Galaxy 24.1 upgrade

galaxy/coralsnp_reports/lib/galaxy/webapps/coralsnp_reports/app.py

@@ -2,40 +2,46 @@
 import sys
 import time
 
-import galaxy.model.corals
 import galaxy.model.corals.mapping
+from galaxy.config import configure_logging
+from galaxy.model.base import SharedModelMapping
 from galaxy.security import idencoding
-from galaxy.web.stack import application_stack_instance
+from galaxy.structured_app import BasicSharedApp
+from galaxy.web_stack import application_stack_instance
 from . import config
 
 log = logging.getLogger(__name__)
 
 
-class UniverseApplication(object):
+class UniverseApplication(BasicSharedApp):
     """Encapsulates the state of a Universe application"""
 
     def __init__(self, **kwargs):
-        log.debug("python path is: %s", ", ".join(sys.path))
+        super().__init__()
+        self[BasicSharedApp] = self
         self.name = "coralsnp_reports"
         # Read config file and check for errors
         self.config = config.Configuration(**kwargs)
         self.config.check()
-        config.configure_logging(self.config)
+        configure_logging(self.config)
+        log.debug("XXX kwargs: %s\n" % str(kwargs))
+        log.debug("XXX self.config: %s\n" % str(self.config))
+        log.debug("XXX self.config.corals_database_connection: %s\n" % self.config.corals_database_connection)
+        log.debug("python path is: %s", ", ".join(sys.path))
         self.application_stack = application_stack_instance()
         # Determine the database url
-        if self.config.database_connection:
-            db_url = self.config.database_connection
+        if self.config.corals_database_connection:
+            db_url = self.config.corals_database_connection
         else:
-            db_url = "postgresql://galaxy:galaxy@localhost/stag"
+            db_url = f"sqlite:///{self.config.database}?isolation_level=IMMEDIATE"
         # Setup the database engine and ORM
-        self.model = galaxy.model.corals.mapping.init(db_url,
-                                                      self.config.database_engine_options)
-        if not self.config.database_connection:
-            self.targets_mysql = False
-        else:
-            self.targets_mysql = 'mysql' in self.config.database_connection
+        self.model = galaxy.model.corals.mapping.init(self.config.file_path, db_url, self.config.database_engine_options)
         # Security helper
         self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret)
+
+        self._register_singleton(idencoding.IdEncodingHelper, self.security)
+        self._register_singleton(SharedModelMapping, self.model)
+
         # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
         self.server_starttime = int(time.time())
 

galaxy/coralsnp_reports/lib/galaxy/webapps/coralsnp_reports/buildapp.py

@@ -8,21 +8,16 @@
 
 from paste import httpexceptions
 
-import galaxy.model.corals
-import galaxy.web.framework.webapp
+import galaxy.webapps.base.webapp
 from galaxy.util import asbool
 from galaxy.util.properties import load_app_properties
-from galaxy.webapps.util import (
-    build_template_error_formatters,
-    MiddlewareWrapUnsupported,
-    wrap_if_allowed,
-    wrap_if_allowed_or_fail
-)
+from galaxy.web.framework.middleware.request_id import RequestIDMiddleware
+from galaxy.webapps.util import wrap_if_allowed
 
 log = logging.getLogger(__name__)
 
 
-class CoralSNPReportsWebApplication(galaxy.web.framework.webapp.WebApplication):
+class CoralSNPReportsWebApplication(galaxy.webapps.base.webapp.WebApplication):
     pass
 
 
@@ -31,9 +26,9 @@ def add_ui_controllers(webapp, app):
     Search for controllers in the 'galaxy.webapps.coralsnp_reports.controllers'
     module and add them to the webapp.
     """
-    #from galaxy.web.base.controller import BaseUIController
     import galaxy.webapps.coralsnp_reports.controllers
-    from galaxy.webapps.coralsnp_reports.controllers import BaseUIController
+    from galaxy.webapps.base.controller import BaseUIController
+
     controller_dir = galaxy.webapps.coralsnp_reports.controllers.__path__[0]
     for fname in os.listdir(controller_dir):
         if not fname.startswith("_") and fname.endswith(".py"):
@@ -52,10 +47,8 @@ def add_ui_controllers(webapp, app):
 def app_factory(global_conf, load_app_kwds={}, **kwargs):
     """Return a wsgi application serving the root object"""
     # Create the Galaxy application unless passed in
-    kwargs = load_app_properties(
-        kwds=kwargs,
-        **load_app_kwds
-    )
+    load_app_kwds = load_app_kwds or {}
+    kwargs = load_app_properties(kwds=kwargs, **load_app_kwds)
     if 'app' in kwargs:
         app = kwargs.pop('app')
     else:
@@ -73,15 +66,7 @@ def app_factory(global_conf, load_app_kwds={}, **kwargs):
     if kwargs.get('middleware', True):
         webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs)
     if asbool(kwargs.get('static_enabled', True)):
-        webapp = wrap_if_allowed(webapp, app.application_stack, wrap_in_static,
-                                 args=(global_conf,),
-                                 kwargs=kwargs)
-    # Close any pooled database connections before forking
-    try:
-        galaxy.model.corals.mapping.metadata.bind.dispose()
-    except Exception:
-        log.exception("Unable to dispose of pooled coralsnp_reports model database connections.")
-    # Return
+        webapp = wrap_if_allowed(webapp, app.application_stack, galaxy.webapps.base.webapp.build_url_map, args=(global_conf,), kwargs=kwargs)
     return webapp
 
 
@@ -91,7 +76,6 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
     # Merge the global and local configurations
     conf = global_conf.copy()
     conf.update(local_conf)
-    debug = asbool(conf.get('debug', False))
     # First put into place httpexceptions, which must be most closely
     # wrapped around the application (it can interact poorly with
     # other middleware):
@@ -101,54 +85,20 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
     if asbool(conf.get('use_recursive', True)):
         from paste import recursive
         app = wrap_if_allowed(app, stack, recursive.RecursiveMiddleware, args=(conf,))
-    # Various debug middleware that can only be turned on if the debug
-    # flag is set, either because they are insecure or greatly hurt
-    # performance
-    if debug:
-        # Middleware to check for WSGI compliance
-        if asbool(conf.get('use_lint', True)):
-            from paste import lint
-            app = wrap_if_allowed(app, stack, lint.make_middleware, name='paste.lint', args=(conf,))
-        # Middleware to run the python profiler on each request
-        if asbool(conf.get('use_profile', False)):
-            import profile
-            app = wrap_if_allowed(app, stack, profile.ProfileMiddleware, args=(conf,))
-        # Middleware that intercepts print statements and shows them on the
-        # returned page
-        if asbool(conf.get('use_printdebug', True)):
-            from paste.debug import prints
-            app = wrap_if_allowed(app, stack, prints.PrintDebugMiddleware, args=(conf,))
-    if debug and asbool(conf.get('use_interactive', False)):
-        # Interactive exception debugging, scary dangerous if publicly
-        # accessible, if not enabled we'll use the regular error printing
-        # middleware.
-        try:
-            from weberror import evalexception
-            app = wrap_if_allowed_or_fail(app, stack, evalexception.EvalException,
-                                          args=(conf,),
-                                          kwargs=dict(templating_formatters=build_template_error_formatters()))
-        except MiddlewareWrapUnsupported as exc:
-            log.warning(str(exc))
-            import galaxy.web.framework.middleware.error
-            app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
-    else:
-        # Not in interactive debug mode, just use the regular error middleware
-        import galaxy.web.framework.middleware.error
-        app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
+    # Error middleware
+    import galaxy.web.framework.middleware.error
+    app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
     # Transaction logging (apache access.log style)
-    if asbool(conf.get('use_translogger', True)):
+    if asbool(conf.get("use_translogger", True)):
         from paste.translogger import TransLogger
         app = wrap_if_allowed(app, stack, TransLogger)
     # X-Forwarded-Host handling
     from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
     app = wrap_if_allowed(app, stack, XForwardedHostMiddleware)
-    return app
-
+    # Request ID middleware
+    app = wrap_if_allowed(app, stack, RequestIDMiddleware)
+    if asbool(conf.get("enable_per_request_sql_debugging", False)):
+        from galaxy.web.framework.middleware.sqldebug import SQLDebugMiddleware
 
-def wrap_in_static(app, global_conf, **local_conf):
-    urlmap, _ = galaxy.web.framework.webapp.build_url_map(app, global_conf, local_conf)
-    return urlmap
-
-
-def uwsgi_app():
-    return galaxy.web.framework.webapp.build_native_uwsgi_app(app_factory, "coralsnp_reports")
+        app = wrap_if_allowed(app, stack, SQLDebugMiddleware, args=(webapp, {}))
+    return app

galaxy/coralsnp_reports/lib/galaxy/webapps/coralsnp_reports/config.py

@@ -11,7 +11,7 @@
 
 def resolve_path(path, root):
     """If 'path' is relative make absolute by prepending 'root'"""
-    if not(os.path.isabs(path)):
+    if not (os.path.isabs(path)):
         path = os.path.join(root, path)
     return path
 
@@ -26,7 +26,7 @@ def __init__(self, **kwargs):
         self.root = kwargs.get('root_dir', '.')
         # Database related configuration
         self.database = resolve_path(kwargs.get("database_file", "database/universe.sqlite"), self.root)
-        self.database_connection = kwargs.get("database_connection", False)
+        self.corals_database_connection = kwargs.get("corals_database_connection", False)
         self.database_engine_options = get_database_engine_options(kwargs)
         # Where dataset files are stored
         self.file_path = resolve_path(kwargs.get("file_path", "database/files"), self.root)
@@ -36,7 +36,7 @@ def __init__(self, **kwargs):
         self.require_login = string_as_bool(kwargs.get("require_login", "False"))
         self.session_duration = kwargs.get("session_duration", "0")
         self.template_path = resolve_path(kwargs.get("template_path", "templates"), self.root)
-        self.template_cache = resolve_path(kwargs.get("template_cache_path", "database/compiled_templates/coralsnp_reports"), self.root)
+        self.template_cache_path = resolve_path(kwargs.get("template_cache_path", "database/compiled_templates/coralsnp_reports"), self.root)
         self.allow_user_creation = string_as_bool(kwargs.get("allow_user_creation", "True"))
         self.allow_user_deletion = string_as_bool(kwargs.get("allow_user_deletion", "False"))
         self.log_actions = string_as_bool(kwargs.get('log_actions', 'False'))

galaxy/coralsnp_reports/lib/galaxy/webapps/coralsnp_reports/controllers/__init__.py

@@ -1,32 +1 @@
 """Galaxy coralsnp reports controllers."""
-import logging
-
-from galaxy import util
-
-log = logging.getLogger(__name__)
-
-
-class BaseController(object):
-    """
-    Base class for CoralSNP Reports web application controllers.
-    """
-
-    def __init__(self, app):
-        """Initialize an interface for application 'app'"""
-        self.app = app
-        self.sa_session = app.model.context
-
-
-class BaseUIController(BaseController):
-
-    def get_object(self, trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None):
-        try:
-            return BaseController.get_object(self, trans, id, class_name, check_ownership=check_ownership,
-                                             check_accessible=check_accessible, deleted=deleted)
-        except Exception:
-            log.exception("Exception in get_object check for %s %s:", class_name, str(id))
-            raise Exception('Server error retrieving %s id ( %s ).' % (class_name, str(id)))
-
-    def message_exception(self, trans, message, sanitize=True):
-        trans.response.status = 400
-        return {'err_msg': util.sanitize_text(message) if sanitize else message}

galaxy/coralsnp_reports/lib/galaxy/webapps/coralsnp_reports/controllers/alleles.py

@@ -3,11 +3,13 @@
 import sqlalchemy as sa
 from markupsafe import escape
 
-import galaxy.model
+from galaxy.model import corals
 from galaxy import util
-from . import BaseUIController
-from galaxy.web.base.controller import web
-from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
+)
+from galaxy.webapps.coralsnp_reports.controllers.query import ReportQueryBuilder
 
 log = logging.getLogger(__name__)
 
@@ -19,14 +21,17 @@ def of_sample(self, trans, **kwd):
         message = escape(util.restore_text(kwd.get('message', '')))
         affy_id = kwd.get('affy_id')
         allele_id = kwd.get('allele_id')
-        q = sa.select((galaxy.model.corals.Allele.table.c.id,
-                       galaxy.model.corals.Allele.table.c.allele),
-                      whereclause=galaxy.model.corals.Allele.table.c.id == allele_id,
-                      from_obj=[galaxy.model.corals.Allele.table])
+        q = (
+            sa.select(
+                corals.Allele.id,
+                corals.Allele.allele
+            )
+            .select_from(corals.Allele.table)
+            .where(corals.Allele.table.c.id == allele_id)
+        )
         alleles = []
-        for row in q.execute():
-            cols_tup = (row.id, row.allele)
-            alleles.append(cols_tup)
+        for row in trans.sa_session.execute(q):
+            alleles.append((row.id, row.allele))
         return trans.fill_template('/webapps/coralsnp_reports/allele_of_sample.mako',
                                    affy_id=affy_id,
                                    alleles=alleles,

galaxy/coralsnp_reports/lib/galaxy/webapps/coralsnp_reports/controllers/collectors.py

@@ -3,11 +3,13 @@
 import sqlalchemy as sa
 from markupsafe import escape
 
-import galaxy.model
+from galaxy.model import corals
 from galaxy import util
-from . import BaseUIController
-from galaxy.web.base.controller import web
-from galaxy.webapps.reports.controllers.query import ReportQueryBuilder
+from galaxy.webapps.base.controller import (
+    BaseUIController,
+    web,
+)
+from galaxy.webapps.coralsnp_reports.controllers.query import ReportQueryBuilder
 
 log = logging.getLogger(__name__)
 
@@ -17,35 +19,32 @@ class Collectors(BaseUIController, ReportQueryBuilder):
     @web.expose
     def all(self, trans, **kwd):
         message = escape(util.restore_text(kwd.get('message', '')))
-        q = sa.select((galaxy.model.corals.Person.table.c.id,
-                       galaxy.model.corals.Person.table.c.last_name,
-                       galaxy.model.corals.Person.table.c.first_name,
-                       galaxy.model.corals.Person.table.c.organization,
-                       galaxy.model.corals.Person.table.c.email),
-                      from_obj=[galaxy.model.corals.Person.table],
-                      order_by=[galaxy.model.corals.Person.table.c.last_name])
         collectors = []
-        for row in q.execute():
-            cols_tup = (row.id, row.last_name, row.first_name, row.organization, row.email)
-            collectors.append(cols_tup)
-        return trans.fill_template('/webapps/coralsnp_reports/collectors.mako', collectors=collectors, message=message)
+        for row in trans.sa_session.query(corals.Person):
+            collectors.append((row.id, row.last_name, row.first_name, row.organization, row.email))
+        return trans.fill_template('/webapps/coralsnp_reports/collectors.mako',
+                                   collectors=collectors,
+                                   message=message)
 
     @web.expose
     def of_sample(self, trans, **kwd):
         message = escape(util.restore_text(kwd.get('message', '')))
         affy_id = kwd.get('affy_id')
         collector_id = kwd.get('collector_id')
-        q = sa.select((galaxy.model.corals.Person.table.c.id,
-                       galaxy.model.corals.Person.table.c.last_name,
-                       galaxy.model.corals.Person.table.c.first_name,
-                       galaxy.model.corals.Person.table.c.organization,
-                       galaxy.model.corals.Person.table.c.email),
-                      whereclause=galaxy.model.corals.Person.table.c.id == collector_id,
-                      from_obj=[galaxy.model.corals.Person.table])
+        q = (
+            sa.select(
+                corals.Person.id,
+                corals.Person.last_name,
+                corals.Person.first_name,
+                corals.Person.organization,
+                corals.Person.email
+            )
+            .select_from(corals.Person.table)
+            .where(corals.Person.table.c.id == collector_id)
+        )
         collectors = []
-        for row in q.execute():
-            cols_tup = (row.last_name, row.first_name, row.organization, row.email)
-            collectors.append(cols_tup)
+        for row in trans.sa_session.execute(q):
+            collectors.append((row.last_name, row.first_name, row.organization, row.email))
         return trans.fill_template('/webapps/coralsnp_reports/collector_of_sample.mako',
                                    affy_id=affy_id,
                                    collectors=collectors,