Content-Type', 'text/plain')
- web.ctx.status = '413 Request entity too large'
- return 'Upload limit exceeded.'
-
- # Non-conforming clients (read: LOVD) might send the form
- # request urlencoded (and not as the requested multipart/
- # form-data). We try to support this anyway.
- if web.ctx.env.get('CONTENT_TYPE', '') == \
- 'application/x-www-form-urlencoded' and \
- isinstance(i.bestandsveld, str):
- UD = R.uploadrecord(i.bestandsveld)
- elif not i.bestandsveld == None and i.bestandsveld.file:
- # Todo: actually we should check if .file exists
- UD = R.uploadrecord(i.bestandsveld.file.read())
- else:
- raise web.badrequest()
-
- elif i.invoermethode == "url":
- UD = R.downloadrecord(i.urlveld)
- elif i.invoermethode == "gene":
- geneName = i.genesymbol
- organism = i.organism
- upStream = _checkInt(i.fiveutr, "5' flanking nucleotides")
- downStream = _checkInt(i.threeutr, "3' flanking nucleotides")
- UD = R.retrievegene(geneName, organism, upStream, downStream)
- elif i.invoermethode == "chr":
- accNo = i.chracc
- start = _checkInt(i.start, "Start position")
- stop = _checkInt(i.stop, "Stop position")
- orientation = int(i.orientation)
- UD = R.retrieveslice(accNo, start, stop, orientation)
- elif i.invoermethode == "chrname":
- name = i.chrname
- start = _checkInt(i.chrnamestart, "Start position")
- stop = _checkInt(i.chrnamestop, "Stop position")
- orientation = int(i.chrnameorientation)
-
- assembly = Assembly.query.filter(
- or_(Assembly.name == assembly_name_or_alias,
- Assembly.alias == assembly_name_or_alias)).first()
- if not assembly:
- raise InputException('Invalid assembly')
-
- if not name.startswith('chr'):
- name = 'chr%s' % name
-
- chromosome = Chromosome.query.filter_by(assembly=assembly,
- name=name).first()
- if not chromosome:
- raise InputException('Chromosome not available for assembly %s: %s' %
- (assembly.name, name))
-
- UD = R.retrieveslice(chromosome.accession, start, stop, orientation)
- else:
- #unknown "invoermethode"
- raise InputException("Wrong method selected")
-
- except InputException, e:
- #DUMB USERS
- errors.append(e)
- finally:
- if not UD:
- #Something went wrong
- errors += ["The request could not be completed"]
- errors.extend(map(lambda m: str(m), O.getMessages()))
-
- args = {
- "UD" : UD,
- 'assemblies' : assemblies,
- 'assembly_name_or_alias' : assembly_name_or_alias,
- "maxSize" : float(maxUploadSize) / 1048576,
- "errors" : errors
- }
-
- O.addMessage(__file__, -1, 'INFO',
- 'Finished request upload(%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s)' \
- % (i.invoermethode, i.urlveld, i.genesymbol, i.organism,
- i.fiveutr, i.threeutr, i.chracc, i.start, i.stop, i.orientation,
- i.chrnameassembly, i.chrname, i.chrnamestart, i.chrnamestop, i.chrnameorientation))
-
- return render.reference_loader(args)
- #POST
-#Uploader
-
-
-class SoapApi:
- """
- SOAP web service documentation.
- """
- def GET(self):
- """
- 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:
-
- http://tomi.vanek.sk/index.php?page=wsdl-viewer
-
- We apply a small patch to this transformation to show newlines in
- the SOAP method docstrings:
-
- Around line 1195, the description <div>, replace
- '<div class="value">' by '<div class="value documentation">'.
-
- In the style sheet, add:
- .documentation { white-space: pre-line; }
-
- @todo: Use some configuration setting for the location of the
- web service.
- @todo: Use configuration value for .xsl location.
- @todo: Cache this transformation.
- """
- url = web.ctx.homedomain + web.ctx.homepath + SERVICE_SOAP_LOCATION
-
- soap_server = HttpBase(soap.application)
- soap_server.doc.wsdl11.build_interface_document(url)
- wsdl_handle = StringIO(soap_server.doc.wsdl11.get_interface_document())
-
- xsl_handle = open(os.path.join(
- pkg_resources.resource_filename('mutalyzer', 'templates'),
- 'wsdl-viewer.xsl'), 'r')
- wsdl_doc = etree.parse(wsdl_handle)
- xsl_doc = etree.parse(xsl_handle)
- transform = etree.XSLT(xsl_doc)
-
- web.header('Content-Type', 'text/html')
- return str(transform(wsdl_doc))
- #GET
-#SoapApi
-
-
-class Static:
- """
- Static page, just render a Jinja2 template on GET.
- """
- def GET(self, page=None):
- """
- Render a Jinja2 template as HTML.
-
- @kwarg page: Page name to render. A Jinja2 template with this name
- must exist. Special case is a page of None, having the
- same effect as 'index'.
- @type page: string
-
- Be careful to only call this method with an argument that is a simple
- template name. For example, make sure this is not called with page
- value '../forbidden'. This check is implemented in the url routing.
- """
- if not page:
- page = 'index'
-
- args = {'location': web.ctx.homedomain + web.ctx.homepath}
-
- return getattr(render, page)(args)
- #GET
-#Static
diff --git a/mutalyzer/website/__init__.py b/mutalyzer/website/__init__.py
new file mode 100644
index 00000000..9a7e122d
--- /dev/null
+++ b/mutalyzer/website/__init__.py
@@ -0,0 +1,83 @@
+"""
+Mutalyzer website interface using the Flask framework.
+"""
+
+
+import pkg_resources
+
+from flask import Flask
+
+from mutalyzer.config import settings
+from mutalyzer.db import session
+
+
+# Todo: Perhaps we also need this for the RPC services?
+class ReverseProxied(object):
+ """
+ Wrap the application in this middleware and configure the front-end server
+ to add these headers, to let you quietly bind this to a URL other than /
+ and to an HTTP scheme that is different than what is used locally.
+
+ Example for nginx::
+
+ location /myprefix {
+ proxy_pass http://192.168.0.1:5001;
+ proxy_set_header Host $host;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ proxy_set_header X-Scheme $scheme;
+ proxy_set_header X-Script-Name /myprefix;
+ }
+
+ `Flask Snippet <http://flask.pocoo.org/snippets/35/>`_ from Peter Hansen.
+ """
+ def __init__(self, app):
+ self.app = app
+
+ def __call__(self, environ, start_response):
+ script_name = environ.get('HTTP_X_SCRIPT_NAME', '')
+ if script_name:
+ environ['SCRIPT_NAME'] = script_name
+ path_info = environ['PATH_INFO']
+ if path_info.startswith(script_name):
+ environ['PATH_INFO'] = path_info[len(script_name):]
+
+ scheme = environ.get('HTTP_X_SCHEME', '')
+ if scheme:
+ environ['wsgi.url_scheme'] = scheme
+ return self.app(environ, start_response)
+
+
+def create_app():
+ """
+ Create a Flask instance for Mutalyzer.
+ """
+ template_folder = pkg_resources.resource_filename(
+ 'mutalyzer', 'website/templates')
+ static_folder = pkg_resources.resource_filename(
+ 'mutalyzer', 'website/templates/static')
+
+ app = Flask('mutalyzer',
+ template_folder=template_folder, static_folder=static_folder)
+
+ app.config.update(DEBUG=settings.DEBUG,
+ TESTING=settings.TESTING,
+ MAX_CONTENT_LENGTH=settings.MAX_FILE_SIZE)
+ from mutalyzer.website.views import website
+ app.register_blueprint(website)
+
+ @app.teardown_appcontext
+ def shutdown_session(exception=None):
+ session.remove()
+
+ return app
+
+
+def create_reverse_proxied_app():
+ """
+ Create a Flask instance for Mutalyzer running behind a reverse proxy.
+
+ See :func:`create_app` and :class:`ReverseProxied`.
+ """
+ app = create_app()
+ app.wsgi_app = ReverseProxied(app.wsgi_app)
+ return app
diff --git a/mutalyzer/templates/about.html b/mutalyzer/website/templates/about.html
similarity index 95%
rename from mutalyzer/templates/about.html
rename to mutalyzer/website/templates/about.html
index dcf17b90..dada9fd4 100644
--- a/mutalyzer/templates/about.html
+++ b/mutalyzer/website/templates/about.html
@@ -6,8 +6,8 @@
{% block content %}
<p>
-Mutalyzer {{ version|e }} is designed and developed by Jeroen F.J. Laros, with
-the following exceptions:
+Mutalyzer {{ mutalyzer_version }} is designed and developed by Jeroen
+F.J. Laros, with the following exceptions:
</p>
<ul>
diff --git a/mutalyzer/templates/base.html b/mutalyzer/website/templates/base.html
similarity index 79%
rename from mutalyzer/templates/base.html
rename to mutalyzer/website/templates/base.html
index f79fff29..826b2604 100644
--- a/mutalyzer/templates/base.html
+++ b/mutalyzer/website/templates/base.html
@@ -6,6 +6,11 @@
<link rel="stylesheet"
type="text/css"
href="static/css/style.css">
+ <script
+ type="text/javascript"
+ language="javascript"
+ src="static/js/jquery-1.10.2.min.js">
+ </script>
<script
type="text/javascript"
language="javascript"
@@ -18,7 +23,7 @@
</script>
<meta http-equiv="Content-Type"
content="text/html; charset=iso-8859-1">
- <title>Mutalyzer {{ version|e }} — {{ page_title|e }}</title>
+ <title>Mutalyzer {{ mutalyzer_version }} — {{ page_title }}</title>
</head>
<body
style="background-image: url('static/images/background.gif');
@@ -39,7 +44,7 @@
<td rowspan="2"
valign="bottom"
width="180">
- <a href="index"
+ <a href="{{ url_for('.homepage') }}"
target="_top"><img
src="static/images/mutalyzer_logo_bw.png" width="180" height="112"
alt="Rauzy fractal" border="0" hspace="0" vspace="0"></a></td>
@@ -54,7 +59,7 @@
width="98%">
<!-- Banner -->
<center>
- <a href="index"><img
+ <a href="{{ url_for('.homepage') }}"><img
src="static/images/mutalyzer_logo.png"
width="90%"
height="90"
@@ -75,11 +80,11 @@
class="hornav">previous page</a>
</td>
<td align="right">
- <a href="index"
+ <a href="{{ url_for('.homepage') }}"
class="hornav">home</a>
- <a href="about"
+ <a href="{{ url_for('.about') }}"
class="hornav">about</a>
- <a href="mailto:{{ contactEmail|e }}"
+ <a href="mailto:{{ contact_email }}"
class="hornav">contact</a>
<a href="#bottom" class="hornav">go to bottom</a>
</td>
@@ -111,37 +116,37 @@
</td>
</tr>
-{# Fields are: url, id, caption, subnav #}
+{# Fields are: view, view_args, id, caption, subnav #}
{% set navigation_menu = [
- ('index', 'homepage', 'Home', False),
- ('check', 'name-checker', 'Name Checker', False),
- ('syntaxCheck', 'syntax-checker', 'Syntax Checker', False),
- ('positionConverter', 'position-converter', 'Position Converter', False),
- ('snp', 'snp-converter', 'SNP Converter', False),
- ('nameGenerator', 'name-generator', 'Name Generator', False),
- ('descriptionExtract', 'description-extractor', 'Description Extractor', False),
- ('upload', 'reference-loader', 'Reference File Loader', False),
- ('batch', 'batch-jobs', 'Batch Jobs', False),
- ('batchNameChecker', 'batch-name-checker', 'Name Checker', True),
- ('batchSyntaxChecker', 'batch-syntax-checker', 'Syntax Checker', True),
- ('batchPositionConverter', 'batch-position-converter', 'Position Converter', True),
- ('batchSnpConverter', 'batch-snp-converter', 'SNP Converter', True),
- ('webservices', 'webservices', 'Web Services', False)
+ ('.homepage', {}, 'homepage', 'Home', False),
+ ('.name_checker', {}, 'name-checker', 'Name Checker', False),
+ ('.syntax_checker', {}, 'syntax-checker', 'Syntax Checker', False),
+ ('.position_converter', {}, 'position-converter', 'Position Converter', False),
+ ('.snp_converter', {}, 'snp-converter', 'SNP Converter', False),
+ ('.name_generator', {}, 'name-generator', 'Name Generator', False),
+ ('.description_extractor', {}, 'description-extractor', 'Description Extractor', False),
+ ('.reference_loader', {}, 'reference-loader', 'Reference File Loader', False),
+ ('.batch_jobs', {}, 'batch-jobs', 'Batch Jobs', False),
+ ('.batch_jobs', {'job_type': 'name-checker'}, 'batch-name-checker', 'Name Checker', True),
+ ('.batch_jobs', {'job_type': 'syntax-checker'}, 'batch-syntax-checker', 'Syntax Checker', True),
+ ('.batch_jobs', {'job_type': 'position-converter'}, 'batch-position-converter', 'Position Converter', True),
+ ('.batch_jobs', {'job_type': 'snp-converter'}, 'batch-snp-converter', 'SNP Converter', True),
+ ('.webservices', {}, 'webservices', 'Web Services', False)
] -%}
{% set active_page = active_page|default('home') -%}
-{% for url, id, caption, subnav in navigation_menu %}
+{% for view, view_args, id, caption, subnav in navigation_menu %}
<tr class="menu{% if id == active_page %} active{% endif %}">
{% if subnav %}
<td></td>
<td valign="baseline" width="10" class="bullet sub"></td>
<td colspan="2">
- <a href="{{ url|e }}">{{ caption|e }}</a>
+ <a href="{{ url_for(view, **view_args) }}">{{ caption }}</a>
</td>
{% else %}
<td valign="top" width="20" class="bullet"></td>
<td colspan="3">
- <a href="{{ url|e }}">{{ caption|e }}</a>
+ <a href="{{ url_for(view, **view_args) }}">{{ caption }}</a>
</td>
{% endif %}
</tr>
@@ -274,21 +279,21 @@
<center>
- <h2>Mutalyzer {{ version|e }}<br>
+ <h2>Mutalyzer {{ mutalyzer_version }}<br>
<small><small><small><small>
{% if release %}
- released on {{ releaseDate|e }}
+ released on {{ release_date }}
{% else %}
development version
{% endif %}
</small></small></small></small>
</h2>
HGVS nomenclature version
- <span>{{ nomenclatureVersion|e }}</span>
+ <span>{{ nomenclature_version }}</span>
</center>
<p>
- <h3><center>{{ page_title|e }}</center></h3>
+ <h3><center>{{ page_title }}</center></h3>
{% block content %}{% endblock %}
@@ -320,7 +325,7 @@
</td>
<td align="middle">
<img src = "static/images/LUMC_24x24.png" align = "middle">
- © {{ copyrightYears[0]|e }}-{{ copyrightYears[1]|e }}
+ © {{ copyright_years[0] }}-{{ copyright_years[1] }}
<a href = "http://www.lumc.nl">LUMC</a>
@@ -352,15 +357,15 @@
{% if piwik %}
<!-- Piwik -->
<script type="text/javascript">
-var pkBaseURL = "{{ piwikBase|e }}/";
+var pkBaseURL = "{{ piwik_base_url }}/";
document.write(unescape("%3Cscript src='" + pkBaseURL + "piwik.js' type='text/javascript'%3E%3C/script%3E"));
</script><script type="text/javascript">
try {
-var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", {{ piwikSite|e }});
+var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", {{ piwik_site_id }});
piwikTracker.trackPageView();
piwikTracker.enableLinkTracking();
} catch( err ) {}
-</script><noscript><p><img src="{{ piwikBase|e }}/piwik.php?idsite={{ piwikSite|e }}" style="border:0" alt="" /></p></noscript>
+</script><noscript><p><img src="{{ piwik_base_url }}/piwik.php?idsite={{ piwik_site_id }}" style="border:0" alt="" /></p></noscript>
<!-- End Piwik Tracking Code -->
{% endif %}
</body>
diff --git a/mutalyzer/website/templates/batch-job-progress.html b/mutalyzer/website/templates/batch-job-progress.html
new file mode 100644
index 00000000..bed41e12
--- /dev/null
+++ b/mutalyzer/website/templates/batch-job-progress.html
@@ -0,0 +1,46 @@
+{% extends "base.html" %}
+
+{% set active_page = "batch-jobs" %}
+
+{% set page_title = "Batch Job Interface" %}
+
+{% block content %}
+
+{% if result_id %}
+ <div id="if_items_left"{% if not items_left %} style="display:none"{% endif %}>
+ <p>Your job is in progress with <span id="items_left">{{ items_left }}</span> items remaining.</p>
+ <p>You will receive an email when the job is finished.</p>
+ </div>
+ <div id="ifnot_items_left"{% if items_left %} style="display:none"{% endif %}>
+ <p>Your job is finished, please download the results:
+ <a href="{{ url_for('.batch_job_result', result_id=result_id) }}">batch-job-{{ result_id }}.txt</a>
+ </p>
+ </div>
+ {% if items_left %}
+ <script type="text/javascript">
+function check_items_left() {
+ $.ajax({
+ type: 'GET',
+ cache: false,
+ url: '{{ url_for('.batch_job_progress') }}',
+ data: { json: 1, result_id: "{{ result_id }}" }
+ }).done(function(data) {
+ if (data.complete) {
+ $('#if_items_left').hide();
+ $('#ifnot_items_left').show();
+ } else {
+ $('#items_left').text(data.items_left);
+ setTimeout(function() {
+ check_items_left();
+ }, 3000);
+ }
+ });
+}
+check_items_left();
+ </script>
+ {% endif %}
+{% else %}
+ <p>Unknow batch job.</p>
+{% endif %}
+
+{% endblock content %}
diff --git a/mutalyzer/templates/batch_jobs.html b/mutalyzer/website/templates/batch-jobs.html
similarity index 59%
rename from mutalyzer/templates/batch_jobs.html
rename to mutalyzer/website/templates/batch-jobs.html
index 848b1d95..0702c382 100644
--- a/mutalyzer/templates/batch_jobs.html
+++ b/mutalyzer/website/templates/batch-jobs.html
@@ -1,13 +1,7 @@
{% extends "base.html" %}
-{% if batchType == "NameChecker" %}
- {% set active_page = "batch-name-checker" %}
-{% elif batchType == "SyntaxChecker" %}
- {% set active_page = "batch-syntax-checker" %}
-{% elif batchType == "PositionConverter" %}
- {% set active_page = "batch-position-converter" %}
-{% elif batchType == "SnpConverter" %}
- {% set active_page = "batch-snp-converter" %}
+{% if job_type %}
+ {% set active_page = "batch-" + job_type %}
{% else %}
{% set active_page = "batch-jobs" %}
{% endif %}
@@ -30,7 +24,7 @@
and the maximum size is <span tal:content = "maxSize"></span> megabytes.
</p>
<h5>We accept two types of input files, you can download examples below</h5>
- <h5>New Style <a href="downloads/batchtestnew.txt">Download Example File</a></h5>
+ <h5>New Style <a href="{{ url_for('.downloads', filename='batchtestnew.txt') }}">Download Example File</a></h5>
<div style="padding-left:20px; width:400px">
<p>This file format has no header-row. Each row consists of one or
more tab delimited fields, where every field contains a single
@@ -42,7 +36,7 @@
</table>
</div>
<h5>Old Style:
- <a href="downloads/batchtestold.txt">Download Example File</a></h5>
+ <a href="{{ url_for('.downloads', filename='batchtestold.txt') }}">Download Example File</a></h5>
<div style="padding-left:20px; width:400px">
<p >This file format has a header-row, which consists of
three tab delimited fields. In each following row the
@@ -67,36 +61,36 @@
</div>
<table id="inputform">
- <form action="" method="post" enctype="multipart/form-data">
+ <form action="{{ url_for('.batch_jobs_submit') }}" method="post" enctype="multipart/form-data">
<tr id="batchRow">
<td><b>BatchType</b></td>
<td>
- <select id="batchType" name="batchType" onchange="return changeBatch(this)">
- <option value="NameChecker">Name Checker</option>
- <option value="SyntaxChecker">Syntax Checker</option>
- <option value="PositionConverter">Position Converter</option>
- <option value="SnpConverter">SNP Converter</option>
+ <select id="job_type" name="job_type" onchange="return changeBatch(this)">
+ <option value="name-checker"{% if job_type == "name-checker" %} selected="selected"{% endif %}>Name Checker</option>
+ <option value="syntax-checker"{% if job_type == "syntax-checker" %} selected="selected"{% endif %}>Syntax Checker</option>
+ <option value="position-converter"{% if job_type == "position-converter" %} selected="selected"{% endif %}>Position Converter</option>
+ <option value="snp-converter"{% if job_type == "snp-converter" %} selected="selected"{% endif %}>SNP Converter</option>
</select>
</td>
</tr>
<tr>
- <tr id="build" style="display:none">
- <td><b>Build</b></td>
+ <tr id="assembly_name_or_alias" style="display:none">
+ <td><b>Assembly</b></td>
<td>
- <select name="arg1">
+ <select name="assembly_name_or_alias">
{% for assembly in assemblies %}
-<option value="{{ assembly.name|e }}"{% if default_assembly in (assembly.name, assembly.alias) %} selected="selected"{% endif %}>{{ assembly.taxonomy_common_name|e }} — {{ assembly.name|e }}{% if assembly.alias %} ({{ assembly.alias|e }}){% endif %}</option>
+<option value="{{ assembly.name }}"{% if assembly_name_or_alias in (assembly.name, assembly.alias) %} selected="selected"{% endif %}>{{ assembly.taxonomy_common_name }} — {{ assembly.name }}{% if assembly.alias %} ({{ assembly.alias }}){% endif %}</option>
{% endfor %}
</select>
</td>
</tr>
<tr>
<td><b>Email</b></td>
- <td><input type="text" name="batchEmail" value="{{ lastpost|e }}" style="width:200px"></td>
+ <td><input type="text" name="email" value="{{ email }}" style="width:200px"></td>
</tr>
<tr>
<td><b>File</b></td>
- <td><input type="file" name="batchFile" style="width:200px"></td>
+ <td><input type="file" name="file" style="width:200px"></td>
</tr>
<tr>
<td colspan="2">
@@ -114,11 +108,6 @@ initpage = function() {
oldload();
onloadBatch();
}
-</script>
-
-<script language="javascript">
-document.getElementById('batchType').selectedIndex = {{ selected|e }};
-document.getElementById('batchRow').style.display = '{{ hideTypes|e }}';
window.onload = initpage;
</script>
@@ -128,8 +117,8 @@ window.onload = initpage;
</p>
<div class="messages">
{% for m in errors %}
- <p class="{{ m.class|e }}" title="{{ m.level|e }} (origin: {{ m.origin|e
- }})">{{ m.description|e }}</p>
+ <p class="{{ m.class }}" title="{{ m.level }} (origin: {{ m.origin
+ }})">{{ m.description }}</p>
{% endfor %}
</div>
{% endif %}
@@ -140,15 +129,10 @@ window.onload = initpage;
</p>
<div class="messages">
{% for m in messages %}
- <p class="{{ m.class|e }}" title="{{ m.level|e }} (origin: {{ m.origin|e }})">{{ m.description|e }}</p>
+ <p class="{{ m.class }}" title="{{ m.level }} (origin: {{ m.origin }})">{{ m.description }}</p>
{% endfor %}
- <p>{{ summary|e }}</p>
+ <p>{{ summary }}</p>
</div>
- {% if resultID %}
- <div id="percent">Your job is in progress and currently at 0%</div>
- <input id="resultID" type="hidden" name="resultID" value="{{ resultID|e }}">
- <input id="totalJobs" type="hidden" name="totalJobs" value="{{ totalJobs|e }}">
- {% endif %}
{% endif %}
{% endblock content %}
diff --git a/mutalyzer/templates/description_extractor.html b/mutalyzer/website/templates/description-extractor.html
similarity index 72%
rename from mutalyzer/templates/description_extractor.html
rename to mutalyzer/website/templates/description-extractor.html
index 61d1be09..2a20e528 100644
--- a/mutalyzer/templates/description_extractor.html
+++ b/mutalyzer/website/templates/description-extractor.html
@@ -31,7 +31,7 @@ algorithm for:
</ul>
<div style="border: 1px solid grey; background-color: aliceblue; padding: 20px;">
- <form action="" method="post">
+ <form action="{{ url_for('.description_extractor') }}" method="get">
Please supply a reference sequence and an observed sequence.<br>
<br>
<div style="border: 1px solid grey; padding: 20px">
@@ -39,8 +39,8 @@ algorithm for:
<br>
Example: <tt>ATGATGATCAGATACAGTGTGATACAGGTAGTTAGACAA</tt><br>
<br>
- <input type="text" name="referenceSeq" value="{{ lastReferenceSeq|e }}" style="width:100%"><br>
- <input type="button" value="Clear field" onclick="clearField(this.form, 'referenceSeq');">
+ <input type="text" name="reference_sequence" value="{{ reference_sequence }}" style="width:100%"><br>
+ <input type="button" value="Clear field" onclick="clearField(this.form, 'reference_sequence');">
</div>
<br>
<div style="border: 1px solid grey; padding: 20px">
@@ -48,8 +48,8 @@ algorithm for:
<br>
Example: <tt>ATGATTTGATCAGATACATGTGATACCGGTAGTTAGGACAA</tt><br>
<br>
- <input type="text" name="variantSeq" value="{{ lastVariantSeq|e }}" style="width:100%"><br>
- <input type="button" value="Clear field" onclick="clearField(this.form, 'variantSeq');">
+ <input type="text" name="variant_sequence" value="{{ variant_sequence }}" style="width:100%"><br>
+ <input type="button" value="Clear field" onclick="clearField(this.form, 'variant_sequence');">
</div>
<br>
<input type="submit" value="Submit">
@@ -57,14 +57,14 @@ algorithm for:
</form>
</div>
-{% if description is defined %}
+{% if description %}
<h3>Variant Description Extractor results:</h3>
<div class="messages">
{% for m in messages %}
- <p class="{{ m.class|e }}" title="{{ m.level|e }} (origin: {{ m.origin|e }})">{{ m.description|e }}</p>
+ <p class="{{ m.class }}" title="{{ m.level }} (origin: {{ m.origin }})">{{ m.description }}</p>
{% endfor %}
- <p>{{ summary|e }}</p>
+ <p>{{ summary }}</p>
</div>
{% if not errors %}
@@ -72,7 +72,7 @@ algorithm for:
<b>Genomic description:</b>
</p>
<p>
- <tt>g.{{ description|e }}</tt>
+ <tt>g.{{ description }}</tt>
</p>
<p>
<b>Overview of the raw variants:</b>
@@ -87,11 +87,15 @@ algorithm for:
<td>Shift</td>
<td>Description</td>
</tr>
- {% for i in visualisation %}
+ {% for raw_var in raw_vars %}
<tr>
- {% for j in i %}
- <td>{{ j|e }}</td>
- {% endfor %}
+ <td>{{ raw_var.start }}</td>
+ <td>{{ raw_var.end }}</td>
+ <td>{{ raw_var.type }}</td>
+ <td>{{ raw_var.deleted }}</td>
+ <td>{{ raw_var.inserted }}</td>
+ <td>{{ raw_var.shift }}</td>
+ <td>{{ raw_var.hgvs }}</td>
</tr>
{% endfor %}
</table>
diff --git a/mutalyzer/templates/downloads/batchtestnew.txt b/mutalyzer/website/templates/downloads/batchtestnew.txt
similarity index 100%
rename from mutalyzer/templates/downloads/batchtestnew.txt
rename to mutalyzer/website/templates/downloads/batchtestnew.txt
diff --git a/mutalyzer/templates/downloads/batchtestold.txt b/mutalyzer/website/templates/downloads/batchtestold.txt
similarity index 100%
rename from mutalyzer/templates/downloads/batchtestold.txt
rename to mutalyzer/website/templates/downloads/batchtestold.txt
diff --git a/mutalyzer/templates/client-mono.cs b/mutalyzer/website/templates/downloads/client-mono.cs
similarity index 80%
rename from mutalyzer/templates/client-mono.cs
rename to mutalyzer/website/templates/downloads/client-mono.cs
index b3baac66..bc4ded94 100644
--- a/mutalyzer/templates/client-mono.cs
+++ b/mutalyzer/website/templates/downloads/client-mono.cs
@@ -2,10 +2,10 @@
Example SOAP client for the Mutalyzer web service in C# for the Mono
platform.
- See {path}/webservices
+ See {{ url_for('.webservices', _external=True) }}
Compilation instructions:
- wsdl '{path}/services/?wsdl'
+ wsdl '{{ soap_wsdl_url }}'
gmcs /target:library Mutalyzer.cs -r:System.Web.Services
gmcs /r:Mutalyzer.dll client-mono.cs
@@ -18,19 +18,19 @@
using System;
-class MutalyzerClient {{
+class MutalyzerClient {
- public static void Main(String [] args) {{
+ public static void Main(String [] args) {
String variant;
checkSyntax argument;
Mutalyzer mutalyzer;
CheckSyntaxOutput result;
- if (args.Length < 1) {{
+ if (args.Length < 1) {
Console.WriteLine("Please provide a variant");
Environment.Exit(1);
- }}
+ }
variant = args[0];
@@ -48,9 +48,9 @@ class MutalyzerClient {{
Console.WriteLine("Not valid!");
foreach (SoapMessage m in result.messages)
- Console.WriteLine(String.Format("Message ({{0}}): {{1}}",
+ Console.WriteLine(String.Format("Message ({0}): {1}",
m.errorcode, m.message));
- }}
+ }
-}}
+}
diff --git a/mutalyzer/templates/client-php.php b/mutalyzer/website/templates/downloads/client-php.php
similarity index 82%
rename from mutalyzer/templates/client-php.php
rename to mutalyzer/website/templates/downloads/client-php.php
index ccf52c85..25408ebe 100644
--- a/mutalyzer/templates/client-php.php
+++ b/mutalyzer/website/templates/downloads/client-php.php
@@ -3,13 +3,13 @@
/*
Example SOAP client for the Mutalyzer web service in PHP.
- See {path}/webservices
+ See {{ url_for('.webservices', _external=True) }}
This code is in the public domain; it can be used for whatever purpose
with absolutely no restrictions.
*/
-$URL = '{path}/services/?wsdl';
+$URL = '{{ soap_wsdl_url }}';
?><!DOCTYPE html>
<html lang="en">
@@ -23,7 +23,7 @@ $URL = '{path}/services/?wsdl';
<?php
-if (isset($_GET['variant']) && $_GET['variant']) {{
+if (isset($_GET['variant']) && $_GET['variant']) {
$variant = $_GET['variant'];
@@ -42,16 +42,16 @@ if (isset($_GET['variant']) && $_GET['variant']) {{
else
echo '<p><b>Not</b> valid!';
- if (isset($result->messages->SoapMessage)) {{
+ if (isset($result->messages->SoapMessage)) {
echo '<p>Messages:<ol>';
- foreach ($result->messages->SoapMessage as $message) {{
+ foreach ($result->messages->SoapMessage as $message) {
echo '<li><code>'.htmlentities($message->errorcode).'</code>: ';
echo htmlentities($message->message);
- }}
+ }
echo '</ol>';
- }}
+ }
-}}
+}
?>
diff --git a/mutalyzer/templates/client-savon.rb b/mutalyzer/website/templates/downloads/client-savon.rb
similarity index 85%
rename from mutalyzer/templates/client-savon.rb
rename to mutalyzer/website/templates/downloads/client-savon.rb
index 5404fba5..9c6532cb 100644
--- a/mutalyzer/templates/client-savon.rb
+++ b/mutalyzer/website/templates/downloads/client-savon.rb
@@ -3,7 +3,7 @@
# Example SOAP client for the Mutalyzer web service in Ruby using the savon
# library.
#
-# See {path}/webservices
+# See {{ url_for('.webservices', _external=True) }}
#
# Usage:
# ruby client-savon.rb 'NM_002001.2:c.1del'
@@ -14,7 +14,7 @@
require 'rubygems'
require 'savon'
-URL = '{path}/services/?wsdl'
+URL = '{{ soap_wsdl_url }}'
HTTPI.log = false
@@ -33,7 +33,7 @@ client = Savon::Client.new do
end
response = client.request :check_syntax do
- soap.body = {{ :variant => ARGV[0] }}
+ soap.body = { :variant => ARGV[0] }
end
result = response.to_hash[:check_syntax_response][:check_syntax_result]
@@ -53,7 +53,7 @@ if result[:messages]
end
result[:messages][:soap_message].each do |m|
- puts "Message (#{{m[:errorcode]}}): #{{m[:message]}}"
+ puts "Message (#{m[:errorcode]}): #{m[:message]}"
end
end
diff --git a/mutalyzer/templates/client-soappy.py b/mutalyzer/website/templates/downloads/client-soappy.py
similarity index 92%
rename from mutalyzer/templates/client-soappy.py
rename to mutalyzer/website/templates/downloads/client-soappy.py
index 4b503dda..e7015331 100644
--- a/mutalyzer/templates/client-soappy.py
+++ b/mutalyzer/website/templates/downloads/client-soappy.py
@@ -3,7 +3,7 @@
# Example SOAP client for the Mutalyzer web service in Python using the
# SOAPpy library.
#
-# See {path}/webservices
+# See {{ url_for('.webservices', _external=True) }}
#
# Usage:
# python client-soappy.py 'NM_002001.2:c.1del'
@@ -14,7 +14,7 @@
import sys
from SOAPpy import WSDL
-URL = '{path}/services/?wsdl'
+URL = '{{ soap_wsdl_url }}'
if len(sys.argv) < 2:
print 'Please provide a variant'
diff --git a/mutalyzer/templates/client-suds.py b/mutalyzer/website/templates/downloads/client-suds.py
similarity index 89%
rename from mutalyzer/templates/client-suds.py
rename to mutalyzer/website/templates/downloads/client-suds.py
index 46ea68f9..e547d008 100644
--- a/mutalyzer/templates/client-suds.py
+++ b/mutalyzer/website/templates/downloads/client-suds.py
@@ -3,7 +3,7 @@
# Example SOAP client for the Mutalyzer web service in Python using the
# suds library.
#
-# See {path}/webservices
+# See {{ url_for('.webservices', _external=True) }}
#
# Usage:
# python client-suds.py 'NM_002001.2:c.1del'
@@ -14,7 +14,7 @@
import sys
from suds.client import Client
-URL = '{path}/services/?wsdl'
+URL = '{{ soap_wsdl_url }}'
if len(sys.argv) < 2:
print 'Please provide a variant'
diff --git a/mutalyzer/templates/textmining.py b/mutalyzer/website/templates/downloads/textmining.py
similarity index 85%
rename from mutalyzer/templates/textmining.py
rename to mutalyzer/website/templates/downloads/textmining.py
index e48fb350..165ffda5 100644
--- a/mutalyzer/templates/textmining.py
+++ b/mutalyzer/website/templates/downloads/textmining.py
@@ -3,7 +3,7 @@
# Example SOAP client for the Mutalyzer web service in Python using the
# SOAPpy library.
#
-# See {path}/webservices
+# See {{ url_for('.webservices', _external=True) }}
#
# Usage:
# python client-soappy.py < textfile
@@ -14,7 +14,7 @@
import sys
from SOAPpy import WSDL
-URL = '{path}/services/?wsdl'
+URL = '{{ soap_wsdl_url }}'
o = WSDL.Proxy(URL)
diff --git a/mutalyzer/templates/downloads/textmining_sample.txt b/mutalyzer/website/templates/downloads/textmining_sample.txt
similarity index 100%
rename from mutalyzer/templates/downloads/textmining_sample.txt
rename to mutalyzer/website/templates/downloads/textmining_sample.txt
diff --git a/mutalyzer/templates/index.html b/mutalyzer/website/templates/homepage.html
similarity index 66%
rename from mutalyzer/templates/index.html
rename to mutalyzer/website/templates/homepage.html
index 15246e76..8b2fd03d 100644
--- a/mutalyzer/templates/index.html
+++ b/mutalyzer/website/templates/homepage.html
@@ -18,43 +18,43 @@ for the checks:
</p>
<ul>
<li>
- The <a href = "check">Name Checker</a> takes the complete sequence
+ The <a href="{{ url_for('.name_checker') }}">Name Checker</a> takes the complete sequence
variant description as input and checks whether it is correct.
</li>
<li>
- The <a href = "syntaxCheck">Syntax Checker</a> takes the complete
+ The <a href="{{ url_for('.syntax_checker') }}">Syntax Checker</a> takes the complete
sequence variant description as input and checks whether the syntax
is correct.
</li>
<li>
- The <a href = "positionConverter">Position Converter</a> can convert
+ The <a href="{{ url_for('.position_converter') }}">Position Converter</a> can convert
chromosomal positions to transcript orientated positions and vice
versa.
</li>
<li>
- The <a href = "snp">SNP converter</a> allows you to convert a
+ The <a href="{{ url_for('.snp_converter') }}">SNP converter</a> allows you to convert a
dbSNP rsId to HGVS notation.
</li>
<li>
- The <a href = "nameGenerator">Name Generator</a> is a user friendly
+ The <a href="{{ url_for('.name_generator') }}">Name Generator</a> is a user friendly
interface that helps to make a valid HGVS variant description.
</li>
<li>
- The <a href = "descriptionExtract">Description Extractor</a> allows
+ The <a href="{{ url_for('.description_extractor') }}">Description Extractor</a> allows
you to generate the HGVS variant description from a reference
sequence and an observed sequence.
</li>
<li>
- The <a href = "upload">Reference File Loader</a> allows you to load and
+ The <a href="{{ url_for('.reference_loader') }}">Reference File Loader</a> allows you to load and
use your own reference sequence.
</li>
<li>
- The <a href="batch">Batch Checkers</a> are interfaces that accept a
+ The <a href="{{ url_for('.batch_jobs') }}">Batch Checkers</a> are interfaces that accept a
list of inputs. These interfaces can be used for large quantities of
checks.
</li>
<li>
- The <a href = "webservices">Web services</a> page provides instructions
+ The <a href="{{ url_for('.webservices') }}">Web services</a> page provides instructions
for the web services.
</li>
</ul>
diff --git a/mutalyzer/templates/name_checker.html b/mutalyzer/website/templates/name-checker.html
similarity index 76%
rename from mutalyzer/templates/name_checker.html
rename to mutalyzer/website/templates/name-checker.html
index 010697cb..e68dc714 100644
--- a/mutalyzer/templates/name_checker.html
+++ b/mutalyzer/website/templates/name-checker.html
@@ -20,19 +20,19 @@
<div id="output">
<div>
Please insert the mutation name using the
- <span class = "helper"
- title = "Human Genome Variation Society standard variant nomenclature">
- <a href = "http://www.hgvs.org/mutnomen">HGVS</a> format</span>:<br>
+ <span class="helper"
+ title="Human Genome Variation Society standard variant nomenclature">
+ <a href="http://www.hgvs.org/mutnomen">HGVS</a> format</span>:<br>
<accession number>.<version
number>(<gene symbol>):<sequence
type>.<variant description>
</div><br>
Example: AB026906.1:c.274G>T<br>
<br>
- <form action="" method="get">
- <input type="text" name="name" value="{{ name|e }}" style="width:100%"><br>
+ <form action="{{ url_for('.name_checker') }}" method="get">
+ <input type="text" name="description" value="{{ description }}" style="width:100%"><br>
<input type="submit" value="Submit">
- <input type="button" value="Clear field" onclick="clearField(this.form, 'name');">
+ <input type="button" value="Clear field" onclick="clearField(this.form, 'description');">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/NameChecker">Help</a>
</form>
</div>
@@ -43,32 +43,32 @@
<b>Overview of the raw variants:</b>
</p>
{% for i in visualisation %}
- <p>Raw variant {{ loop.index }}: {{ i[0]|e }}</p>
- <pre>{{ i[1]|e }}<br>{{ i[2]|e }}</pre>
+ <p>Raw variant {{ loop.index }}: {{ i[0] }}</p>
+ <pre>{{ i[1] }}<br>{{ i[2] }}</pre>
{% endfor %}
{% endif %}
{% if browserLink %}
<p>
- <a href="{{ browserLink|e }}">View original variant in UCSC Genome Browser</a>
+ <a href="{{ browserLink }}">View original variant in UCSC Genome Browser</a>
</p>
{% endif %}
</div>
-{% if name %}
+{% if description %}
<h3>Name checker results:</h3>
<div class="messages">
{% for m in messages %}
- <p class="{{ m.class|e }}" title="{{ m.level|e }} (origin: {{ m.origin|e
- }})">{{ m.description|e }}</p>
+ <p class="{{ m.class }}" title="{{ m.level }} (origin: {{ m.origin
+ }})">{{ m.description }}</p>
{% endfor %}
- <p>{{ summary|e }}</p>
+ <p>{{ summary }}</p>
</div>
- {% if parseError %}
+ {% if parse_error %}
<h4>Details of the parse error:</h4>
- <pre>{{ parseError[0]|e }}<br>{{ parseError[1]|e }}</pre>
+ <pre>{{ parse_error[0] }}<br>{{ parse_error[1] }}</pre>
<p>
The "^" indicates the position where the error occurred.
</p>
@@ -82,14 +82,14 @@
(Not for use in LSDBs in case of protein-coding transcripts).</p>
{% endif %}
<p>
- <tt><a href="check?name={{ genomicDescription|urlencode }}">{{ genomicDescription|e }}</a></tt>
+ <tt><a href="{{ url_for('.name_checker', description=genomicDescription) }}">{{ genomicDescription }}</a></tt>
</p>
{% endif %}
{% if chromDescription %}
<p>Alternative chromosomal position:</p>
<p>
- <tt>{{ chromDescription|e }}</tt>
+ <tt>{{ chromDescription }}</tt>
</p>
{% endif %}
@@ -98,9 +98,9 @@
<p>
{% for i in descriptions %}
{% if i.endswith('?') %}
- <tt>{{ i|e }}</tt>
+ <tt>{{ i }}</tt>
{% else %}
- <tt><a href="check?name={{ i|urlencode }}">{{ i|e }}</a></tt>
+ <tt><a href="{{ url_for('.name_checker', description=i) }}">{{ i }}</a></tt>
{% endif %}
<br>
{% endfor %}
@@ -113,7 +113,7 @@
</p>
<p>
{% for i in protDescriptions %}
- <tt>{{ i|e }}</tt><br>
+ <tt>{{ i }}</tt><br>
{% endfor %}
</p>
{% endif %}
@@ -126,7 +126,7 @@
<p><b>Reference protein:</b></p>
<pre>
{%- for i in oldProtein -%}
- {{- i -}}<br>
+ {{- i|safe -}}<br>
{%- endfor -%}
</pre>
@@ -135,7 +135,7 @@
{% if newProtein %}
<pre>
{%- for i in newProtein -%}
- {{- i -}}<br>
+ {{- i|safe -}}<br>
{%- endfor -%}
</pre>
{% else %}
@@ -146,11 +146,11 @@
{% endif %}
{% if altStart %}
- <p><b>Alternative protein using start codon {{ altStart|e }}</b></p>
+ <p><b>Alternative protein using start codon {{ altStart }}</b></p>
{% if altProtein %}
<pre>
{%- for i in altProtein -%}
- {{- i -}}<br>
+ {{- i|safe -}}<br>
{%- endfor -%}
</pre>
{% else %}
@@ -172,7 +172,7 @@
<tr>
<td>{{ loop.index }}</td>
{% for j in i %}
- <td>{{ j|e }}</td>
+ <td>{{ j }}</td>
{% endfor %}
</tr>
{% endfor %}
@@ -188,13 +188,13 @@
</tr>
<tr>
<td>Start</td>
- <td>{{ cdsStart_g|e }}</td>
- <td>{{ cdsStart_c|e }}</td>
+ <td>{{ cdsStart_g }}</td>
+ <td>{{ cdsStart_c }}</td>
</tr>
<tr>
<td>Stop</td>
- <td>{{ cdsStop_g|e }}</td>
- <td>{{ cdsStop_c|e }}</td>
+ <td>{{ cdsStop_g }}</td>
+ <td>{{ cdsStop_c }}</td>
</tr>
<tr>
</tr>
@@ -216,12 +216,12 @@
<td>{{ loop.index }}</td>
<td>
{% for j in i[0] %}
- {{ j|e }}{{ ',' if not loop.last }}
+ {{ j }}{{ ',' if not loop.last }}
{% endfor %}
</td>
<td>
{% for j in i[1] %}
- {{ j|e }}{{ ',' if not loop.last }}
+ {{ j }}{{ ',' if not loop.last }}
{% endfor %}
</td>
</tr>
@@ -242,7 +242,7 @@
{% for i in legends %}
<tr>
{% for j in i %}
- <td>{{ j|e if j else '' }}</td>
+ <td>{{ j if j else '' }}</td>
{% endfor %}
</tr>
{% endfor %}
@@ -253,14 +253,14 @@
<p><b>Links:</b></p>
<p>
Download this reference sequence file:
- <a href="Reference/{{ reference|urlencode }}">{{ reference|e }}</a>
+ <a href="{{ url_for('.reference', filename=reference_filename) }}">{{ reference_filename }}</a>
</p>
{% endif %}
{% if extractedDescription %}
<p><b>Experimental services:</b></p>
- <p>Genomic description: <tt>{{ extractedDescription|e }}</tt></p>
- <p>Protein description: <tt>{{ extractedProtein|e }}</tt></p>
+ <p>Genomic description: <tt>{{ extractedDescription }}</tt></p>
+ <p>Protein description: <tt>{{ extractedProtein }}</tt></p>
{% endif %}
{% endif %}
diff --git a/mutalyzer/templates/nameGenerator.html b/mutalyzer/website/templates/name-generator.html
similarity index 100%
rename from mutalyzer/templates/nameGenerator.html
rename to mutalyzer/website/templates/name-generator.html
diff --git a/mutalyzer/templates/position_converter.html b/mutalyzer/website/templates/position-converter.html
similarity index 61%
rename from mutalyzer/templates/position_converter.html
rename to mutalyzer/website/templates/position-converter.html
index 1a1f45c1..12f498b1 100644
--- a/mutalyzer/templates/position_converter.html
+++ b/mutalyzer/website/templates/position-converter.html
@@ -12,7 +12,7 @@
</p>
<p>
<b>Note:</b> The Position Converter does NOT check the description or
- normalize it to HGVS. Use the <a href="check">Name Checker</a> for this.
+ normalize it to HGVS. Use the <a href="{{ url_for('.name_checker') }}">Name Checker</a> for this.
</p>
<p>
Example: NM_003002.2:c.274G>T<br>
@@ -20,25 +20,25 @@
or: NC_000011.9:g.111959693G>T<br>
</p>
<table id="inputform">
- <form action="" method="post" enctype="multipart/form-data">
+ <form action="{{ url_for('.position_converter') }}" method="get" enctype="multipart/form-data">
<tr>
<td><b>Assembly</b></td>
<td>
<select name="assembly_name_or_alias">
{% for assembly in assemblies %}
-<option value="{{ assembly.name|e }}"{% if assembly_name_or_alias in (assembly.name, assembly.alias) %} selected="selected"{% endif %}>{{ assembly.taxonomy_common_name|e }} — {{ assembly.name|e }}{% if assembly.alias %} ({{ assembly.alias|e }}){% endif %}</option>
+<option value="{{ assembly.name }}"{% if assembly_name_or_alias in (assembly.name, assembly.alias) %} selected="selected"{% endif %}>{{ assembly.taxonomy_common_name }} — {{ assembly.name }}{% if assembly.alias %} ({{ assembly.alias }}){% endif %}</option>
{% endfor %}
</select>
</td>
</tr>
<tr>
<td><b>Variant</b></td>
- <td><input type="text" name="variant" value="{{ variant|e }}" style="width:500px"></td>
+ <td><input type="text" name="description" value="{{ description }}" style="width:500px"></td>
</tr>
<tr>
<td colspan="2">
<input type="submit" value="Submit">
- <input type="button" value="Clear field" onclick="clearField(this.form, 'variant');">
+ <input type="button" value="Clear field" onclick="clearField(this.form, 'description');">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/PositionConverter">Help</a>
</td>
@@ -47,34 +47,34 @@
</table> <!-- inputform -->
</div>
-{% if variant %}
+{% if description %}
<h3>Results:</h3>
<div class="messages">
{% for m in messages %}
- <p class="{{ m.class|e }}" title="{{ m.level|e }} (origin: {{ m.origin|e
- }})">{{ m.description|e }}</p>
+ <p class="{{ m.class }}" title="{{ m.level }} (origin: {{ m.origin
+ }})">{{ m.description }}</p>
{% endfor %}
- <p>{{ summary|e }}</p>
+ <p>{{ summary }}</p>
</div>
- {% if gName %}
+ {% if chromosomal_description %}
<p>
<b>Chromosomal Variant:</b>
</p>
- <pre>{{ gName|e }}</pre>
- {% if not cNames %}
+ <pre>{{ chromosomal_description }}</pre>
+ {% if not transcript_descriptions %}
<p>
<b>No transcripts found in mutation region</b>
</p>
{% endif %}
{% endif %}
- {% if cNames %}
+ {% if transcript_descriptions %}
<p>
<b>Found transcripts in mutation region:</b>
</p>
- <pre>{% for i in cNames %}{{ i|e }}<br>{% endfor %}</pre>
+ <pre>{% for d in transcript_descriptions %}{{ d }}<br>{% endfor %}</pre>
{% endif %}
{% endif %}
diff --git a/mutalyzer/templates/reference_loader.html b/mutalyzer/website/templates/reference-loader.html
similarity index 68%
rename from mutalyzer/templates/reference_loader.html
rename to mutalyzer/website/templates/reference-loader.html
index ddf05ab2..44045ce4 100644
--- a/mutalyzer/templates/reference_loader.html
+++ b/mutalyzer/website/templates/reference-loader.html
@@ -19,23 +19,23 @@ sequence when no appropriate RefSeq, GenBank or LRG file is available.
</p>
<p>
Please select one of the options below to upload or retrieve your reference
-sequence (maximum size is {{ maxSize|e }} megabytes):
+sequence (maximum size is {{ max_file_size }} megabytes):
</p>
-<form name="invoer" enctype="multipart/form-data" action="" method="post">
+<form name="invoer" enctype="multipart/form-data" action="{{ url_for('.reference_loader') }}" method="post">
<table border="0" cellpadding="0" cellspacing="0">
<tr valign="top">
<th width="100" style="text-align: left; padding-left : 70px">Options</th>
<td>
- <input type="radio" name="invoermethode" value="file" checked onClick="updateVisibility();">
+ <input type="radio" name="method" value="upload" checked onClick="updateVisibility();">
The reference sequence file is a local file<br>
- <input type="radio" name="invoermethode" value="url" onClick="updateVisibility();">
+ <input type="radio" name="method" value="url" onClick="updateVisibility();">
The reference sequence file can be found at the following URL<br>
- <input type="radio" name="invoermethode" value="gene" onClick="updateVisibility();">
+ <input type="radio" name="method" value="slice_gene" onClick="updateVisibility();">
Retrieve part of the reference genome for a (HGNC) gene symbol<br>
- <input type="radio" name="invoermethode" value="chr" onClick="updateVisibility();">
+ <input type="radio" name="method" value="slice_accession" onClick="updateVisibility();">
Retrieve a range of a chromosome by accession number<br>
- <input type="radio" name="invoermethode" value="chrname" onClick="updateVisibility();">
+ <input type="radio" name="method" value="slice_chromosome" onClick="updateVisibility();">
Retrieve a range of a chromosome by name<br>
</td>
</tr>
@@ -44,17 +44,17 @@ sequence (maximum size is {{ maxSize|e }} megabytes):
<th width="100" style="text-align : left; padding-left : 70px">Input
</th>
<td>
- <span id="file_label">
+ <span id="upload_label">
<i>Please select the GenBank file in plain text format</i><br>
- <input type="file" name="bestandsveld"><br>
+ <input type="file" name="file"><br>
</span>
<span id="url_label">
<i>Please enter the URL of the GenBank file in plain text
(including http://)</i>
<br>
- <input type="text" name="urlveld"><br>
+ <input type="text" name="url"><br>
</span>
- <span id="gene_label">
+ <span id="slice_gene_label">
<i>Please enter the Gene symbol and organism name without spaces
and specify the length of the flanking sequences</i>
<br>
@@ -73,33 +73,33 @@ sequence (maximum size is {{ maxSize|e }} megabytes):
</tr>
<tr>
<td>Number of 5' flanking nucleotides</td>
- <td><input type="text" name="fiveutr" value="5000"></td>
+ <td><input type="text" name="upstream" value="5000"></td>
</tr>
<tr><td>Number of 3' flanking nucleotides</td>
- <td><input type="text" name="threeutr" value="2000"></td>
+ <td><input type="text" name="downstream" value="2000"></td>
</tr>
</table>
</span>
- <span id="range_label">
+ <span id="slice_accession_label">
<i>Please enter the accession number of the chromosome or contig
and specify the range</i><br>
<table>
<tr>
<td>Chromosome accession number</td>
- <td><input type="text" name="chracc"></td>
+ <td><input type="text" name="accession"></td>
</tr>
<tr>
<td>Start position</td>
- <td><input type="text" name="start"></td>
+ <td><input type="text" name="accession_start"></td>
</tr>
<tr>
<td>Stop position</td>
- <td><input type="text" name="stop"></td>
+ <td><input type="text" name="accession_stop"></td>
</tr>
<tr>
<td>Orientation</td>
<td>
- <select name="orientation">
+ <select name="accession_orientation">
<option value="1">Forward</option>
<option value="2">Reverse</option>
</select>
@@ -107,36 +107,36 @@ sequence (maximum size is {{ maxSize|e }} megabytes):
</tr>
</table>
</span>
- <span id="chrname_label">
+ <span id="slice_chromosome_label">
<i>Please enter the name of the chromosome
and specify the range</i><br>
<table>
<tr>
<td>Assembly</td>
<td>
- <select name="chrnameassembly">
+ <select name="assembly_name_or_alias">
{% for assembly in assemblies %}
-<option value="{{ assembly.name|e }}"{% if assembly_name_or_alias in (assembly.name, assembly.alias) %} selected="selected"{% endif %}>{{ assembly.taxonomy_common_name|e }} — {{ assembly.name|e }}{% if assembly.alias %} ({{assembly.alias|e }}){% endif %}</option>
+<option value="{{ assembly.name }}"{% if assembly_name_or_alias in (assembly.name, assembly.alias) %} selected="selected"{% endif %}>{{ assembly.taxonomy_common_name }} — {{ assembly.name }}{% if assembly.alias %} ({{assembly.alias }}){% endif %}</option>
{% endfor %}
</select>
</td>
</tr>
<tr>
<td>Chromosome name</td>
- <td><input type="text" name="chrname"></td>
+ <td><input type="text" name="chromosome"></td>
</tr>
<tr>
<td>Start position</td>
- <td><input type="text" name="chrnamestart"></td>
+ <td><input type="text" name="chromosome_start"></td>
</tr>
<tr>
<td>Stop position</td>
- <td><input type="text" name="chrnamestop"></td>
+ <td><input type="text" name="chromosome_stop"></td>
</tr>
<tr>
<td>Orientation</td>
<td>
- <select name="chrnameorientation">
+ <select name="chromosome_orientation">
<option value="1">Forward</option>
<option value="2">Reverse</option>
</select>
@@ -144,10 +144,6 @@ sequence (maximum size is {{ maxSize|e }} megabytes):
</tr>
</table>
</span>
- <input type="hidden" name="method" value="gbupload">
- <input type="hidden" name="client" value="human">
- <input type="hidden" name="location" value="file">
- <input type="hidden" name="bestandsnaam" value="">
</td>
</tr>
<tr height="20px"></tr>
@@ -168,22 +164,22 @@ sequence (maximum size is {{ maxSize|e }} megabytes):
<pre>
{% for i in errors %}
- {{ i|e }}<br>
+ {{ i }}<br>
{% endfor %}
</pre>
{% endif %}
-{% if UD %}
+{% if ud %}
<p>
<b>Output:</b>
</p>
<p>
Your reference sequence was loaded successfully.<br>
You now can use mutalyzer with the following accession number as
- reference: <b>{{ UD|e }}</b>
+ reference: <b>{{ ud }}</b>
</p>
<p>
- <a href="Reference/{{ UD|urlencode }}.gb">Download this reference sequence.</a>
+ <a href="{{ url_for('.reference', filename=ud + '.gb') }}">Download this reference sequence.</a>
</p>
{% endif %}
diff --git a/mutalyzer/templates/snp_converter.html b/mutalyzer/website/templates/snp-converter.html
similarity index 65%
rename from mutalyzer/templates/snp_converter.html
rename to mutalyzer/website/templates/snp-converter.html
index b729715a..5c0af32d 100644
--- a/mutalyzer/templates/snp_converter.html
+++ b/mutalyzer/website/templates/snp-converter.html
@@ -8,40 +8,40 @@
<div style="border: 1px solid grey; background-color: aliceblue; padding: 20px;">
<p>
Please insert the
- <a href = "http://www.ncbi.nlm.nih.gov/projects/SNP/">dbSNP</a> rs
+ <a href="http://www.ncbi.nlm.nih.gov/projects/SNP/">dbSNP</a> rs
number below. Mutalyzer will retrieve the HGVS description of the SNP
specified on the reference sequence(s) used by dbSNP.
</p>
<p>
Example: rs9919552
</p>
- <form action="" method="post">
- <input type="text" name="rsId" style="width:25%"><br>
+ <form action="{{ url_for('.snp_converter') }}" method="get">
+ <input type="text" name="rs_id" value="{{ rs_id }}" style="width:25%"><br>
<input type="submit" value="Submit">
- <input type="button" value="Clear field" onclick="clearField(this.form, 'rsId');">
+ <input type="button" value="Clear field" onclick="clearField(this.form, 'rs_id');">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/SnpConverter">Help</a>
</form>
</div>
-{% if lastpost %}
+{% if rs_id %}
<h3>SNP converter results:</h3>
<div class="messages">
{% for m in messages %}
- <p class="{{ m.class|e }}" title="{{ m.level|e }} (origin: {{ m.origin|e
- }})">{{ m.description|e }}</p>
+ <p class="{{ m.class }}" title="{{ m.level }} (origin: {{ m.origin
+ }})">{{ m.description }}</p>
{% endfor %}
- <p>{{ summary|e }}</p>
+ <p>{{ summary }}</p>
</div>
<h4>dbSNP rs ID:</h4>
<p>
- <tt>{{ lastpost|e }}</tt>
+ <tt>{{ rs_id }}</tt>
</p>
<h4>HGVS descriptions:</h4>
<p>
- {% for i in snp %}
- <tt>{{ i|e }}</tt><br>
+ {% for d in descriptions %}
+ <tt>{{ d }}</tt><br>
{% endfor %}
</p>
{% endif %}
diff --git a/mutalyzer/templates/static/css/style.css b/mutalyzer/website/templates/static/css/style.css
similarity index 100%
rename from mutalyzer/templates/static/css/style.css
rename to mutalyzer/website/templates/static/css/style.css
diff --git a/mutalyzer/templates/static/images/1x1b.gif b/mutalyzer/website/templates/static/images/1x1b.gif
similarity index 100%
rename from mutalyzer/templates/static/images/1x1b.gif
rename to mutalyzer/website/templates/static/images/1x1b.gif
diff --git a/mutalyzer/templates/static/images/1x1w.gif b/mutalyzer/website/templates/static/images/1x1w.gif
similarity index 100%
rename from mutalyzer/templates/static/images/1x1w.gif
rename to mutalyzer/website/templates/static/images/1x1w.gif
diff --git a/mutalyzer/templates/static/images/Eurogentest.png b/mutalyzer/website/templates/static/images/Eurogentest.png
similarity index 100%
rename from mutalyzer/templates/static/images/Eurogentest.png
rename to mutalyzer/website/templates/static/images/Eurogentest.png
diff --git a/mutalyzer/templates/static/images/LUMC_24x24.png b/mutalyzer/website/templates/static/images/LUMC_24x24.png
similarity index 100%
rename from mutalyzer/templates/static/images/LUMC_24x24.png
rename to mutalyzer/website/templates/static/images/LUMC_24x24.png
diff --git a/mutalyzer/templates/static/images/background.gif b/mutalyzer/website/templates/static/images/background.gif
similarity index 100%
rename from mutalyzer/templates/static/images/background.gif
rename to mutalyzer/website/templates/static/images/background.gif
diff --git a/mutalyzer/templates/static/images/background.gif.old b/mutalyzer/website/templates/static/images/background.gif.old
similarity index 100%
rename from mutalyzer/templates/static/images/background.gif.old
rename to mutalyzer/website/templates/static/images/background.gif.old
diff --git a/mutalyzer/templates/static/images/banner.jpg b/mutalyzer/website/templates/static/images/banner.jpg
similarity index 100%
rename from mutalyzer/templates/static/images/banner.jpg
rename to mutalyzer/website/templates/static/images/banner.jpg
diff --git a/mutalyzer/templates/static/images/bullit.gif b/mutalyzer/website/templates/static/images/bullit.gif
similarity index 100%
rename from mutalyzer/templates/static/images/bullit.gif
rename to mutalyzer/website/templates/static/images/bullit.gif
diff --git a/mutalyzer/templates/static/images/bullitdonker.gif b/mutalyzer/website/templates/static/images/bullitdonker.gif
similarity index 100%
rename from mutalyzer/templates/static/images/bullitdonker.gif
rename to mutalyzer/website/templates/static/images/bullitdonker.gif
diff --git a/mutalyzer/templates/static/images/bullitlicht1.gif b/mutalyzer/website/templates/static/images/bullitlicht1.gif
similarity index 100%
rename from mutalyzer/templates/static/images/bullitlicht1.gif
rename to mutalyzer/website/templates/static/images/bullitlicht1.gif
diff --git a/mutalyzer/templates/static/images/bullitlicht2.gif b/mutalyzer/website/templates/static/images/bullitlicht2.gif
similarity index 100%
rename from mutalyzer/templates/static/images/bullitlicht2.gif
rename to mutalyzer/website/templates/static/images/bullitlicht2.gif
diff --git a/mutalyzer/templates/static/images/bullitmiddel.gif b/mutalyzer/website/templates/static/images/bullitmiddel.gif
similarity index 100%
rename from mutalyzer/templates/static/images/bullitmiddel.gif
rename to mutalyzer/website/templates/static/images/bullitmiddel.gif
diff --git a/mutalyzer/templates/static/images/bullitmiddel.gif.old b/mutalyzer/website/templates/static/images/bullitmiddel.gif.old
similarity index 100%
rename from mutalyzer/templates/static/images/bullitmiddel.gif.old
rename to mutalyzer/website/templates/static/images/bullitmiddel.gif.old
diff --git a/mutalyzer/templates/static/images/commit_logo.png b/mutalyzer/website/templates/static/images/commit_logo.png
similarity index 100%
rename from mutalyzer/templates/static/images/commit_logo.png
rename to mutalyzer/website/templates/static/images/commit_logo.png
diff --git a/mutalyzer/templates/static/images/cubic4-17.gif b/mutalyzer/website/templates/static/images/cubic4-17.gif
similarity index 100%
rename from mutalyzer/templates/static/images/cubic4-17.gif
rename to mutalyzer/website/templates/static/images/cubic4-17.gif
diff --git a/mutalyzer/templates/static/images/cubic4-17c.gif b/mutalyzer/website/templates/static/images/cubic4-17c.gif
similarity index 100%
rename from mutalyzer/templates/static/images/cubic4-17c.gif
rename to mutalyzer/website/templates/static/images/cubic4-17c.gif
diff --git a/mutalyzer/templates/static/images/debug.png b/mutalyzer/website/templates/static/images/debug.png
similarity index 100%
rename from mutalyzer/templates/static/images/debug.png
rename to mutalyzer/website/templates/static/images/debug.png
diff --git a/mutalyzer/templates/static/images/detailkaart.jpg b/mutalyzer/website/templates/static/images/detailkaart.jpg
similarity index 100%
rename from mutalyzer/templates/static/images/detailkaart.jpg
rename to mutalyzer/website/templates/static/images/detailkaart.jpg
diff --git a/mutalyzer/templates/static/images/error.png b/mutalyzer/website/templates/static/images/error.png
similarity index 100%
rename from mutalyzer/templates/static/images/error.png
rename to mutalyzer/website/templates/static/images/error.png
diff --git a/mutalyzer/templates/static/images/favicon.ico b/mutalyzer/website/templates/static/images/favicon.ico
similarity index 100%
rename from mutalyzer/templates/static/images/favicon.ico
rename to mutalyzer/website/templates/static/images/favicon.ico
diff --git a/mutalyzer/templates/static/images/gen_2_phen_logo_print.png b/mutalyzer/website/templates/static/images/gen_2_phen_logo_print.png
similarity index 100%
rename from mutalyzer/templates/static/images/gen_2_phen_logo_print.png
rename to mutalyzer/website/templates/static/images/gen_2_phen_logo_print.png
diff --git a/mutalyzer/templates/static/images/info.png b/mutalyzer/website/templates/static/images/info.png
similarity index 100%
rename from mutalyzer/templates/static/images/info.png
rename to mutalyzer/website/templates/static/images/info.png
diff --git a/mutalyzer/templates/static/images/logoULE.gif b/mutalyzer/website/templates/static/images/logoULE.gif
similarity index 100%
rename from mutalyzer/templates/static/images/logoULE.gif
rename to mutalyzer/website/templates/static/images/logoULE.gif
diff --git a/mutalyzer/templates/static/images/mutalyzer_logo.png b/mutalyzer/website/templates/static/images/mutalyzer_logo.png
similarity index 100%
rename from mutalyzer/templates/static/images/mutalyzer_logo.png
rename to mutalyzer/website/templates/static/images/mutalyzer_logo.png
diff --git a/mutalyzer/templates/static/images/mutalyzer_logo_bw.png b/mutalyzer/website/templates/static/images/mutalyzer_logo_bw.png
similarity index 100%
rename from mutalyzer/templates/static/images/mutalyzer_logo_bw.png
rename to mutalyzer/website/templates/static/images/mutalyzer_logo_bw.png
diff --git a/mutalyzer/templates/static/images/nbic_logo.png b/mutalyzer/website/templates/static/images/nbic_logo.png
similarity index 100%
rename from mutalyzer/templates/static/images/nbic_logo.png
rename to mutalyzer/website/templates/static/images/nbic_logo.png
diff --git a/mutalyzer/templates/static/images/project-1.jpg b/mutalyzer/website/templates/static/images/project-1.jpg
similarity index 100%
rename from mutalyzer/templates/static/images/project-1.jpg
rename to mutalyzer/website/templates/static/images/project-1.jpg
diff --git a/mutalyzer/templates/static/images/warning.png b/mutalyzer/website/templates/static/images/warning.png
similarity index 100%
rename from mutalyzer/templates/static/images/warning.png
rename to mutalyzer/website/templates/static/images/warning.png
diff --git a/mutalyzer/templates/static/js/generator.js b/mutalyzer/website/templates/static/js/generator.js
similarity index 99%
rename from mutalyzer/templates/static/js/generator.js
rename to mutalyzer/website/templates/static/js/generator.js
index ceeecdd6..7971a98f 100644
--- a/mutalyzer/templates/static/js/generator.js
+++ b/mutalyzer/website/templates/static/js/generator.js
@@ -449,7 +449,7 @@ function update(){
var vari = hgvs[1];
var encVar = encodeURIComponent(vari);
- var url = "check?name="+ref+encVar;
+ var url = "name-checker?description="+ref+encVar;
var link = ref+vari;
var Output = "<a href=\""+url+"\">"+link+"</a>";
diff --git a/mutalyzer/website/templates/static/js/interface.js b/mutalyzer/website/templates/static/js/interface.js
new file mode 100644
index 00000000..5d83b1f2
--- /dev/null
+++ b/mutalyzer/website/templates/static/js/interface.js
@@ -0,0 +1,58 @@
+function updateVisibility() {
+ document.getElementById('upload_label').style.display = "none";
+ document.getElementById('url_label').style.display = "none";
+ document.getElementById('slice_gene_label').style.display = "none";
+ document.getElementById('slice_accession_label').style.display = "none";
+ document.getElementById('slice_chromosome_label').style.display = "none";
+
+ for (i = 0; i < document.invoer.method.length; i++) {
+ if (document.invoer.method[i].checked) {
+ if (document.invoer.method[i].value == 'upload') {
+ document.getElementById('upload_label').style.display = "";
+ }
+ else if (document.invoer.method[i].value == 'url') {
+ document.getElementById('url_label').style.display = "";
+ }
+ else if (document.invoer.method[i].value == 'slice_gene') {
+ document.getElementById('slice_gene_label').style.display = "";
+ }
+ else if (document.invoer.method[i].value == 'slice_accession') {
+ document.getElementById('slice_accession_label').style.display = "";
+ }
+ else if (document.invoer.method[i].value == 'slice_chromosome') {
+ document.getElementById('slice_chromosome_label').style.display = "";
+ }
+ }//if
+ }//for
+}//updateVisibility
+
+//Toggle the build option in the batch.html page
+function changeBatch(sel) {
+ var opt = sel.options[sel.selectedIndex].value;
+ if(opt=='position-converter') {
+ document.getElementById('assembly_name_or_alias').style.display = "";
+ } else {
+ document.getElementById('assembly_name_or_alias').style.display = "none";
+ }
+}
+
+function toggle_visibility(id) {
+ var e = document.getElementById(id);
+ if (e.style.display == 'block') {
+ e.style.display = 'none';
+ } else {
+ e.style.display = 'block';
+ }
+}
+
+function onloadBatch() {
+ changeBatch(document.getElementById('job_type'));
+}
+
+function clearField(form, fieldName) {
+ for (var i = 0; i < form.elements.length; i++) {
+ if (form.elements[i].name == fieldName) {
+ form.elements[i].value = '';
+ }
+ }
+}
diff --git a/mutalyzer/website/templates/static/js/jquery-1.10.2.min.js b/mutalyzer/website/templates/static/js/jquery-1.10.2.min.js
new file mode 100644
index 00000000..da417064
--- /dev/null
+++ b/mutalyzer/website/templates/static/js/jquery-1.10.2.min.js
@@ -0,0 +1,6 @@
+/*! jQuery v1.10.2 | (c) 2005, 2013 jQuery Foundation, Inc. | jquery.org/license
+//@ sourceMappingURL=jquery-1.10.2.min.map
+*/
+(function(e,t){var n,r,i=typeof t,o=e.location,a=e.document,s=a.documentElement,l=e.jQuery,u=e.$,c={},p=[],f="1.10.2",d=p.concat,h=p.push,g=p.slice,m=p.indexOf,y=c.toString,v=c.hasOwnProperty,b=f.trim,x=function(e,t){return new x.fn.init(e,t,r)},w=/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/.source,T=/\S+/g,C=/^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,N=/^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/,k=/^<(\w+)\s*\/?>(?:<\/\1>|)$/,E=/^[\],:{}\s]*$/,S=/(?:^|:|,)(?:\s*\[)+/g,A=/\\(?:["\\\/bfnrt]|u[\da-fA-F]{4})/g,j=/"[^"\\\r\n]*"|true|false|null|-?(?:\d+\.|)\d+(?:[eE][+-]?\d+|)/g,D=/^-ms-/,L=/-([\da-z])/gi,H=function(e,t){return t.toUpperCase()},q=function(e){(a.addEventListener||"load"===e.type||"complete"===a.readyState)&&(_(),x.ready())},_=function(){a.addEventListener?(a.removeEventListener("DOMContentLoaded",q,!1),e.removeEventListener("load",q,!1)):(a.detachEvent("onreadystatechange",q),e.detachEvent("onload",q))};x.fn=x.prototype={jquery:f,constructor:x,init:function(e,n,r){var i,o;if(!e)return 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diff --git a/mutalyzer/templates/syntax_checker.html b/mutalyzer/website/templates/syntax-checker.html
similarity index 69%
rename from mutalyzer/templates/syntax_checker.html
rename to mutalyzer/website/templates/syntax-checker.html
index 5e748c8c..9efe75eb 100644
--- a/mutalyzer/templates/syntax_checker.html
+++ b/mutalyzer/website/templates/syntax-checker.html
@@ -10,33 +10,33 @@
Please insert the mutation name using the
<span class = "helper" title =
"Human Genome Variation Society standard variant nomenclature">
- <a href = "http://www.hgvs.org/mutnomen">HGVS</a> format</span>:<br>
+ <a href="http://www.hgvs.org/mutnomen">HGVS</a> format</span>:<br>
<accession number>.<version
number>(<gene symbol>):<sequence
type>.<variant description>
</div><br>
Example: AB026906.1:c.274G>T<br>
<br>
- <form action="" method="post">
- <input type="text" name="variant" value="{{ variant|e }}" style="width:100%"><br>
+ <form action="{{ url_for('.syntax_checker') }}" method="get">
+ <input type="text" name="description" value="{{ description }}" style="width:100%"><br>
<input type="submit" value="Submit">
- <input type="button" value="Clear field" onclick="clearField(this.form, 'variant');">
+ <input type="button" value="Clear field" onclick="clearField(this.form, 'description');">
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/SyntaxChecker">Help</a>
</form>
</div>
<br>
-{% if variant %}
+{% if description %}
<h3>Variant syntax checker results:</h3>
- {% if parseError %}
+ {% if parse_error %}
<div class="messages">
{% for m in messages %}
- <p class="{{ m.class|e }}" title="{{ m.level|e }} (origin: {{ m.origin|e }})">{{ m.description|e }}</p>
+ <p class="{{ m.class }}" title="{{ m.level }} (origin: {{ m.origin }})">{{ m.description }}</p>
{% endfor %}
- <p>{{ summary|e }}</p>
+ <p>{{ summary }}</p>
<br>
</div>
<h4>Details of the parse error:</h4>
- <pre>{{- parseError[0]|e }}<br>{{- parseError[1]|e }}</pre>
+ <pre>{{- parse_error[0] }}<br>{{- parse_error[1] }}</pre>
<p>The "^" indicates the position where the error occurred.</p>
{% else %}
<p>The syntax of this variant is OK!</p>
diff --git a/mutalyzer/website/templates/webservices.html b/mutalyzer/website/templates/webservices.html
new file mode 100644
index 00000000..3303d92c
--- /dev/null
+++ b/mutalyzer/website/templates/webservices.html
@@ -0,0 +1,71 @@
+{% extends "base.html" %}
+
+{% set active_page = "webservices" %}
+{% set page_title = "Web Services" %}
+
+{% block content %}
+
+<p>
+Most Mutalyzer functionality is programmatically available through two
+interfaces: a SOAP web service and a HTTP/RPC+JSON web service.
+</p>
+
+<h3>SOAP web service</h3>
+
+<p>
+A <a href="services/?wsdl">WSDL description</a> is available
+for easy generation of client programs in many languages. See the
+<a href="{{ url_for('.soap_api') }}">annotated API</a> for detailed
+documentation.
+</p>
+
+<p>
+The following are some example client programs for SOAP web service. They
+use the <a href="{{ url_for('.soap_api', _anchor='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">
+<a href="http://www.hgvs.org/mutnomen">HGVS</a> format</span>.
+</p>
+
+<ul>
+ <li>Python client using the suds library:
+ <a href="{{ url_for('.downloads', filename='client-suds.py') }}"><tt>client-suds.py</tt></a>
+ <li>Python client using the soappy library:
+ <a href="{{ url_for('.downloads', filename='client-soappy.py') }}"><tt>client-soappy.py</tt></a>
+ <li>Ruby client using the Savon library:
+ <a href="{{ url_for('.downloads', filename='client-savon.rb') }}"><tt>client-savon.rb</tt></a>
+ <li>Mono client in C#:
+ <a href="{{ url_for('.downloads', filename='client-mono.cs') }}"><tt>client-mono.cs</tt></a>
+ <li>PHP client using the PHP5 SOAP extension:
+ <a href="{{ url_for('.downloads', filename='client-php.php') }}"><tt>client-php.php</tt></a>
+</ul>
+
+<p>
+Here is an example that could be used for
+<a href="{{ url_for('.downloads', filename='textmining.py') }}">text
+ mining</a> on a <a href="{{ url_for('.downloads',
+ filename='textmining_sample.txt') }}">sample</a> input file.
+</p>
+
+<h3>HTTP/RPC+JSON web service</h3>
+
+<p>
+The HTTP/RPC+JSON web service is experimental and currently undocumented.
+It can be called using HTTP GET requests on
+<code>{{ json_root_url }}/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.
+</p>
+
+<p>
+Example: <a href="{{ json_root_url }}/checkSyntax?variant=AB026906.1:c.274del"><tt>checkSyntax?variant=AB026906.1:c.274del</tt></a>
+</p>
+
+<p>
+For now, you can work from this example using the above mentioned
+<a href="{{ url_for('.soap_api') }}">annotated SOAP API</a>, since the
+HTTP/RPC+JSON web service mirrors the functionality of the SOAP web service.
+</p>
+
+{% endblock content %}
diff --git a/mutalyzer/templates/wsdl-viewer.xsl b/mutalyzer/website/templates/wsdl-viewer.xsl
similarity index 100%
rename from mutalyzer/templates/wsdl-viewer.xsl
rename to mutalyzer/website/templates/wsdl-viewer.xsl
diff --git a/mutalyzer/website/views.py b/mutalyzer/website/views.py
new file mode 100644
index 00000000..2c0a3f58
--- /dev/null
+++ b/mutalyzer/website/views.py
@@ -0,0 +1,1060 @@
+"""
+Mutalyzer website views.
+"""
+
+
+import bz2
+import os
+import pkg_resources
+import re
+from cStringIO import StringIO
+import urllib
+
+from flask import Blueprint
+from flask import (abort, current_app, jsonify, make_response, redirect,
+ render_template, request, send_from_directory, url_for)
+import jinja2
+from lxml import etree
+from spyne.server.http import HttpBase
+from sqlalchemy import and_, or_
+
+import mutalyzer
+from mutalyzer import (describe, File, Retriever, Scheduler, stats, util,
+ variantchecker)
+from mutalyzer.config import settings
+from mutalyzer.db import session
+from mutalyzer.db.models import BATCH_JOB_TYPES
+from mutalyzer.db.models import Assembly, BatchJob, BatchQueueItem
+from mutalyzer.grammar import Grammar
+from mutalyzer.mapping import Converter
+from mutalyzer.output import Output
+from mutalyzer.services import soap
+
+
+website = Blueprint('website', __name__)
+
+
+@website.context_processor
+def add_globals():
+ return {'mutalyzer_version' : mutalyzer.__version__,
+ 'nomenclature_version': mutalyzer.NOMENCLATURE_VERSION,
+ 'release_date' : mutalyzer.__date__,
+ 'release' : mutalyzer.RELEASE,
+ 'copyright_years' : mutalyzer.COPYRIGHT_YEARS,
+ 'contact_email' : settings.EMAIL,
+ 'soap_wsdl_url' : settings.SOAP_WSDL_URL,
+ 'json_root_url' : settings.JSON_ROOT_URL,
+ 'piwik' : settings.PIWIK,
+ 'piwik_base_url' : settings.PIWIK_BASE_URL,
+ 'piwik_site_id' : settings.PIWIK_SITE_ID}
+
+
+@website.route('/')
+def homepage():
+ """
+ Website homepage.
+ """
+ return render_template('homepage.html')
+
+
+@website.route('/about')
+def about():
+ """
+ About page.
+ """
+ return render_template('about.html')
+
+
+@website.route('/name-generator')
+def name_generator():
+ """
+ Name generator page.
+ """
+ return render_template('name-generator.html')
+
+
+@website.route('/webservices')
+def webservices():
+ """
+ Webservices documentation page.
+ """
+ return render_template('webservices.html')
+
+
+@website.route('/soap-api')
+def soap_api():
+ """
+ SOAP web service documentation by rendering the WSDL document as HTML.
+
+ Generate the documentation by a XSL transform of the WSDL document.
+ The XSL transformation used is `WSDL viewer
+ <http://tomi.vanek.sk/index.php?page=wsdl-viewer>`_ by Tomi Vanek.
+
+ We apply a small patch to this transformation to show newlines in
+ the SOAP method docstrings:
+
+ 1. Around line 1195, the description ``<div>``, replace
+ ``<div class="value">`` by ``<div class="value documentation">``.
+
+ 2. In the style sheet, add:
+
+ .documentation { white-space: pre-line; }
+ """
+ soap_server = HttpBase(soap.application)
+ soap_server.doc.wsdl11.build_interface_document(settings.SOAP_WSDL_URL)
+ wsdl_handle = StringIO(soap_server.doc.wsdl11.get_interface_document())
+
+ xsl_handle = open(os.path.join(
+ pkg_resources.resource_filename('mutalyzer', 'website/templates'),
+ 'wsdl-viewer.xsl'), 'r')
+ wsdl_doc = etree.parse(wsdl_handle)
+ xsl_doc = etree.parse(xsl_handle)
+ transform = etree.XSLT(xsl_doc)
+
+ return make_response(str(transform(wsdl_doc)))
+
+
+@website.route('/downloads/<string:filename>')
+def downloads(filename):
+ """
+ Files for download, such as example webservice client scripts and batch
+ job input files.
+ """
+ try:
+ response = make_response(render_template(os.path.join('downloads',
+ filename)))
+ except jinja2.exceptions.TemplateNotFound:
+ abort(404)
+
+ response.headers['Content-Type'] = 'text/plain'
+ response.headers['Content-Disposition'] = ('attachment; filename="%s"'
+ % filename)
+ return response
+
+
+@website.route('/syntax-checker')
+def syntax_checker():
+ """
+ Parse the given variant and render the syntax checker HTML form.
+ """
+ # Backwards compatibility.
+ if 'variant' in request.args:
+ return redirect(url_for('.syntax_checker',
+ description=request.args['variant']),
+ code=301)
+
+ description = request.args.get('description')
+
+ if not description:
+ return render_template('syntax-checker.html')
+
+ output = Output(__file__)
+ output.addMessage(__file__, -1, 'INFO',
+ 'Received request syntaxCheck(%s) from %s'
+ % (description, request.remote_addr))
+ stats.increment_counter('syntax-checker/website')
+
+ # Todo: This doesn't belong here.
+ if ',' in description:
+ output.addMessage(__file__, 2, 'WCOMMASYNTAX',
+ 'Comma\'s are not allowed in the syntax, '
+ 'autofixed.')
+ description = description.replace(',', '')
+
+ grammar = Grammar(output)
+ grammar.parse(description)
+
+ parse_error = output.getOutput('parseError')
+ messages = map(util.message_info, output.getMessages())
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished request syntaxCheck(%s)' % description)
+
+ return render_template('syntax-checker.html',
+ description=description,
+ messages=messages,
+ parse_error=parse_error)
+
+
+@website.route('/name-checker')
+def name_checker():
+ """
+ Name checker.
+ """
+ # For backwards compatibility with older LOVD versions, we support the
+ # `mutationName` argument. If present, we redirect and add `standalone=1`.
+ #
+ # Also for backwards compatibility, we support the `name` argument as an
+ # alias for `description`.
+ if 'name' in request.args:
+ return redirect(url_for('.name_checker',
+ description=request.args['name'],
+ standalone=request.args.get('standalone')),
+ code=301)
+ if 'mutationName' in request.args:
+ return redirect(url_for('.name_checker',
+ description=request.args['mutationName'],
+ standalone=1),
+ code=301)
+
+ description = request.args.get('description')
+
+ if not description:
+ return render_template('name-checker.html')
+
+ output = Output(__file__)
+ output.addMessage(__file__, -1, 'INFO', 'Received variant %s from %s'
+ % (description, request.remote_addr))
+ stats.increment_counter('name-checker/website')
+
+ # Todo: The following is probably a problem elsewhere too. We stringify
+ # the variant, because a unicode string crashes BioPython's
+ # `reverse_complement`.
+ variantchecker.check_variant(str(description), output)
+
+ errors, warnings, summary = output.Summary()
+ parse_error = output.getOutput('parseError')
+
+ record_type = output.getIndexedOutput('recordType', 0, '')
+ reference = output.getIndexedOutput('reference', 0, '')
+ if reference:
+ if record_type == 'LRG':
+ reference_filename = reference + '.xml'
+ else :
+ reference_filename = reference + '.gb'
+ else:
+ reference_filename = None
+
+ genomic_dna = output.getIndexedOutput('molType', 0) != 'n'
+ genomic_description = output.getIndexedOutput('genomicDescription', 0, '')
+
+ # Create a link to the UCSC Genome Browser.
+ browser_link = None
+ raw_variants = output.getIndexedOutput('rawVariantsChromosomal', 0)
+ if raw_variants:
+ positions = [pos
+ for descr, (first, last) in raw_variants[2]
+ for pos in (first, last)]
+ bed_url = url_for('.bed', description=description, _external=True)
+ browser_link = ('http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&'
+ 'position={chromosome}:{start}-{stop}&hgt.customText='
+ '{bed_file}'.format(chromosome=raw_variants[0],
+ start=min(positions) - 10,
+ stop=max(positions) + 10,
+ bed_file=urllib.quote(bed_url)))
+
+ # Experimental description extractor.
+ if (output.getIndexedOutput('original', 0) and
+ output.getIndexedOutput('mutated', 0)):
+ allele = describe.describe(output.getIndexedOutput('original', 0),
+ output.getIndexedOutput('mutated', 0))
+ prot_allele = describe.describe(
+ output.getIndexedOutput('oldprotein', 0),
+ output.getIndexedOutput('newprotein', 0, default=''),
+ DNA=False)
+
+ extracted = extractedProt = '(skipped)'
+ if allele:
+ extracted = describe.alleleDescription(allele)
+ if prot_allele:
+ extractedProt = describe.alleleDescription(prot_allele)
+
+ else:
+ extracted = extractedProt = ''
+
+ # Todo: Generate the fancy HTML views for the proteins here instead of in
+ # `mutalyzer.variantchecker`.
+ arguments = {
+ 'description' : description,
+ 'messages' : map(util.message_info, output.getMessages()),
+ 'summary' : summary,
+ 'parse_error' : parse_error,
+ 'errors' : errors,
+ 'genomicDescription' : genomic_description,
+ 'chromDescription' : output.getIndexedOutput(
+ 'genomicChromDescription', 0),
+ 'genomicDNA' : genomic_dna,
+ 'visualisation' : output.getOutput('visualisation'),
+ 'descriptions' : output.getOutput('descriptions'),
+ 'protDescriptions' : output.getOutput('protDescriptions'),
+ 'oldProtein' : output.getOutput('oldProteinFancy'),
+ 'altStart' : output.getIndexedOutput('altStart', 0),
+ 'altProtein' : output.getOutput('altProteinFancy'),
+ 'newProtein' : output.getOutput('newProteinFancy'),
+ 'transcriptInfo' : output.getIndexedOutput('hasTranscriptInfo',
+ 0, False),
+ 'transcriptCoding' : output.getIndexedOutput('transcriptCoding', 0,
+ False),
+ 'exonInfo' : output.getOutput('exonInfo'),
+ 'cdsStart_g' : output.getIndexedOutput('cdsStart_g', 0),
+ 'cdsStart_c' : output.getIndexedOutput('cdsStart_c', 0),
+ 'cdsStop_g' : output.getIndexedOutput('cdsStop_g', 0),
+ 'cdsStop_c' : output.getIndexedOutput('cdsStop_c', 0),
+ 'restrictionSites' : output.getOutput('restrictionSites'),
+ 'legends' : output.getOutput('legends'),
+ 'reference_filename' : reference_filename,
+ 'browserLink' : browser_link,
+ 'extractedDescription': extracted,
+ 'extractedProtein' : extractedProt,
+ 'standalone' : bool(request.args.get('standalone'))
+ }
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished variant %s' % description)
+
+ return render_template('name-checker.html', **arguments)
+
+
+@website.route('/bed')
+def bed():
+ """
+ Create a BED track for the given variant, listing the positions of its raw
+ variants, e.g., for use in the UCSC Genome Browser.
+
+ This basically just runs the variant checker and extracts the raw variants
+ with positions.
+ """
+ # Backwards compatibility.
+ if 'name' in request.args:
+ return redirect(url_for('.bed',
+ description=request.args['name']),
+ code=301)
+
+ description = request.args.get('description')
+
+ if not description:
+ abort(404)
+ return render_template('name-checker.html')
+
+ output = Output(__file__)
+
+ variantchecker.check_variant(str(description), output)
+
+ raw_variants = output.getIndexedOutput('rawVariantsChromosomal', 0)
+ if not raw_variants:
+ abort(404)
+
+ # Todo: Hard-coded hg19.
+ fields = {
+ 'name' : 'Mutalyzer',
+ 'description': 'Mutalyzer track for ' + description,
+ 'visibility' : 'pack',
+ 'db' : 'hg19',
+ 'url' : url_for('.name_checker',
+ description=description,
+ _external=True),
+ 'color': '255,0,0'}
+
+ bed = ' '.join(['track'] +
+ ['%s="%s"' % field for field in fields.items()]) + '\n'
+
+ for descr, positions in raw_variants[2]:
+ bed += '\t'.join([raw_variants[0],
+ str(min(positions) - 1),
+ str(max(positions)),
+ descr,
+ '0',
+ raw_variants[1]]) + '\n'
+
+ response = make_response(bed)
+ response.headers['Content-Type'] = 'text/plain'
+ return response
+
+
+@website.route('/position-converter')
+def position_converter():
+ """
+ Position converter.
+ """
+ # Backwards compatibility.
+ if 'variant' in request.args:
+ return redirect(url_for('.position_converter',
+ description=request.args['variant']),
+ code=301)
+
+ assemblies = Assembly.query \
+ .order_by(Assembly.taxonomy_common_name.asc(),
+ Assembly.name.asc()) \
+ .all()
+
+ assembly_name_or_alias = request.args.get('assembly_name_or_alias',
+ settings.DEFAULT_ASSEMBLY)
+ description = request.args.get('description')
+
+ if not description:
+ return render_template('position-converter.html',
+ assemblies=assemblies,
+ assembly_name_or_alias=assembly_name_or_alias)
+
+ output = Output(__file__)
+ output.addMessage(__file__, -1, 'INFO',
+ 'Received request positionConverter(%s, %s) from %s'
+ % (assembly_name_or_alias, description,
+ request.remote_addr))
+ stats.increment_counter('position-converter/website')
+
+ chromosomal_description = None
+ transcript_descriptions = None
+
+ assembly = Assembly.query.filter(
+ or_(Assembly.name == assembly_name_or_alias,
+ Assembly.alias == assembly_name_or_alias)).first()
+ if not assembly:
+ output.addMessage(__file__, 3, 'ENOASSEMBLY',
+ 'Not a valid assembly.')
+ else:
+ converter = Converter(assembly, output)
+
+ # Convert chromosome name to accession number.
+ corrected_description = converter.correctChrVariant(description)
+
+ if corrected_description:
+ # Now we're ready to actually do position conversion.
+ if not(':c.' in corrected_description or
+ ':n.' in corrected_description or
+ ':g.' in corrected_description or
+ ':m.' in corrected_description):
+ grammar = Grammar(output)
+ grammar.parse(corrected_description)
+
+ if (':c.' in corrected_description or
+ ':n.' in corrected_description):
+ corrected_description = converter.c2chrom(
+ corrected_description)
+
+ chromosomal_description = corrected_description
+
+ if corrected_description and (':g.' in corrected_description or
+ ':m.' in corrected_description):
+ descriptions = converter.chrom2c(corrected_description, 'dict')
+ if descriptions is None:
+ chromosomal_description = None
+ elif descriptions:
+ transcript_descriptions = [
+ '%-10s:\t%s' % (key[:10], '\n\t\t'.join(value))
+ for key, value in descriptions.items()]
+
+ messages = map(util.message_info, output.getMessages())
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished request positionConverter(%s, %s)'
+ % (assembly_name_or_alias, description))
+
+ return render_template('position-converter.html',
+ assemblies=assemblies,
+ assembly_name_or_alias=assembly_name_or_alias,
+ description=description,
+ chromosomal_description=chromosomal_description,
+ transcript_descriptions=transcript_descriptions,
+ messages=messages)
+
+
+@website.route('/snp-converter')
+def snp_converter():
+ """
+ SNP converter.
+
+ Convert a dbSNP rs number to HGVS description(s) of the SNP specified on
+ the reference sequence(s) used by dbSNP.
+ """
+ # Backwards compatibility.
+ if 'rsId' in request.args:
+ return redirect(url_for('.snp_converter',
+ rs_id=request.args['rsId']),
+ code=301)
+
+ rs_id = request.args.get('rs_id')
+
+ if not rs_id:
+ return render_template('snp-converter.html')
+
+ output = Output(__file__)
+ output.addMessage(__file__, -1, 'INFO',
+ 'Received request snpConvert(%s) from %s'
+ % (rs_id, request.remote_addr))
+ stats.increment_counter('snp-converter/website')
+
+ retriever = Retriever.Retriever(output)
+ descriptions = retriever.snpConvert(rs_id)
+
+ messages = map(util.message_info, output.getMessages())
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished request snpConvert(%s)' % rs_id)
+
+ return render_template('snp-converter.html',
+ rs_id=rs_id,
+ descriptions=descriptions,
+ messages=messages,
+ summary=output.Summary()[2])
+
+
+@website.route('/reference-loader')
+def reference_loader():
+ """
+ Reference sequence loader form.
+ """
+ assemblies = Assembly.query \
+ .order_by(Assembly.taxonomy_common_name.asc(),
+ Assembly.name.asc()) \
+ .all()
+
+ return render_template('reference-loader.html',
+ assemblies=assemblies,
+ assembly_name_or_alias=settings.DEFAULT_ASSEMBLY,
+ max_file_size=settings.MAX_FILE_SIZE // 1048576)
+
+
+@website.route('/reference-loader', methods=['POST'])
+def reference_loader_submit():
+ """
+ Reference sequence loader.
+
+ There are five ways for the user to load a reference sequence,
+ corresponding to values for the `method` field, each requiring some
+ additional fields to be defined.:
+
+ `method=upload`
+ The reference sequence file is uploaded from a local file.
+
+ - `file`: Reference sequence file to upload.
+
+ `method=url`
+ The reference sequence file can be found at the specified URL.
+
+ - `url`: URL of reference sequence file to load.
+
+ `method=slice_gene`
+ Retrieve part of the reference genome for an HGNC gene symbol.
+
+ - `genesymbol`: Gene symbol.
+ - `organism`: Organism.
+ - `upstream`: Number of 5' flanking nucleotides.
+ - `downstream`: Number of 3' flanking nucleotides.
+
+ `method=slice_accession`
+ Retrieve a range of a chromosome by accession number.
+
+ - `accession`: Chromosome Accession Number.
+ - `accession_start`: Start position.
+ - `accession_stop`: Stop position.
+ - `accession_orientation`: Orientation.
+
+ `method=slice_chromosome`
+ Retrieve a range of a chromosome by name.
+
+ - `assembly_name_or_alias`: Genome assembly by name or by alias.
+ - `chromosome`: Chromosome name.
+ - `chromosome_start`: Start position.
+ - `chromosome_stop`: Stop position.
+ - `chromosome_orientation`: Orientation.
+ """
+ method = request.form.get('method')
+
+ output = Output(__file__)
+ output.addMessage(__file__, -1, 'INFO',
+ 'Received request upload(%s) with arguments %s from %s'
+ % (method, str(request.form), request.remote_addr))
+
+ assemblies = Assembly.query \
+ .order_by(Assembly.taxonomy_common_name.asc(),
+ Assembly.name.asc()) \
+ .all()
+
+ retriever = Retriever.GenBankRetriever(output)
+ ud, errors = '', []
+
+ class InputException(Exception):
+ pass
+
+ def check_position(position, field):
+ position = position.replace(',', '').replace('.', '').replace('-', '')
+ try:
+ return int(position)
+ except AttributeError, ValueError:
+ raise InputException('Expected an integer in field: %s' % field)
+
+ try:
+ if method == 'upload':
+ # Todo: Non-conforming clients (read: LOVD) might send the form
+ # request urlencoded (and not as the requested multipart/
+ # form-data).
+ file = request.files.get('file')
+ if not file:
+ raise InputException('Please select a local file for upload.')
+
+ ud = retriever.uploadrecord(file.read())
+
+ elif method == 'url':
+ ud = retriever.downloadrecord(request.form.get('url'))
+
+ elif method == 'slice_gene':
+ genesymbol = request.form.get('genesymbol')
+ organism = request.form.get('organism')
+ upstream = check_position(request.form.get('upstream', ''),
+ '5\' flanking nucleotides')
+ downstream = check_position(request.form.get('downstream', ''),
+ '3\' flanking nucleotides')
+ ud = retriever.retrievegene(genesymbol, organism, upstream,
+ downstream)
+
+ elif method == 'slice_accession':
+ accession = request.form.get('accession')
+ start = check_position(request.form.get('accession_start', ''),
+ 'Start position')
+ stop = check_position(request.form.get('accession_stop', ''),
+ 'Stop position')
+ orientation = int(request.form.get('accession_orientation'))
+ ud = retriever.retrieveslice(accession, start, stop, orientation)
+
+ elif method == 'slice_chromosome':
+ chromosome_name = request.form.get('chromosome')
+ start = check_position(request.form.get('chromosome_start', ''),
+ 'Start position')
+ stop = check_position(request.form.get('chromosome_stop', ''),
+ 'Stop position')
+ orientation = int(request.form.get('chromosome_orientation'))
+
+ assembly_name_or_alias = request.form.get('assembly_name_or_alias',
+ settings.DEFAULT_ASSEMBLY)
+ assembly = Assembly.query.filter(
+ or_(Assembly.name == assembly_name_or_alias,
+ Assembly.alias == assembly_name_or_alias)).first()
+ if not assembly:
+ raise InputException('Invalid assembly')
+
+ if not chromosome_name.startswith('chr'):
+ chromosome_name = 'chr%s' % chromosome_name
+
+ chromosome = assembly.chromosomes \
+ .filter_by(name=chromosome_name) \
+ .first()
+ if not chromosome:
+ raise InputException('Chromosome not available for assembly '
+ '%s: %s' % (assembly.name, name))
+
+ ud = retriever.retrieveslice(chromosome.accession, start, stop,
+ orientation)
+
+ else:
+ raise InputException('Invalid method')
+
+ except InputException as e:
+ errors.append(e)
+
+ if not ud:
+ errors.append('The request could not be completed')
+ errors.extend(str(m) for m in output.getMessages())
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished request upload(%s) with arguments %s from %s'
+ % (method, str(request.form), request.remote_addr))
+
+ return render_template('reference-loader.html',
+ assemblies=assemblies,
+ assembly_name_or_alias=settings.DEFAULT_ASSEMBLY,
+ max_file_size=settings.MAX_FILE_SIZE // 1048576,
+ ud=ud,
+ errors=errors)
+
+
+@website.route('/description-extractor')
+def description_extractor():
+ """
+ The Variant Description Extractor (experimental service).
+ """
+ reference_sequence = request.args.get('reference_sequence')
+ variant_sequence = request.args.get('variant_sequence')
+
+ if not (reference_sequence and variant_sequence):
+ return render_template('description-extractor.html')
+
+ output = Output(__file__)
+ output.addMessage(__file__, -1, 'INFO',
+ 'Received Description Extract request from %s'
+ % request.remote_addr)
+
+ # Todo: Move this to the describe module.
+ if not util.is_dna(reference_sequence):
+ output.addMessage(__file__, 3, 'ENODNA',
+ 'Reference sequence is not DNA.')
+ if not util.is_dna(variant_sequence):
+ output.addMessage(__file__, 3, 'ENODNA',
+ 'Variant sequence is not DNA.')
+
+ raw_vars = describe.describe(reference_sequence, variant_sequence)
+ description = describe.alleleDescription(raw_vars)
+
+ errors, warnings, summary = output.Summary()
+ messages = map(util.message_info, output.getMessages())
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished Description Extract request')
+
+ return render_template('description-extractor.html',
+ reference_sequence=reference_sequence,
+ variant_sequence=variant_sequence,
+ raw_vars=raw_vars,
+ description=description,
+ errors=errors,
+ summary=summary,
+ messages=messages)
+
+
+@website.route('/reference/<string:filename>')
+def reference(filename):
+ """
+ Download reference file from cache.
+ """
+ file_path = os.path.join(settings.CACHE_DIR, '%s.bz2' % filename)
+
+ if not os.path.isfile(file_path):
+ abort(404)
+
+ response = make_response(bz2.BZ2File(file_path, 'r').read())
+
+ response.headers['Content-Type'] = 'text/plain'
+ response.headers['Content-Disposition'] = ('attachment; filename="%s"'
+ % filename)
+ return response
+
+
+@website.route('/batch-jobs')
+def batch_jobs():
+ """
+ Batch jobs form.
+ """
+ job_type = request.args.get('job_type', 'name-checker')
+
+ assemblies = Assembly.query \
+ .order_by(Assembly.taxonomy_common_name.asc(),
+ Assembly.name.asc()) \
+ .all()
+ assembly_name_or_alias = request.args.get('assembly_name_or_alias',
+ settings.DEFAULT_ASSEMBLY)
+
+ return render_template('batch-jobs.html',
+ assemblies=assemblies,
+ assembly_name_or_alias=assembly_name_or_alias,
+ job_type=job_type,
+ max_file_size=settings.MAX_FILE_SIZE // 1048576)
+
+
+@website.route('/batch-jobs', methods=['POST'])
+def batch_jobs_submit():
+ """
+ Run batch jobs and render batch checker HTML form. The batch jobs are
+ added to the database by the scheduler and ran by the BatchChecker
+ daemon.
+ """
+ job_type = request.form.get('job_type')
+ email = request.form.get('email')
+ file = request.files.get('file')
+
+ assemblies = Assembly.query \
+ .order_by(Assembly.taxonomy_common_name.asc(),
+ Assembly.name.asc()) \
+ .all()
+ assembly_name_or_alias = request.form.get('assembly_name_or_alias',
+ settings.DEFAULT_ASSEMBLY)
+
+ errors = []
+
+ if not email:
+ errors.append('Please provide an email address.')
+
+ if job_type not in BATCH_JOB_TYPES:
+ errors.append('Invalid batch job type.')
+
+ if not file:
+ errors.append('Please select a local file for upload.')
+
+ if job_type == 'position-converter':
+ if not Assembly.query.filter(
+ or_(Assembly.name == assembly_name_or_alias,
+ Assembly.alias == assembly_name_or_alias)).first():
+ errors.append('Not a valid assembly.')
+ argument = assembly_name_or_alias
+ else:
+ argument = None
+
+ output = Output(__file__)
+
+ if not errors:
+ stats.increment_counter('batch-job/website')
+
+ scheduler = Scheduler.Scheduler()
+ file_instance = File.File(output)
+ job, columns = file_instance.parseBatchFile(file)
+
+ if job is None:
+ errors.append('Could not parse input file, please check your '
+ 'file format.')
+ else:
+ # Creates the result download URL from a job result_id.
+ def create_download_url(result_id):
+ return url_for('.batch_job_result',
+ result_id=result_id,
+ _external=True)
+
+ result_id = scheduler.addJob(
+ email, job, columns, job_type, argument=argument,
+ create_download_url=create_download_url)
+
+ # Todo: We now assume that the job was not scheduled if there are
+ # messages, which is probably not correct.
+ if not output.getMessages():
+ return redirect(url_for('.batch_job_progress',
+ result_id=result_id))
+
+ for error in errors:
+ output.addMessage(__file__, 3, 'EBATCHJOB', error)
+
+ errors = map(util.message_info, output.getMessages())
+
+ return render_template('batch-jobs.html',
+ assemblies=assemblies,
+ assembly_name_or_alias=assembly_name_or_alias,
+ job_type=job_type,
+ max_file_size=settings.MAX_FILE_SIZE // 1048576,
+ errors=errors)
+
+
+@website.route('/batch-job-progress')
+def batch_job_progress():
+ """
+ Batch jobs progress viewer.
+ """
+ result_id = request.args.get('result_id')
+ json = bool(request.args.get('json'))
+
+ if not result_id:
+ return render_template('batch-job-progress.html')
+
+ batch_job = BatchJob.query.filter_by(result_id=result_id).first()
+
+ if not batch_job:
+ # Only now, the job can be complete. But since we don't keep completed
+ # jobs in the database, we can only see if it ever existed by checking
+ # the result file.
+ path = os.path.join(settings.CACHE_DIR, 'batch-job-%s.txt' % result_id)
+ if os.path.isfile(path):
+ if json:
+ return jsonify(items_left=1, complete=True)
+ return render_template('batch-job-progress.html',
+ result_id=result_id)
+ else:
+ return render_template('batch-job-progress.html')
+
+ items_left = batch_job.batch_queue_items.count()
+
+ if json:
+ return jsonify(items_left=items_left, complete=False)
+ return render_template('batch-job-progress.html',
+ result_id=result_id,
+ items_left=items_left)
+
+
+@website.route('/batch-job-result/batch-job-<string:result_id>.txt')
+def batch_job_result(result_id):
+ """
+ Batch job result file download.
+ """
+ if not result_id:
+ abort(404)
+
+ batch_job = BatchJob.query.filter_by(result_id=result_id).first()
+ if batch_job:
+ # If the batch job exists, it is not done yet.
+ abort(404)
+
+ return send_from_directory(settings.CACHE_DIR,
+ 'batch-job-%s.txt' % result_id,
+ mimetype='text/plain',
+ as_attachment=True)
+
+
+# Todo: Is this obsolete?
+@website.route('/getGS')
+def lovd_get_gs():
+ """
+ LOVD bypass to get the correct GeneSymbol incl Transcript variant.
+
+ Used by LOVD to get the correct transcript variant out of a genomic
+ record. LOVD uses a genomic reference (NC_?) in combination with a gene
+ symbol to pass variant info to mutalyzer. Mutalyzer 1.0 was only using
+ the first transcript. LOVD supplies the NM of the transcript needed but
+ this was ignored. This helper allows LOVD to get the requested
+ transcript variant from a genomic reference.
+
+ Parameters:
+
+ - `mutationName`: The mutationname without gene symbol.
+ - `variantRecord`: The NM reference of the variant.
+ - `forward`: If set this forwards the request to the name checker.
+
+ Returns: Output of name checker if `forward` is set, otherwise the
+ gene symbol with the variant notation as string.
+ """
+ mutation_name = request.args['mutationName']
+ variant_record = request.args['variantRecord']
+ forward = request.args.get('forward')
+
+ output = Output(__file__)
+ output.addMessage(__file__, -1, 'INFO',
+ 'Received request getGS(%s, %s, %s) from %s'
+ % (mutation_name, variant_record, forward,
+ request.remote_addr))
+
+ # Todo: The following is probably a problem elsewhere too.
+ # We stringify the variant, because a unicode string crashes
+ # Bio.Seq.reverse_complement in mapping.py:607.
+ variantchecker.check_variant(str(mutation_name), output)
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished request getGS(%s, %s, %s)'
+ % (mutation_name, variant_record, forward))
+
+ legends = output.getOutput('legends')
+
+ # Filter the transcript from the legend.
+ legends = [l for l in legends if '_v' in l[0]]
+ for l in legends:
+ if l[1] == variant_record:
+ if forward:
+ p, a = mutation_name.split(':')
+ return redirect(url_for('.name_checker',
+ description='%s(%s):%s' % (p, l[0], a),
+ standalone=1))
+ else:
+ response = make_response(l[0])
+ response.headers['Content-Type'] = 'text/plain'
+ return response
+
+ response = make_response('Transcript not found')
+ response.headers['Content-Type'] = 'text/plain'
+ return response
+
+
+# Todo: Is this obsolete?
+@website.route('/Variant_info')
+def lovd_variant_info():
+ """
+ The chromosomal to coding and vice versa conversion interface for LOVD.
+
+ Search for an NM number in the database, if the version number matches,
+ get the start and end positions in a variant and translate these positions
+ to chromosomal notation if the variant is in coding notation and vice
+ versa.
+
+ - If no end position is present, the start position is assumed to be the
+ end position.
+ - If the version number is not found in the database, an error message is
+ generated and a suggestion for an other version is given.
+ - If the reference sequence is not found at all, an error is returned.
+ - If no variant is present, the transcription start and end and CDS end
+ in coding notation is returned.
+ - If the variant is not accepted by the nomenclature parser, a parse error
+ will be printed.
+
+ Get variant info and return the result as plain text.
+
+ Parameters:
+
+ - `LOVD_ver`: The version of the calling LOVD.
+ - `build`: The human genome build (hg19 assumed).
+ - `acc`: The accession number (NM number).
+ - `var`: A description of the variant.
+
+ Returns:
+ - start_main ; The main coordinate of the start position in I{c.}
+ (non-star) notation.
+ - start_offset ; The offset coordinate of the start position in I{c.}
+ notation (intronic position).
+ - end_main ; The main coordinate of the end position in I{c.}
+ (non-star) notation.
+ - end_offset ; The offset coordinate of the end position in I{c.}
+ notation (intronic position).
+ - start_g ; The I{g.} notation of the start position.
+ - end_g ; The I{g.} notation of the end position.
+ - type ; The mutation type.
+
+ Returns (alternative):
+ - trans_start ; Transcription start in I{c.} notation.
+ - trans_stop ; Transcription stop in I{c.} notation.
+ - CDS_stop ; CDS stop in I{c.} notation.
+ """
+ lovd_version = request.args['LOVD_ver']
+ build = request.args['build']
+ accession = request.args['acc']
+ description = request.args.get('var')
+
+ output = Output(__file__)
+ output.addMessage(__file__, -1, 'INFO',
+ 'Received request variantInfo(%s:%s (LOVD_ver %s, '
+ 'build %s)) from %s'
+ % (accession, description, lovd_version, build,
+ request.remote_addr))
+
+ assembly = Assembly.query.filter(or_(Assembly.name == build,
+ Assembly.alias == build)).first()
+ if not assembly:
+ response = make_response('invalid build')
+ response.headers['Content-Type'] = 'text/plain'
+ return response
+
+ converter = Converter(assembly, output)
+
+ result = ''
+
+ # If no variant is given, return transcription start, transcription
+ # end and CDS stop in c. notation.
+ if description:
+ ret = converter.mainMapping(accession, description)
+ else:
+ ret = converter.giveInfo(accession)
+ if ret:
+ result = '%i\n%i\n%i' % ret
+
+ if not result and not getattr(ret, 'startmain', None):
+ out = output.getOutput('LOVDERR')
+ if out:
+ result = out[0]
+ else:
+ result = 'Unknown error occured'
+
+ output.addMessage(__file__, -1, 'INFO',
+ 'Finished request variantInfo(%s:%s (LOVD_ver %s, '
+ 'build %s))'
+ % (accession, description, lovd_version, build))
+
+ if not result and getattr(ret, 'startmain', None):
+ result = '%i\n%i\n%i\n%i\n%i\n%i\n%s' % (
+ ret.startmain, ret.startoffset, ret.endmain, ret.endoffset,
+ ret.start_g, ret.end_g, ret.mutationType)
+
+ # Todo: Obsoleted error messages, remove soon.
+ if lovd_version == '2.0-23':
+ response = re.sub('^Error \(.*\):', 'Error:', result)
+
+ response = make_response(result)
+ response.headers['Content-Type'] = 'text/plain'
+ return response
+
+
+# Register redirects for backwards compatibility.
+website.add_url_route('/index', 'homepage', homepage, alias=True)
+website.add_url_route('/nameGenerator', name_generator, alias=True)
+website.add_url_route('/syntaxCheck', syntax_checker, alias=True)
+website.add_url_route('/check', name_checker, alias=True)
+website.add_url_route('/checkForward', name_checker, alias=True)
+website.add_url_route('/positionConverter', position_converter, alias=True)
+website.add_url_route('/snp', snp_converter, alias=True)
+website.add_url_route('/upload', reference_loader, alias=True)
+website.add_url_route('/descriptionExtract', description_extractor, alias=True)
+website.add_url_route('/Reference/<string:filename>', reference, alias=True)
+website.add_url_route('/batch', batch_jobs, alias=True)
+website.add_url_route('/batchNameChecker', batch_jobs, alias=True)
+website.add_url_route('/batchSyntaxChecker', batch_jobs, alias=True)
+website.add_url_route('/batchPositionConverter', batch_jobs, alias=True)
+website.add_url_route('/batchSnpConverter', batch_jobs, alias=True)
diff --git a/requirements.txt b/requirements.txt
index 09b01f8d..5e5f2130 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -8,7 +8,6 @@ requests==2.0.1
simplejson==3.3.1
spyne==2.10.9
suds==0.4
-web.py==0.37
wsgiref==0.1.2
xlrd==0.9.2
WebOb==1.1.1
diff --git a/setup.py b/setup.py
index 5cbe5d59..5d132cfa 100644
--- a/setup.py
+++ b/setup.py
@@ -45,7 +45,8 @@ setup(
'mutalyzer.db',
'mutalyzer.entrypoints',
'mutalyzer.parsers',
- 'mutalyzer.services'],
+ 'mutalyzer.services',
+ 'mutalyzer.website'],
include_package_data=True,
entry_points = {'console_scripts': [
'mutalyzer = mutalyzer.entrypoints.mutalyzer:main',
--
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