Merge branch 'release_23.2' into dev

CONTRIBUTORS.md

@@ -69,11 +69,12 @@ The following individuals have contributed code to Galaxy:
 * Ben Fulton <[email protected]>
 * Carrie Ganote <[email protected]>
 * Ryan Golhar <[email protected]>
-* Jeremy Goecks <[email protected]> 
+* Jeremy Goecks <[email protected]>
 * Nuwan Goonasekera <[email protected]>
 * Björn Grüning <[email protected]> <[email protected]>
 * Aysam Guerler <[email protected]>
 * Simon Guest <[email protected]>
+* Nalin Gupta <[email protected]>
 * Jianbin He <[email protected]>
 * Peter van Heusden <[email protected]>
 * Morita Hideyuki <[email protected]>

lib/galaxy/app.py

@@ -144,10 +144,7 @@
 from galaxy.visualization.data_providers.registry import DataProviderRegistry
 from galaxy.visualization.genomes import Genomes
 from galaxy.visualization.plugins.registry import VisualizationsRegistry
-from galaxy.web import (
-    legacy_url_for,
-    url_for,
-)
+from galaxy.web import url_for
 from galaxy.web.framework.base import server_starttime
 from galaxy.web.proxy import ProxyManager
 from galaxy.web_stack import (
@@ -795,7 +792,6 @@ def __init__(self, **kwargs) -> None:
         # Inject url_for for components to more easily optionally depend
         # on url_for.
         self.url_for = url_for
-        self.legacy_url_for = legacy_url_for
 
         self.server_starttime = server_starttime  # used for cachebusting
         # Limit lifetime of tool shed repository cache to app startup

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -779,10 +779,11 @@
     </datatype>
     <datatype extension="pdbqt" type="galaxy.datatypes.molecules:PDBQT" display_in_upload="true"/>
     <datatype extension="pqr" type="galaxy.datatypes.molecules:PQR" display_in_upload="true" />
-    <datatype extension="cell" type="galaxy.datatypes.molecules:Cell" display_in_upload="true"/>
-    <datatype extension="cif" type="galaxy.datatypes.molecules:CIF" display_in_upload="true"/>
-    <datatype extension="xyz" type="galaxy.datatypes.molecules:XYZ" display_in_upload="true"/>
-    <datatype extension="extxyz" type="galaxy.datatypes.molecules:ExtendedXYZ" display_in_upload="true"/>
+    <datatype extension="cell" type="galaxy.datatypes.molecules:Cell" display_in_upload="true" description="The .cell file contains geometry information, including cell parameters, atomic coordinates, and k-point coordinates and weights. The file consists of lines containing keywords and data blocks, and associated values" description_url="https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/expcastepfilecell.htm"/>
+    <datatype extension="cif" type="galaxy.datatypes.molecules:CIF" display_in_upload="true" description="CIF or Crystallographic Information File is the standard format for storing crystallographic structural data" description_url="https://www.iucr.org/resources/cif"/>
+    <datatype extension="xyz" type="galaxy.datatypes.molecules:XYZ" display_in_upload="true" description="Basic format for atomic positions in a structure" description_url="https://open-babel.readthedocs.io/en/latest/FileFormats/XYZ_cartesian_coordinates_format.html"/>
+    <datatype extension="extxyz" type="galaxy.datatypes.molecules:ExtendedXYZ" display_in_upload="true" description="Extended XYZ format is an enhanced version of the basic XYZ format that allows extra columns to be present in the file for additonal per-atom properties as well as standardising the format of the comment line to include the cell lattice and other per-frame parameters" description_url="https://wiki.fysik.dtu.dk/ase/ase/io/formatoptions.html#extxyz"/>
+    <datatype extension="magres" type="galaxy.datatypes.molecules:Magres" display_in_upload="true" description="Ab initio Nuclear Magnetic Resonance file format providing a complete archival and data processing format for the results of first principles calculation of NMR parameters" description_url="https://www.ccpnc.ac.uk/docs/magres"/>
     <datatype extension="trr" type="galaxy.datatypes.binary:Trr" display_in_upload="true">
       <converter file="mdconvert.xml" target_datatype="xtc"/>
       <converter file="mdconvert.xml" target_datatype="dcd"/>
@@ -963,9 +964,9 @@
     <datatype extension="storm.check" type="galaxy.datatypes.text:StormCheck" display_in_upload="true"/>
     <datatype extension="ctl.result" type="galaxy.datatypes.text:CTLresult" display_in_upload="true"/>
     <!-- CASTEP types -->
-    <datatype extension="castep" type="galaxy.datatypes.text:Castep" display_in_upload="true"/>
-    <datatype extension="param" type="galaxy.datatypes.text:Param" display_in_upload="true"/>
-    <datatype extension="den_fmt" type="galaxy.datatypes.text:FormattedDensity" display_in_upload="true"/>
+    <datatype extension="castep" type="galaxy.datatypes.text:Castep" display_in_upload="true" description="numerical output of a CASTEP job in ASCII format" description_url="https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/expcastepfilecastep.htm"/>
+    <datatype extension="param" type="galaxy.datatypes.text:Param" display_in_upload="true" description="the param file contains all the input control parameters required to run a CASTEP job. Consists of lines containing keywords and associated values" description_url="https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/expcastepfileparam.htm"/>
+    <datatype extension="den_fmt" type="galaxy.datatypes.text:FormattedDensity" display_in_upload="true" description="formatted electronic density file output by CASTEP containing value of electron density for a grid of points"/>
     <!-- Larch types -->
     <datatype extension="prj" type="galaxy.datatypes.larch:AthenaProject" display_in_upload="true" description="Athena project file."/>
     <datatype extension="inp" type="galaxy.datatypes.larch:FEFFInput" display_in_upload="true" description="FEFF input file."/>
@@ -1141,6 +1142,7 @@
     <sniffer type="galaxy.datatypes.molecules:CIF"/>
     <sniffer type="galaxy.datatypes.molecules:ExtendedXYZ"/>
     <sniffer type="galaxy.datatypes.molecules:XYZ"/>
+    <sniffer type="galaxy.datatypes.molecules:Magres" />
     <sniffer type="galaxy.datatypes.molecules:MOL2"/>
     <sniffer type="galaxy.datatypes.molecules:InChI"/>
     <sniffer type="galaxy.datatypes.molecules:FPS"/>

lib/galaxy/datatypes/data.py

@@ -783,7 +783,7 @@ def as_display_type(self, dataset: DatasetProtocol, type: str, **kwd) -> Union[F
         return f"This display type ({type}) is not implemented for this datatype ({dataset.ext})."
 
     def get_display_links(
-        self, dataset: DatasetProtocol, type: str, app, base_url: str, request, target_frame: str = "_blank", **kwd
+        self, dataset: DatasetProtocol, type: str, app, base_url: str, target_frame: str = "_blank", **kwd
     ):
         """
         Returns a list of tuples of (name, link) for a particular display type.  No check on
@@ -794,7 +794,7 @@ def get_display_links(
         try:
             if app.config.enable_old_display_applications and type in self.get_display_types():
                 return target_frame, getattr(self, self.supported_display_apps[type]["links_function"])(
-                    dataset, type, app, base_url, request, **kwd
+                    dataset, type, app, base_url, **kwd
                 )
         except Exception:
             log.exception(

lib/galaxy/datatypes/display_applications/application.py

@@ -53,16 +53,14 @@ def __init__(self, display_application):
 
     def get_display_url(self, data, trans):
         dataset_hash, user_hash = encode_dataset_user(trans, data, None)
-        return trans.app.legacy_url_for(
-            mapper=trans.app.legacy_mapper,
+        return trans.app.url_for(
             controller="dataset",
             action="display_application",
             dataset_id=dataset_hash,
             user_id=user_hash,
             app_name=quote_plus(self.display_application.id),
             link_name=quote_plus(self.id),
             app_action=None,
-            environ=trans.request.environ,
         )
 
     def get_inital_values(self, data, trans):

lib/galaxy/datatypes/display_applications/parameters.py

@@ -272,8 +272,7 @@ def url(self):
             base_url = f"http{base_url[5:]}"
         return "{}{}".format(
             base_url,
-            self.trans.app.legacy_url_for(
-                mapper=self.trans.app.legacy_mapper,
+            self.trans.app.url_for(
                 controller="dataset",
                 action="display_application",
                 dataset_id=self._dataset_hash,
@@ -282,7 +281,6 @@ def url(self):
                 link_name=quote_plus(self.parameter.link.id),
                 app_action=self.action_name,
                 action_param=self._url,
-                environ=self.trans.request.environ,
             ),
         )
 

lib/galaxy/datatypes/genetics.py

@@ -91,7 +91,7 @@ def as_ucsc_display_file(self, dataset: DatasetProtocol, **kwd) -> Union[FileObj
         """
         return open(dataset.get_file_name(), "rb")
 
-    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         """
         from the ever-helpful angie hinrichs [email protected]
         a genome graphs call looks like this
@@ -115,17 +115,15 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, re
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
                 if site_name in app.datatypes_registry.get_display_sites("ucsc"):
                     site_url = site_url.replace("/hgTracks?", "/hgGenome?")  # for genome graphs
-                    internal_url = "%s" % app.legacy_url_for(
-                        mapper=app.legacy_mapper,
-                        environ=request.environ,
+                    internal_url = app.url_for(
                         controller="dataset",
                         dataset_id=dataset.id,
                         action="display_at",
                         filename=f"ucsc_{site_name}",
                     )
                     display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (
                         base_url,
-                        app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                        app.url_for(controller="root"),
                         dataset.id,
                         type,
                     )

lib/galaxy/datatypes/interval.py

@@ -316,7 +316,7 @@ def display_peek(self, dataset: DatasetProtocol) -> str:
             },
         )
 
-    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         """
         Generate links to UCSC genome browser sites based on the dbkey
         and content of dataset.
@@ -338,9 +338,7 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, re
         # Accumulate links for valid sites
         ret_val = []
         for site_name, site_url in valid_sites:
-            internal_url = app.legacy_url_for(
-                mapper=app.legacy_mapper,
-                environ=request.environ,
+            internal_url = app.url_for(
                 controller="dataset",
                 dataset_id=dataset.id,
                 action="display_at",
@@ -350,7 +348,7 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, re
                 "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
                 % (
                     base_url,
-                    app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                    app.url_for(controller="root"),
                     dataset.id,
                     type,
                 )
@@ -769,20 +767,26 @@ class Bed12(BedStrict):
 
 class _RemoteCallMixin:
     def _get_remote_call_url(
-        self, redirect_url: str, site_name: str, dataset: HasId, type: str, app, base_url: str, request
+        self,
+        redirect_url: str,
+        site_name: str,
+        dataset: HasId,
+        type: str,
+        app,
+        base_url: str,
     ) -> str:
         """Retrieve the URL to call out to an external site and retrieve data.
         This routes our external URL through a local galaxy instance which makes
         the data available, followed by redirecting to the remote site with a
         link back to the available information.
         """
-        internal_url = f"{app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller='dataset', dataset_id=dataset.id, action='display_at', filename=f'{type}_{site_name}')}"
+        internal_url = f"{app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename=f'{type}_{site_name}')}"
         base_url = app.config.get("display_at_callback", base_url)
         display_url = quote_plus(
             "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
             % (
                 base_url,
-                app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                app.url_for(controller="root"),
                 dataset.id,
                 type,
             )
@@ -970,7 +974,7 @@ def get_estimated_display_viewport(
                 log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
-    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport(dataset)
         if seqid is not None:
@@ -979,11 +983,11 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, re
                     redirect_url = quote_plus(
                         f"{site_url}db={dataset.dbkey}&position={seqid}:{start}-{stop}&hgt.customText=%s"
                     )
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
 
-    def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport(dataset)
         if seqid is not None:
@@ -992,7 +996,7 @@ def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str,
                     if seqid.startswith("chr") and len(seqid) > 3:
                         seqid = seqid[3:]
                     redirect_url = quote_plus(f"{site_url}/?q={seqid}:{start}..{stop}&eurl=%s")
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
 
@@ -1372,7 +1376,7 @@ def get_estimated_display_viewport(
                 log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
-    def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
@@ -1381,11 +1385,11 @@ def gbrowse_links(self, dataset: DatasetProtocol, type: str, app, base_url: str,
                     if chrom.startswith("chr") and len(chrom) > 3:
                         chrom = chrom[3:]
                     redirect_url = quote_plus(f"{site_url}/?q={chrom}:{start}..{stop}&eurl=%s")
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
 
-    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
@@ -1394,7 +1398,7 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, re
                     redirect_url = quote_plus(
                         f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s"
                     )
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))
         return ret_val
 
@@ -1554,18 +1558,18 @@ def get_estimated_display_viewport(
                 log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
-    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str, request) -> List:
+    def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) -> List:
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
                 if site_name in app.datatypes_registry.get_display_sites("ucsc"):
-                    internal_url = f"{app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name)}"
+                    internal_url = f"{app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name)}"
                     display_url = quote_plus(
                         "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
                         % (
                             base_url,
-                            app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                            app.url_for(controller="root"),
                             dataset.id,
                             type,
                         )