Re: [spctools-discuss] reposting: 64-bit windows 7 installation cannot view html output files

[Joseph Slagel]

Hi Suzanne,

Are you getting this error when you click on the pep.xml file in the Petunia interface?

-Joe

On Wed, Sep 26, 2012 at 8:46 AM, Suzanne <szac...@gmail.com> wrote:

Hello. I wondered whether someone can help me determine why I cannot view the output files when I run the same expt on a 32 bit xp installation and can view the output files.

Thank you.

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[Suzanne]

Yes. When I click in the pep.xml file in the Petunia interface, I rec'd an "unable to access file via webserver..." and it shows me a non-interactive version of the pep.xml. (On the 32bit computer (slow processor), I can view every file so far. I transferred the files from the 64-bit to the 32-bit computer which was a silly thing to do because the Apache servers are different!)

When I click on either the xinteract or prot.shtml (or prot.html) links I rec'd an "The webpage cannot be found". The address it sends it to is, "http://localhost/ISB/data/...*.interact.prot.html".

Suzanne

[Brian Hampton]

Suzanne,

Not certain if the below apply to your case but good to know...

Keep in mind that directory paths to file locations are hard coded in the files themselves e.g. all files created after the database search such as .pep.xml and onward.  So if you moved files and the directory paths in their new location differs from where they were when the database search was performed you will get file not found errors or similar.  I wrote a series of bash shell commands that will change the directory statements in the files to your specified new location.  This is using Ubuntu 12.04.  Not sure if this would work in Windows.

Also make certain the apache config has mod_inculdes enabled or the xml files won't be loaded.  They are processed by the Apache server first and the output is sent to the browser.  Depending on your install of Apache, they may need to be loaded.  If you are using the Windows self installing version of TPP this should already be taken care of.  

Brian Hampton

University of Maryland School of Medicine

To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/_2o8-PZMGgIJ.

[Suzanne]

Hello Brian. Thank you. I rec'd the message while opening the file using the link present in the Petunia interface, i.e. just after the file was created (on the 64 bit computer). I only copied the files to the 32 but computer when I could not determine a way to view the files through the webserver.

I will check apache config as I believe the problem is with this module.

Suzanne

[Suzanne]

"LoadModule include_module modules/mod_include.so" is enabled. I reinstalled apache but still no luck loading the output, whether it is .pep.xml or interact.pep.shtml

 

 

 

 

 

 

 

On Wednesday, September 26, 2012 3:44:45 PM UTC-4, Brian Hampton wrote:

[Joseph Slagel]

Do you get a directory listing when you navigate to http://localhost/ISB?

To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/t85CJOKPn_0J.

[Suzanne]

No. I see "Webpage cannot be found"

[Joseph Slagel]

Suzanne,

It sounds as your Apache isn't configured to allow browsing of the data folder, hence the reason why the pep.xml viewer can't load the file.  I'm guessing your missing the directives in the Apache configuration file. They should look something like:

Alias /ISB "C:/Inetpub/wwwroot/ISB"

Alias /schema "C:/Inetpub/wwwroot/schema"

<Directory "C:/Inetpub/wwwroot">
    Options Indexes MultiViews Includes
    AllowOverride None
    Order allow,deny
    Allow from all

    AddType text/html .shtml
    AddHandler server-parsed .shtml

    PassEnv WEBSERVER_ROOT
    PassEnv WEBSERVER_TMP
</Directory>

To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/WhN5aL8CsH8J.

[Suzanne]

 

It looks exactly like below.

[Suzanne]

Here it is:

 

#
# This is the main Apache HTTP server configuration file.  It contains the
# configuration directives that give the server its instructions.
# See <URL:http://httpd.apache.org/docs/2.2> for detailed information.
# In particular, see
# <URL:http://httpd.apache.org/docs/2.2/mod/directives.html>
# for a discussion of each configuration directive.
#
# Do NOT simply read the instructions in here without understanding
# what they do.  They're here only as hints or reminders.  If you are unsure
# consult the online docs. You have been warned. 
#
# Configuration and logfile names: If the filenames you specify for many
# of the server's control files begin with "/" (or "drive:/" for Win32), the
# server will use that explicit path.  If the filenames do *not* begin
# with "/", the value of ServerRoot is prepended -- so "logs/foo.log"
# with ServerRoot set to "C:/Program Files (x86)/Apache Software Foundation/Apache2.2" will be interpreted by the
# server as "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/logs/foo.log".
#
# NOTE: Where filenames are specified, you must use forward slashes
# instead of backslashes (e.g., "c:/apache" instead of "c:\apache").
# If a drive letter is omitted, the drive on which Apache.exe is located
# will be used by default.  It is recommended that you always supply
# an explicit drive letter in absolute paths to avoid confusion.

#
# ServerRoot: The top of the directory tree under which the server's
# configuration, error, and log files are kept.
#
# Do not add a slash at the end of the directory path.  If you point
# ServerRoot at a non-local disk, be sure to point the LockFile directive
# at a local disk.  If you wish to share the same ServerRoot for multiple
# httpd daemons, you will need to change at least LockFile and PidFile.
#
ServerRoot "C:/Program Files (x86)/Apache Software Foundation/Apache2.2"

#
# Listen: Allows you to bind Apache to specific IP addresses and/or
# ports, instead of the default. See also the <VirtualHost>
# directive.
#
# Change this to Listen on specific IP addresses as shown below to
# prevent Apache from glomming onto all bound IP addresses.
#
#Listen 12.34.56.78:80
Listen 80

#
# Dynamic Shared Object (DSO) Support
#
# To be able to use the functionality of a module which was built as a DSO you
# have to place corresponding `LoadModule' lines at this location so the
# directives contained in it are actually available _before_ they are used.
# Statically compiled modules (those listed by `httpd -l') do not need
# to be loaded here.
#
# Example:
# LoadModule foo_module modules/mod_foo.so
#
LoadModule actions_module modules/mod_actions.so
LoadModule alias_module modules/mod_alias.so
LoadModule asis_module modules/mod_asis.so
LoadModule auth_basic_module modules/mod_auth_basic.so
#LoadModule auth_digest_module modules/mod_auth_digest.so
#LoadModule authn_alias_module modules/mod_authn_alias.so
#LoadModule authn_anon_module modules/mod_authn_anon.so
#LoadModule authn_dbd_module modules/mod_authn_dbd.so
#LoadModule authn_dbm_module modules/mod_authn_dbm.so
LoadModule authn_default_module modules/mod_authn_default.so
LoadModule authn_file_module modules/mod_authn_file.so
#LoadModule authnz_ldap_module modules/mod_authnz_ldap.so
#LoadModule authz_dbm_module modules/mod_authz_dbm.so
LoadModule authz_default_module modules/mod_authz_default.so
LoadModule authz_groupfile_module modules/mod_authz_groupfile.so
LoadModule authz_host_module modules/mod_authz_host.so
#LoadModule authz_owner_module modules/mod_authz_owner.so
LoadModule authz_user_module modules/mod_authz_user.so
LoadModule autoindex_module modules/mod_autoindex.so
#LoadModule cache_module modules/mod_cache.so
#LoadModule cern_meta_module modules/mod_cern_meta.so
LoadModule cgi_module modules/mod_cgi.so
#LoadModule charset_lite_module modules/mod_charset_lite.so
#LoadModule dav_module modules/mod_dav.so
#LoadModule dav_fs_module modules/mod_dav_fs.so
#LoadModule dav_lock_module modules/mod_dav_lock.so
#LoadModule dbd_module modules/mod_dbd.so
#LoadModule deflate_module modules/mod_deflate.so
LoadModule dir_module modules/mod_dir.so
#LoadModule disk_cache_module modules/mod_disk_cache.so
#LoadModule dumpio_module modules/mod_dumpio.so
LoadModule env_module modules/mod_env.so
#LoadModule expires_module modules/mod_expires.so
#LoadModule ext_filter_module modules/mod_ext_filter.so
#LoadModule file_cache_module modules/mod_file_cache.so
#LoadModule filter_module modules/mod_filter.so
#LoadModule headers_module modules/mod_headers.so
#LoadModule ident_module modules/mod_ident.so
#LoadModule imagemap_module modules/mod_imagemap.so
LoadModule include_module modules/mod_include.so
#LoadModule info_module modules/mod_info.so
LoadModule isapi_module modules/mod_isapi.so
#LoadModule ldap_module modules/mod_ldap.so
#LoadModule logio_module modules/mod_logio.so
LoadModule log_config_module modules/mod_log_config.so
#LoadModule log_forensic_module modules/mod_log_forensic.so
#LoadModule mem_cache_module modules/mod_mem_cache.so
LoadModule mime_module modules/mod_mime.so
#LoadModule mime_magic_module modules/mod_mime_magic.so
LoadModule negotiation_module modules/mod_negotiation.so
#LoadModule proxy_module modules/mod_proxy.so
#LoadModule proxy_ajp_module modules/mod_proxy_ajp.so
#LoadModule proxy_balancer_module modules/mod_proxy_balancer.so
#LoadModule proxy_connect_module modules/mod_proxy_connect.so
#LoadModule proxy_ftp_module modules/mod_proxy_ftp.so
#LoadModule proxy_http_module modules/mod_proxy_http.so
#LoadModule rewrite_module modules/mod_rewrite.so
LoadModule setenvif_module modules/mod_setenvif.so
#LoadModule speling_module modules/mod_speling.so
#LoadModule ssl_module modules/mod_ssl.so
#LoadModule status_module modules/mod_status.so
#LoadModule substitute_module modules/mod_substitute.so
#LoadModule unique_id_module modules/mod_unique_id.so
#LoadModule userdir_module modules/mod_userdir.so
#LoadModule usertrack_module modules/mod_usertrack.so
#LoadModule version_module modules/mod_version.so
#LoadModule vhost_alias_module modules/mod_vhost_alias.so

<IfModule !mpm_netware_module>
<IfModule !mpm_winnt_module>
#
# If you wish httpd to run as a different user or group, you must run
# httpd as root initially and it will switch. 
#
# User/Group: The name (or #number) of the user/group to run httpd as.
# It is usually good practice to create a dedicated user and group for
# running httpd, as with most system services.
#
User daemon
Group daemon

</IfModule>
</IfModule>

# 'Main' server configuration
#
# The directives in this section set up the values used by the 'main'
# server, which responds to any requests that aren't handled by a
# <VirtualHost> definition.  These values also provide defaults for
# any <VirtualHost> containers you may define later in the file.
#
# All of these directives may appear inside <VirtualHost> containers,
# in which case these default settings will be overridden for the
# virtual host being defined.
#

#
# ServerAdmin: Your address, where problems with the server should be
# e-mailed.  This address appears on some server-generated pages, such
# as error documents.  e.g. ad...@your-domain.com
#
ServerAdmin webm...@gmail.com

#
# ServerName gives the name and port that the server uses to identify itself.
# This can often be determined automatically, but we recommend you specify
# it explicitly to prevent problems during startup.
#
# If your host doesn't have a registered DNS name, enter its IP address here.
#
#ServerName localhost:80

#
# DocumentRoot: The directory out of which you will serve your
# documents. By default, all requests are taken from this directory, but
# symbolic links and aliases may be used to point to other locations.
#
DocumentRoot "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/htdocs"

#
# Each directory to which Apache has access can be configured with respect
# to which services and features are allowed and/or disabled in that
# directory (and its subdirectories).
#
# First, we configure the "default" to be a very restrictive set of
# features. 
#
<Directory />
    Options FollowSymLinks
    AllowOverride None
    Order deny,allow
    Deny from all
</Directory>

#
# Note that from this point forward you must specifically allow
# particular features to be enabled - so if something's not working as
# you might expect, make sure that you have specifically enabled it
# below.
#

#
# This should be changed to whatever you set DocumentRoot to.
#
<Directory "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/htdocs">
    #
    # Possible values for the Options directive are "None", "All",
    # or any combination of:
    #   Indexes Includes FollowSymLinks SymLinksifOwnerMatch ExecCGI MultiViews
    #
    # Note that "MultiViews" must be named *explicitly* --- "Options All"
    # doesn't give it to you.
    #
    # The Options directive is both complicated and important.  Please see
    # http://httpd.apache.org/docs/2.2/mod/core.html#options
    # for more information.
    #
    Options Indexes FollowSymLinks

    #
    # AllowOverride controls what directives may be placed in .htaccess files.
    # It can be "All", "None", or any combination of the keywords:
    #   Options FileInfo AuthConfig Limit
    #
    AllowOverride None

    #
    # Controls who can get stuff from this server.
    #

    Order allow,deny
    Allow from all

</Directory>

#
# DirectoryIndex: sets the file that Apache will serve if a directory
# is requested.
#
<IfModule dir_module>
    DirectoryIndex index.html
</IfModule>

#
# The following lines prevent .htaccess and .htpasswd files from being
# viewed by Web clients.
#
<FilesMatch "^\.ht">
    Order allow,deny
    Deny from all
    Satisfy All
</FilesMatch>

#
# ErrorLog: The location of the error log file.
# If you do not specify an ErrorLog directive within a <VirtualHost>
# container, error messages relating to that virtual host will be
# logged here.  If you *do* define an error logfile for a <VirtualHost>
# container, that host's errors will be logged there and not here.
#
ErrorLog "logs/error.log"

#
# LogLevel: Control the number of messages logged to the error_log.
# Possible values include: debug, info, notice, warn, error, crit,
# alert, emerg.
#
LogLevel warn

<IfModule log_config_module>
    #
    # The following directives define some format nicknames for use with
    # a CustomLog directive (see below).
    #
    LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\"" combined
    LogFormat "%h %l %u %t \"%r\" %>s %b" common

    <IfModule logio_module>
      # You need to enable mod_logio.c to use %I and %O
      LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" %I %O" combinedio
    </IfModule>

    #
    # The location and format of the access logfile (Common Logfile Format).
    # If you do not define any access logfiles within a <VirtualHost>
    # container, they will be logged here.  Contrariwise, if you *do*
    # define per-<VirtualHost> access logfiles, transactions will be
    # logged therein and *not* in this file.
    #
    CustomLog "logs/access.log" common

    #
    # If you prefer a logfile with access, agent, and referer information
    # (Combined Logfile Format) you can use the following directive.
    #
    #CustomLog "logs/access.log" combined
</IfModule>

<IfModule alias_module>
    #
    # Redirect: Allows you to tell clients about documents that used to
    # exist in your server's namespace, but do not anymore. The client
    # will make a new request for the document at its new location.
    # Example:
    # Redirect permanent /foo http://localhost/bar

    #
    # Alias: Maps web paths into filesystem paths and is used to
    # access content that does not live under the DocumentRoot.
    # Example:
    # Alias /webpath /full/filesystem/path
    #
    # If you include a trailing / on /webpath then the server will
    # require it to be present in the URL.  You will also likely
    # need to provide a <Directory> section to allow access to
    # the filesystem path.

    #
    # ScriptAlias: This controls which directories contain server scripts.
    # ScriptAliases are essentially the same as Aliases, except that
    # documents in the target directory are treated as applications and
    # run by the server when requested rather than as documents sent to the
    # client.  The same rules about trailing "/" apply to ScriptAlias
    # directives as to Alias.
    #
    ScriptAlias /cgi-bin/ "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/cgi-bin/"

</IfModule>

<IfModule cgid_module>
    #
    # ScriptSock: On threaded servers, designate the path to the UNIX
    # socket used to communicate with the CGI daemon of mod_cgid.
    #
    #Scriptsock logs/cgisock
</IfModule>

#
# "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/cgi-bin" should be changed to whatever your ScriptAliased
# CGI directory exists, if you have that configured.
#
<Directory "C:/Program Files (x86)/Apache Software Foundation/Apache2.2/cgi-bin">
    AllowOverride None
    Options None

    Order allow,deny
    Allow from all

</Directory>

#
# DefaultType: the default MIME type the server will use for a document
# if it cannot otherwise determine one, such as from filename extensions.
# If your server contains mostly text or HTML documents, "text/plain" is
# a good value.  If most of your content is binary, such as applications
# or images, you may want to use "application/octet-stream" instead to
# keep browsers from trying to display binary files as though they are
# text.
#
DefaultType text/plain

<IfModule mime_module>
    #
    # TypesConfig points to the file containing the list of mappings from
    # filename extension to MIME-type.
    #
    TypesConfig conf/mime.types

    #
    # AddType allows you to add to or override the MIME configuration
    # file specified in TypesConfig for specific file types.
    #
    #AddType application/x-gzip .tgz
    #
    # AddEncoding allows you to have certain browsers uncompress
    # information on the fly. Note: Not all browsers support this.
    #
    #AddEncoding x-compress .Z
    #AddEncoding x-gzip .gz .tgz
    #
    # If the AddEncoding directives above are commented-out, then you
    # probably should define those extensions to indicate media types:
    #
    AddType application/x-compress .Z
    AddType application/x-gzip .gz .tgz

    #
    # AddHandler allows you to map certain file extensions to "handlers":
    # actions unrelated to filetype. These can be either built into the server
    # or added with the Action directive (see below)
    #
    # To use CGI scripts outside of ScriptAliased directories:
    # (You will also need to add "ExecCGI" to the "Options" directive.)
    #
    #AddHandler cgi-script .cgi

    # For type maps (negotiated resources):
    #AddHandler type-map var

    #
    # Filters allow you to process content before it is sent to the client.
    #
    # To parse .shtml files for server-side includes (SSI):
    # (You will also need to add "Includes" to the "Options" directive.)
    #
    #AddType text/html .shtml
    #AddOutputFilter INCLUDES .shtml
</IfModule>

#
# The mod_mime_magic module allows the server to use various hints from the
# contents of the file itself to determine its type.  The MIMEMagicFile
# directive tells the module where the hint definitions are located.
#
#MIMEMagicFile conf/magic

#
# Customizable error responses come in three flavors:
# 1) plain text 2) local redirects 3) external redirects
#
# Some examples:
#ErrorDocument 500 "The server made a boo boo."
#ErrorDocument 404 /missing.html
#ErrorDocument 404 "/cgi-bin/missing_handler.pl"
#ErrorDocument 402 http://localhost/subscription_info.html
#

#
# EnableMMAP and EnableSendfile: On systems that support it,
# memory-mapping or the sendfile syscall is used to deliver
# files.  This usually improves server performance, but must
# be turned off when serving from networked-mounted
# filesystems or if support for these functions is otherwise
# broken on your system.
#
#EnableMMAP off
#EnableSendfile off

# Supplemental configuration
#
# The configuration files in the conf/extra/ directory can be
# included to add extra features or to modify the default configuration of
# the server, or you may simply copy their contents here and change as
# necessary.

# Server-pool management (MPM specific)
#Include conf/extra/httpd-mpm.conf

# Multi-language error messages
#Include conf/extra/httpd-multilang-errordoc.conf

# Fancy directory listings
#Include conf/extra/httpd-autoindex.conf

# Language settings
#Include conf/extra/httpd-languages.conf

# User home directories
#Include conf/extra/httpd-userdir.conf

# Real-time info on requests and configuration
#Include conf/extra/httpd-info.conf

# Virtual hosts
#Include conf/extra/httpd-vhosts.conf

# Local access to the Apache HTTP Server Manual
#Include conf/extra/httpd-manual.conf

# Distributed authoring and versioning (WebDAV)
#Include conf/extra/httpd-dav.conf

# Various default settings
#Include conf/extra/httpd-default.conf

# Secure (SSL/TLS) connections
#Include conf/extra/httpd-ssl.conf
#
# Note: The following must must be present to support
#       starting without SSL on platforms with no /dev/random equivalent
#       but a statically compiled-in mod_ssl.
#
<IfModule ssl_module>
SSLRandomSeed startup builtin
SSLRandomSeed connect builtin
</IfModule>

#
# Begin settings for the Trans Proteomic Pipeline
#

# Add 5-hour timeout
Timeout 18000

Alias /tpp-bin "C:/Inetpub/tpp-bin"
<Directory "C:/Inetpub/tpp-bin">
    Options Indexes MultiViews ExecCGI

    AllowOverride None
    Order allow,deny
    Allow from all

    AddHandler cgi-script .cgi .pl
    ScriptInterpreterSource Registry

    PassEnv WEBSERVER_ROOT
    PassEnv WEBSERVER_TMP
</Directory>

Alias /ISB "C:/Inetpub/wwwroot/ISB"

Alias /schema "C:/Inetpub/wwwroot/schema"

<Directory "C:/Inetpub/wwwroot">
    Options MultiViews Includes

    AllowOverride None
    Order allow,deny
    Allow from all

    AddType text/html .shtml
    AddHandler server-parsed .shtml

    PassEnv WEBSERVER_ROOT
    PassEnv WEBSERVER_TMP
</Directory>

#
# End settings for the Trans Proteomic Pipeline
#

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

On Thursday, September 27, 2012 1:31:36 PM UTC-4, jsl...@systemsbiology.org wrote:

[Brian Hampton]

Try uncommenting the line 

#ServerName localhost:80

Reboot or restart apache.  For some reason windows needs a reboot to restart apache.

You should be able to connect to your server at http://localhost. Or http://127.0.0.1 and get a page that says "It works!".

Also, your server admin email is listed as webm...@gmail.com.  Is that your email address?  Probably not.  

Brian

To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/GwiLAH9JzCkJ.

[Suzanne]

I have always observed the "It works" message. Otherwise I will not be able to access Petunia. I simply can't view the results. I will try the un-comment you suggest. 

I did not think that a valid email address was necessary. (?)

[Suzanne]

To follow up: The un-comment did not help. I also shut-down the computer but still no luck viewing the files or the directory list when I navigate to  http://localhost/ISB as Joe suggested yesterday.

[Vishal Swaroop]

Hi Suzanne,

First, there are references to dependent files in pep/ prot xmls like (shtml, xsl, xml.index etc...) so copying from one server to other will screw the things.

Can you right click the pep/prot link and check the what path it is using, then see if that file is physically present, if pressent then open the file in any editor and see referenced files.

Example : I have a link which I can see in Petunia (sample_interact.prot.xml)

sample_interact.prot.xml [ View | Edit ]

If you are not able to "view" this file then either click "Edit" link or open the file in editor and check if paths are correct.

Verfify all the attributes path.... example 

<?xml version="1.0" encoding="UTF-8"?>

<?xml-stylesheet type="text/xsl" href="http://localhost/ISB/data/...

...

summary_xml="c:/Inetpub/wwwroot/ISB

...

reference_database="c:/Inetpub...

source_files="c:/Inetpub/

source_files_alt="c:/Inetpub

Let me know.

Thanks

Vishal

To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/FFO4Fo55dzwJ.

[Vishal Swaroop]

Hi Suzanne,

Adding to my email below...

a) You are using petunia on the server itself using localhost, right ?

b) Which browser you are using ? So if you open pep.xml are you getting this error message ?

"Unable to access xml file via webserver, so cannot check xml file for changes ()

Check webserver configuration if desired.

(URL: undefined)"

c) Just try to open one 1 prot.xml and check the corresponding xsl path used in it

d) If possible send the screen shot of the error and corresponding xml and xsl file

Thanks