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Reintroduce nginx upload module support.

Browse Source 
http://www.grid.net.ru/nginx/upload.en.html

The following config variables are added to universe_wsgi.ini:

    nginx_upload_store = Path to nginx upload store
        ex: = database/upload_store
    nginx_upload_path = URL (from root of the Galaxy server) to direct upload POSTs to
        ex: = /_upload

The following nginx config supports such a configuration:

    location /_upload {
        upload_store /path/to/galaxy/database/upload_store;
        upload_pass_form_field "tool_id";
        upload_pass_form_field "tool_state";
        upload_pass_form_field "async_datasets";
        upload_pass_form_field "^files_[0-9]+\|.*";
        upload_pass_form_field "file_type";
        upload_pass_form_field "dbkey";
        upload_pass_form_field "runtool_btn";
        upload_pass_form_field "ajax_upload";
        upload_pass_form_field "upload_option";
        upload_pass_form_field "library_id";
        upload_pass_form_field "folder_id";
        upload_pass_form_field "message";
        upload_pass_form_field "roles";
        upload_set_form_field "__${upload_field_name}__is_composite" "true";
        upload_set_form_field "__${upload_field_name}__keys" "name path";
        upload_set_form_field "${upload_field_name}_name" "$upload_file_name";
        upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path";
        upload_pass_args on;
        upload_pass /_upload_done;
    }

    location /_upload_done {
        set $dst /tool_runner/index;
        if ($args ~ nginx_redir=([^&]+)) {
            set $dst $1;
        }
        rewrite "" $dst;
    }
This commit is contained in:
Nate Coraor
2009-09-29 17:14:20 -04:00
parent 0630363c48
commit d14eb4d653
10 changed files with 39 additions and 23 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/config.py
+4 -3
View File
@@ -89,9 +89,10 @@ class Configuration( object ):
raise ConfigurationError( "user_library_import_dir specified in config (%s) does not exist" % self.user_library_import_dir )
# Configuration options for taking advantage of nginx features
self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False )
self.nginx_upload_location = kwargs.get( 'nginx_upload_store', False )
if self.nginx_upload_location:
self.nginx_upload_location = os.path.abspath( self.nginx_upload_location )
self.nginx_upload_store = kwargs.get( 'nginx_upload_store', False )
self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False )
if self.nginx_upload_store:
self.nginx_upload_store = os.path.abspath( self.nginx_upload_store )
# Parse global_conf and save the parser
global_conf = kwargs.get( 'global_conf', None )
global_conf_parser = ConfigParser.ConfigParser()
lib/galaxy/tools/__init__.py
+5 -1
View File
@@ -464,7 +464,11 @@ class Tool:
if input_elem:
# Handle properties of the input form
self.check_values = util.string_as_bool( input_elem.get("check_values", "true") )
self.action = input_elem.get( "action", "/tool_runner/index")
self.nginx_upload = util.string_as_bool( input_elem.get( "nginx_upload", "false" ) )
if self.nginx_upload and self.app.config.nginx_upload_path:
self.action = input_elem.get( "action", self.app.config.nginx_upload_path + "?nginx_redir=/tool_runner/index" )
else:
self.action = input_elem.get( "action", "/tool_runner/index")
self.target = input_elem.get( "target", "galaxy_main" )
self.method = input_elem.get( "method", "post" )
# Parse the actual parameters
lib/galaxy/tools/actions/upload_common.py
+2
View File
@@ -23,6 +23,8 @@ def persist_uploads( params ):
f.file.close()
upload_dataset['file_data'] = dict( filename = f.filename,
local_filename = local_filename )
elif type( f ) == dict and 'filename' and 'local_filename' not in f:
raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' )
if upload_dataset['url_paste'].strip() != '':
upload_dataset['url_paste'] = datatypes.sniff.stream_to_file( StringIO.StringIO( upload_dataset['url_paste'] ), prefix="strio_url_paste_" )[0]
else:
lib/galaxy/tools/parameters/basic.py
+13 -14
View File
@@ -304,22 +304,21 @@ class FileToolParameter( ToolParameter ):
def get_html_field( self, trans=None, value=None, other_values={} ):
return form_builder.FileField( self.name, ajax = self.ajax, value = value )
def from_html( self, value, trans=None, other_values={} ):
# TODO: Fix nginx upload module support
# Middleware or proxies may encode files in special ways (TODO: this
# should be pluggable)
#if type( value ) == dict:
# upload_location = self.tool.app.config.nginx_upload_location
# assert upload_location, \
# "Request appears to have been processed by nginx_upload_module \
# but Galaxy is not configured to recgonize it"
# # Check that the file is in the right location
# local_filename = os.path.abspath( value['path'] )
# assert local_filename.startswith( upload_location ), \
# "Filename provided by nginx is not in correct directory"
# value = Bunch(
# filename = value["name"],
# local_filename = local_filename
# )
if type( value ) == dict:
upload_store = self.tool.app.config.nginx_upload_store
assert upload_store, \
"Request appears to have been processed by nginx_upload_module \
but Galaxy is not configured to recognize it"
# Check that the file is in the right location
local_filename = os.path.abspath( value['path'] )
assert local_filename.startswith( upload_store ), \
"Filename provided by nginx is not in correct directory"
value = dict(
filename = value["name"],
local_filename = local_filename
)
return value
def get_required_enctype( self ):
"""
lib/galaxy/web/controllers/library.py
+5
View File
@@ -792,8 +792,13 @@ class Library( BaseController ):
# Send the current history to the form to enable importing datasets from history to library
history = trans.get_history()
history.refresh()
# If we're using nginx upload, override the form action
action = web.url_for( controller='library', action='library_dataset_dataset_association' )
if upload_option == 'upload_file' and trans.app.config.nginx_upload_path:
action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action
return trans.fill_template( '/library/upload.mako',
upload_option=upload_option,
action=action,
library_id=library_id,
folder_id=folder_id,
replace_dataset=replace_dataset,
lib/galaxy/web/controllers/library_admin.py
+5
View File
@@ -487,8 +487,13 @@ class LibraryAdmin( BaseController ):
# Send the current history to the form to enable importing datasets from history to library
history = trans.get_history()
history.refresh()
# If we're using nginx upload, override the form action
action = web.url_for( controller='library_admin', action='library_dataset_dataset_association' )
if upload_option == 'upload_file' and trans.app.config.nginx_upload_path:
action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action
return trans.fill_template( '/admin/library/upload.mako',
upload_option=upload_option,
action=action,
library_id=library_id,
folder_id=folder_id,
replace_dataset=replace_dataset,
templates/admin/library/upload.mako
+1 -1
View File
@@ -32,4 +32,4 @@
${render_msg( msg, messagetype )}
%endif
${render_upload_form( 'library_admin', upload_option, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )}
${render_upload_form( 'library_admin', upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )}
templates/library/library_dataset_common.mako
+2 -2
View File
@@ -1,4 +1,4 @@
<%def name="render_upload_form( controller, upload_option, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history )">
<%def name="render_upload_form( controller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history )">
<% import os, os.path %>
%if upload_option in [ 'upload_file', 'upload_directory' ]:
<div class="toolForm" id="upload_library_dataset">
@@ -8,7 +8,7 @@
<div class="toolFormTitle">Upload a directory of files</div>
%endif
<div class="toolFormBody">
<form name="upload_library_dataset" action="${h.url_for( controller=controller, action='library_dataset_dataset_association' )}" enctype="multipart/form-data" method="post">
<form name="upload_library_dataset" action="${action}" enctype="multipart/form-data" method="post">
<input type="hidden" name="tool_id" value="upload1"/>
<input type="hidden" name="tool_state" value="None"/>
<input type="hidden" name="library_id" value="${library_id}"/>
templates/library/upload.mako
+1 -1
View File
@@ -32,4 +32,4 @@
${render_msg( msg, messagetype )}
%endif
${render_upload_form( 'library', upload_option, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )}
${render_upload_form( 'library', upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )}
tools/data_source/upload.xml
+1 -1
View File
@@ -14,7 +14,7 @@
${output.dataset.dataset.id}:${output}
#end while
</command>
<inputs>
<inputs nginx_upload="true">
<param name="file_type" type="select" label="File Format" help="Which format? See help below">
<options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ &quot;%s%s%s&quot; % ( line, self.separator, line ) for line in obj ]">
<column name="value" index="1"/>