Initial commit.

.gitignore

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+# Don't ever commit your settings
+config.py
+
+# vim remenants
+*.swp
+*.swo
+*~
+
+# Python remenants
+*.pyc
+*.pyo

.htaccess

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+Options +ExecCGI
+DirectoryIndex index.xhtml

abbreviations.conf

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+# Abbreviation definitions for display.
+
+### Entity types
+
+Gene_or_gene_product : GGP
+
+Protein : Pro, Pr, P
+Entity  : Ent, En, E
+
+Multicellular_organism_natural : M-C Organism, MCOrg
+Organism             : Org
+Chemical             : Chem
+Two-component-system : 2-comp-sys, 2CS
+Regulon-operon       : Reg/op
+
+### Event types
+
+Protein_catabolism   : Catabolism, Catab
+Gene_expression      : Expression, Expr
+Binding              : Bind
+Transcription        : Trns
+Localization         : Locl
+Regulation           : Reg
+Positive_regulation  : +Regulation, +Reg
+Negative_regulation  : -Regulation, -Reg
+Phosphorylation      : Phos
+Dephosphorylation    : -Phos
+Acetylation          : Acet
+Deacetylation        : -Acet
+Hydroxylation        : Hydr
+Dehydroxylation      : -Hydr
+Glycosylation        : Glyc
+Deglycosylation      : -Glyc
+Methylation          : Meth
+Demethylation        : -Meth
+Ubiquitination       : Ubiq
+Deubiquitination     : -Ubiq
+DNA_methylation      : DNA meth
+DNA_demethylation    : DNA -meth
+Catalysis            : Catal
+Biological_process   : Biol proc
+Cellular_physiological_process: Cell phys proc
+Protein_molecule     : Prot mol
+Protein_family_or_group: PFG
+DNA_domain_or_region : DDR
+Protein_domain_or_region: PDR
+Amino_acid_monomer   : AA
+Carbohydrate         : Carb
+
+Acylation            : Acyl
+Deacylation          : -Acyl
+Alkylation           : Alkyl
+Dealkylation         : -Alkyl
+Palmitoylation       : Palm
+Depalmitoylation     : -Palm
+Lipidation           : Lipid
+Delipidation         : -Lipid
+Prenylation          : Prenyl
+Deprenylation        : -Prenyl
+Neddylation          : Nedd
+Deneddylation        : -Nedd
+Sumoylation          : Sumo
+Desumoylation        : -Sumo
+
+# AZ additions
+Drug_or_compound     : Drug/comp, D/C
+Other_pharmaceutical_agent : Other_pharm
+# end AZ additions
+
+### Role types
+
+Theme : Th
+Theme1: Th1
+Theme2: Th2
+Theme3: Th3
+Theme4: Th4
+Cause : Ca
+Site  : Si
+Site1 : Si1
+Site2 : Si2
+Site3 : Si3
+Site4 : Si4
+Equiv : Eq
+Contextgene : CGn
+Sidechain   : SCh
+Participant : Pa

ajax.cgi

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+#!/usr/bin/env python
+# -*- Mode: Python; tab-width: 4; indent-tabs-mode: nil; -*- 
+# vim:set ft=python ts=4 sw=4 sts=4 autoindent:
+
+'''
+Entry for cgi calls to the application. This is a simple wrapper that
+only imports a bare minimum and ensures that the web-based UI gets a proper
+response even when the server crashes. If in debug mode it returns any errors
+that occur using the established messaging API.
+
+This file should stay compatible with Python 2.3 and upwards until it has done
+the version checking in order to assure that we can return sensible results
+to the user and administrators.
+
+Author:     Pontus  Stenetorp   <pontus is s u tokyo ac jp>
+Version:    2010-02-07
+'''
+
+from cgi import escape, FieldStorage
+from os.path import dirname
+from os.path import join as path_join
+from sys import path as sys_path
+from sys import version_info
+
+sys_path.append(path_join(dirname(__file__), 'server/lib/simplejson-2.1.5'))
+sys_path.append(path_join(dirname(__file__), 'server/src'))
+
+from common import ProtocolError, NoPrintJSONError
+from message import add_messages_to_json, display_message
+from session import get_session
+
+### Constants
+# This handling of version_info is strictly for backwards compability
+PY_VER_STR = '%d.%d.%d-%s-%d' % tuple(version_info)
+REQUIRED_PY_VERSION_MAJOR = 2
+REQUIRED_PY_VERSION_MINOR = 5
+INVALID_PY_JSON = '''
+{
+  "messages": [
+    [
+      "Incompatible Python version (%s), %d.%d or above is supported",
+      "error",
+      -1
+    ]
+  ]
+}
+''' % (PY_VER_STR, REQUIRED_PY_VERSION_MAJOR, REQUIRED_PY_VERSION_MINOR)
+CONF_FNAME = 'config.py'
+CONF_TEMPLATE_FNAME = 'config_template.py'
+###
+
+def _miss_var_msg(var):
+    #TODO: DOC!
+    return ('Missing variable "%s" in %s, make sure that you have '
+            'not made any errors to your configurations and to start over '
+            'copy the template file %s to %s in your '
+            'installation directory and edit it to suit your environment'
+            ) % (var, CONF_FNAME, CONF_TEMPLATE_FNAME, CONF_FNAME)
+
+def _miss_config_msg():
+    #TODO: DOC!
+    return ('Missing file %s in the installation dir. If this is a new '
+            'installation, copy the template file %s to %s in '
+            'your installation directory ("cp %s %s") and edit '
+            'it to suit your environment.'
+            ) % (CONF_FNAME, CONF_TEMPLATE_FNAME, CONF_FNAME, CONF_FNAME, CONF_TEMPLATE_FNAME)
+
+# TODO: Split up main or somehow make it more read-able
+def main(args):
+    # Check the Python version, if it is incompatible print a manually crafted
+    # json error. This needs to be updated manually as the protocol changes.
+    if (version_info[0] != REQUIRED_PY_VERSION_MAJOR or 
+        version_info[1] < REQUIRED_PY_VERSION_MINOR):
+        print 'Content-Type: application/json\n'
+        print INVALID_PY_JSON
+        return -1
+
+    # NOTE: It is essential to parse the request before anything else, if
+    #       we fail with any kind of error this ensures us that the client
+    #       will get the response back.
+    # TODO: wrap this in try (not protected now)
+    params = FieldStorage()
+
+    # From now on we know we have access to dumps
+    from jsonwrap import dumps
+
+    # Do configuration checking and importing
+    from sys import path
+    from copy import deepcopy
+    from os.path import dirname
+    # Reset the path to force config.py to be in this dir (could be hacked
+    #       using __init__.py, but we can be monkey-patched anyway)
+    orig_path = deepcopy(path)
+    # Can't you empty in O(1) instead of O(N)?
+    while path:
+        path.pop()
+    path.append(dirname(__file__))
+    # Check if we have a config, otherwise whine
+    try:
+        import config
+        del config
+    except ImportError:
+        path.extend(orig_path)
+        print 'Content-Type: application/json\n'
+        display_message(_miss_config_msg(),
+            type='error', duration=-1)
+        print dumps(add_messages_to_json({}))
+        raise
+    # Try importing the config entries we need
+    try:
+        from config import DEBUG
+    except ImportError:
+        path.extend(orig_path)
+        print 'Content-Type: application/json\n'
+        display_message(_miss_var_msg('DEBUG'),
+            type='error', duration=-1)
+        print dumps(add_messages_to_json({}))
+        raise
+    try:
+        from config import ADMIN_CONTACT_EMAIL
+    except ImportError:
+        path.extend(orig_path)
+        print 'Content-Type: application/json\n'
+        display_message(_miss_var_msg('ADMIN_CONTACT_EMAIL'),
+            type='error', duration=-1)
+        print dumps(add_messages_to_json({}))
+        raise
+    # Remove our entry to the path
+    path.pop()
+    # Then restore it
+    path.extend(orig_path)
+
+    try:
+        try:
+            # Dispatch the request and get the corresponding json dictionary
+            from dispatch import dispatch
+            json_dic = dispatch(params)
+            # TODO: Possibly a check here that what we got back was dictionary:ish
+
+            get_session().print_cookie()
+
+            print 'Content-Type: application/json\n'
+            print dumps(add_messages_to_json(json_dic))
+        except ProtocolError, e:
+            # Internal exception, notify the client but don't log to stderr
+            json_dic = {}
+            e.json(json_dic)
+            print 'Content-Type: application/json\n'
+            print dumps(add_messages_to_json(json_dic))
+        except NoPrintJSONError:
+            pass # We are simply to exit and do nothing
+    except BaseException, e:
+        # Catches even an interpreter crash and syntax error
+        if DEBUG:
+            # Send back the stack-trace as json
+            from traceback import print_exc
+            try:
+                from cStringIO import StringIO
+            except ImportError:
+                from StringIO import StringIO
+
+            # Getting the stack-trace requires a small trick
+            buf = StringIO()
+            print_exc(file=buf)
+            buf.seek(0)
+            error_msg = '<br/>'.join((
+                'Server Python crash, stacktrace is:\n',
+                escape(buf.read()))).replace('\n', '\n<br/>\n')
+            display_message(error_msg, type='error', duration=-1)
+        else:
+            # Give the user an error message
+            from time import time
+            # Use the current time since epoch as an id for later log look-up
+            error_msg = ('The server encountered a serious error, '
+                    'please contact the administrators at %s '
+                    'and give the id #%d'
+                    ) % (ADMIN_CONTACT_EMAIL, int(time()))
+            display_message(error_msg, type='error', duration=-1)
+
+        # Allow the exception to fall through so it is logged by Apache
+        print 'Content-Type: application/json\n'
+        print dumps(add_messages_to_json({}))
+        raise 
+    return 0
+
+if __name__ == '__main__':
+    from sys import argv, exit
+    exit(main(argv))