--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/galaxy/util/dbkeys.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,94 @@
+"""
+Functionality for dealing with dbkeys.
+"""
+# dbkeys read from disk using builds.txt
+from __future__ import absolute_import
+
+import os.path
+from json import loads
+
+from galaxy.util import read_dbnames
+from galaxy.util.object_wrapper import sanitize_lists_to_string
+
+
+class GenomeBuilds(object):
+    default_value = "?"
+    default_name = "unspecified (?)"
+
+    def __init__(self, app, data_table_name="__dbkeys__", load_old_style=True):
+        self._app = app
+        self._data_table_name = data_table_name
+        self._static_chrom_info_path = app.config.len_file_path
+        # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups
+        if load_old_style:
+            self._static_dbkeys = list(read_dbnames(app.config.builds_file_path))
+        else:
+            self._static_dbkeys = []
+
+    def get_genome_build_names(self, trans=None):
+        # FIXME: how to deal with key duplicates?
+        rval = []
+        # load user custom genome builds
+        if trans is not None:
+            if trans.history:
+                # This is a little bit Odd. We are adding every .len file in the current history to dbkey list,
+                # but this is previous behavior from trans.db_names, so we'll continue to do it.
+                # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering,
+                # so a len file will be listed twice (as the build name and again as dataset name),
+                # if custom dbkey creation/conversion occurred within the current history.
+                datasets = trans.sa_session.query(self._app.model.HistoryDatasetAssociation) \
+                                .filter_by(deleted=False, history_id=trans.history.id, extension="len")
+                for dataset in datasets:
+                    rval.append((dataset.dbkey, "%s (%s) [History]" % (dataset.name, dataset.dbkey)))
+            user = trans.user
+            if user and hasattr(user, 'preferences') and 'dbkeys' in user.preferences:
+                user_keys = loads(user.preferences['dbkeys'])
+                for key, chrom_dict in user_keys.items():
+                    rval.append((key, "%s (%s) [Custom]" % (chrom_dict['name'], key)))
+        # Load old builds.txt static keys
+        rval.extend(self._static_dbkeys)
+        # load dbkeys from dbkey data table
+        dbkey_table = self._app.tool_data_tables.get(self._data_table_name, None)
+        if dbkey_table is not None:
+            for field_dict in dbkey_table.get_named_fields_list():
+                rval.append((field_dict['value'], field_dict['name']))
+        return rval
+
+    def get_chrom_info(self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True):
+        # FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required
+        chrom_info = None
+        db_dataset = None
+        # Collect chromInfo from custom builds
+        if trans:
+            db_dataset = trans.db_dataset_for(dbkey)
+            if db_dataset:
+                chrom_info = db_dataset.file_name
+            else:
+                # Do Custom Build handling
+                if trans.user and ('dbkeys' in trans.user.preferences) and (dbkey in loads(trans.user.preferences['dbkeys'])):
+                    custom_build_dict = loads(trans.user.preferences['dbkeys'])[dbkey]
+                    # HACK: the attempt to get chrom_info below will trigger the
+                    # fasta-to-len converter if the dataset is not available or,
+                    # which will in turn create a recursive loop when
+                    # running the fasta-to-len tool. So, use a hack in the second
+                    # condition below to avoid getting chrom_info when running the
+                    # fasta-to-len converter.
+                    if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion:
+                        # Build is defined by fasta; get len file, which is obtained from converting fasta.
+                        build_fasta_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(custom_build_dict['fasta'])
+                        chrom_info = build_fasta_dataset.get_converted_dataset(trans, 'len').file_name
+                    elif 'len' in custom_build_dict:
+                        # Build is defined by len file, so use it.
+                        chrom_info = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(custom_build_dict['len']).file_name
+        # Check Data table
+        if not chrom_info:
+            dbkey_table = self._app.tool_data_tables.get(self._data_table_name, None)
+            if dbkey_table is not None:
+                chrom_info = dbkey_table.get_entry('value', dbkey, 'len_path', default=None)
+        # use configured server len path
+        if not chrom_info:
+            # Default to built-in build.
+            # Since we are using an unverified dbkey, we will sanitize the dbkey before use
+            chrom_info = os.path.join(self._static_chrom_info_path, "%s.len" % sanitize_lists_to_string(dbkey))
+        chrom_info = os.path.abspath(chrom_info)
+        return (chrom_info, db_dataset)