From 098b31f5df650e3233cfe022b28d8850cc03c6c0 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 27 Jan 2021 15:58:58 -0500
Subject: [PATCH 01/17] Add MissingDataError to galaxy exceptions

Intended to be raised when data required for processing a request is
missing.

Example: when accessing `api/genomes/foo`, this error will be
raised if the foo.len file has not been generated.
---
 lib/galaxy/exceptions/__init__.py      | 5 +++++
 lib/galaxy/exceptions/error_codes.json | 5 +++++
 2 files changed, 10 insertions(+)

diff --git a/lib/galaxy/exceptions/__init__.py b/lib/galaxy/exceptions/__init__.py
index 14bd2a7b539..34c02448e14 100644
--- a/lib/galaxy/exceptions/__init__.py
+++ b/lib/galaxy/exceptions/__init__.py
@@ -221,6 +221,11 @@ class InvalidFileFormatError(MessageException):
     err_code = error_codes_by_name['INVALID_FILE_FORMAT']
 
 
+class MissingDataError(MessageException):
+    status_code = 500
+    err_code = error_codes_by_name['MISSING_DATA_ERROR']
+
+
 # non-web exceptions
 
 class ContainerCLIError(Exception):
diff --git a/lib/galaxy/exceptions/error_codes.json b/lib/galaxy/exceptions/error_codes.json
index 629d799ea5d..054f8ee999c 100644
--- a/lib/galaxy/exceptions/error_codes.json
+++ b/lib/galaxy/exceptions/error_codes.json
@@ -159,6 +159,11 @@
     "code": 500005,
     "message": "File format not supported for this operation."
    },
+   {
+    "name": "MISSING_DATA_ERROR",
+    "code": 500006,
+    "message": "Data required for program execution is missing."
+   },
    {
     "name": "NOT_IMPLEMENTED",
     "code": 501001,

From 47e37cddda77a053b9283574ae444cb54834fcff Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 27 Jan 2021 23:09:48 -0500
Subject: [PATCH 02/17] Do not use @web decorators in api controllers

@web decorator will cause json content to be sent to the client as html,
including html-formatted errors, which is incorrect.
---
 lib/galaxy/webapps/galaxy/api/genomes.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/genomes.py b/lib/galaxy/webapps/galaxy/api/genomes.py
index ec8e06e7659..453a53e0b49 100644
--- a/lib/galaxy/webapps/galaxy/api/genomes.py
+++ b/lib/galaxy/webapps/galaxy/api/genomes.py
@@ -1,4 +1,7 @@
-from galaxy import web
+from galaxy.web import (
+    expose_api_anonymous,
+    expose_api_raw_anonymous,
+)
 from galaxy.web.framework.helpers import is_true
 from galaxy.webapps.base.controller import BaseAPIController
 
@@ -15,15 +18,14 @@ class GenomesController(BaseAPIController):
     RESTful controller for interactions with genome data.
     """
 
-    @web.legacy_expose_api_anonymous
+    @expose_api_anonymous
     def index(self, trans, **kwd):
         """
         GET /api/genomes: returns a list of installed genomes
         """
-
         return self.app.genomes.get_dbkeys(trans, **kwd)
 
-    @web.json
+    @expose_api_anonymous
     def show(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd):
         """
         GET /api/genomes/{id}
@@ -44,7 +46,7 @@ class GenomesController(BaseAPIController):
             rval = self.app.genomes.chroms(trans, dbkey=id, num=num, chrom=chrom, low=low)
         return rval
 
-    @web.legacy_expose_api_raw_anonymous
+    @expose_api_raw_anonymous
     def indexes(self, trans, id, **kwd):
         """
         GET /api/genomes/{id}/indexes?type={table name}
@@ -62,7 +64,7 @@ class GenomesController(BaseAPIController):
         if_open = open(index_file_name + index_extensions[index_type], mode='r')
         return if_open.read()
 
-    @web.legacy_expose_api_raw_anonymous
+    @expose_api_raw_anonymous
     def sequences(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd):
         """
         GET /api/genomes/{id}/sequences

From 5a1459f8db5abc4fdb96994e9c3c0a5cc820fd33 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 27 Jan 2021 23:11:55 -0500
Subject: [PATCH 03/17] Raise appropriate exception; add test

/api/genomes/foo should raise ObjectNotFound exception if foo is not a
valid id.
---
 lib/galaxy/visualization/genomes.py | 11 ++++-------
 lib/galaxy_test/api/test_genomes.py | 15 +++++++++++++++
 2 files changed, 19 insertions(+), 7 deletions(-)
 create mode 100644 lib/galaxy_test/api/test_genomes.py

diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index ed1b8cd30d1..527d7b8a74c 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -6,6 +6,7 @@ from json import loads
 
 from bx.seq.twobit import TwoBitFile
 
+from galaxy.exceptions import ObjectNotFound
 from galaxy.util.bunch import Bunch
 
 log = logging.getLogger(__name__)
@@ -325,14 +326,10 @@ class Genomes:
             elif dbkey in self.genomes:
                 genome = self.genomes[dbkey]
 
-        # Set up return value or log exception if genome not found for key.
-        rval = None
-        if genome:
-            rval = genome.to_dict(num=num, chrom=chrom, low=low)
-        else:
-            log.exception('genome not found for key %s', dbkey)
+        if not genome:
+            raise ObjectNotFound(f'genome not found for key {dbkey}')
 
-        return rval
+        return genome.to_dict(num=num, chrom=chrom, low=low)
 
     def has_reference_data(self, dbkey, dbkey_owner=None):
         """
diff --git a/lib/galaxy_test/api/test_genomes.py b/lib/galaxy_test/api/test_genomes.py
new file mode 100644
index 00000000000..d5ba568373b
--- /dev/null
+++ b/lib/galaxy_test/api/test_genomes.py
@@ -0,0 +1,15 @@
+from galaxy.exceptions import ObjectNotFound
+from ._framework import ApiTestCase
+
+
+class GenomesApiTestCase(ApiTestCase):
+
+    def test_index(self):
+        response = self._get('genomes')
+        self._assert_status_code_is(response, 200)
+        assert response.json()[0][0] == 'unspecified (?)'
+
+    def test_show_invalid(self):
+        response = self._get('genomes/invalid')
+        self._assert_status_code_is(response, 404)
+        assert response.json()['err_code'] == ObjectNotFound.err_code.code

From 94e2cc7fd75d6029afc4869a565b937261ba99f4 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 27 Jan 2021 23:53:51 -0500
Subject: [PATCH 04/17] Handle error for missing len_file; add test

---
 lib/galaxy/visualization/genomes.py |  8 +++++++-
 lib/galaxy_test/api/test_genomes.py | 11 ++++++++++-
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 527d7b8a74c..23483a500b3 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -6,7 +6,10 @@ from json import loads
 
 from bx.seq.twobit import TwoBitFile
 
-from galaxy.exceptions import ObjectNotFound
+from galaxy.exceptions import (
+    MissingDataError,
+    ObjectNotFound,
+)
 from galaxy.util.bunch import Bunch
 
 log = logging.getLogger(__name__)
@@ -118,6 +121,9 @@ class Genome:
         #   (b) whether there are previous, next chroms;
         #   (c) index of start chrom.
         #
+        if not self.len_file:
+            raise MissingDataError(f'len_file not set for {self.key}')
+
         len_file_enumerate = enumerate(open(self.len_file))
         chroms = {}
         prev_chroms = False
diff --git a/lib/galaxy_test/api/test_genomes.py b/lib/galaxy_test/api/test_genomes.py
index d5ba568373b..b50af8b8bfe 100644
--- a/lib/galaxy_test/api/test_genomes.py
+++ b/lib/galaxy_test/api/test_genomes.py
@@ -1,4 +1,7 @@
-from galaxy.exceptions import ObjectNotFound
+from galaxy.exceptions import (
+    MissingDataError,
+    ObjectNotFound,
+)
 from ._framework import ApiTestCase
 
 
@@ -13,3 +16,9 @@ class GenomesApiTestCase(ApiTestCase):
         response = self._get('genomes/invalid')
         self._assert_status_code_is(response, 404)
         assert response.json()['err_code'] == ObjectNotFound.err_code.code
+
+    def test_show_missing_data(self):
+        # 'anoGam3' is a valid id, but its anoGam3.len file will be missing on a new instance
+        response = self._get('genomes/anoGam3')
+        self._assert_status_code_is(response, 500)
+        assert response.json()['err_code'] == MissingDataError.err_code.code

From a18eafdd880be3c8204b02bf177b971da237d551 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 28 Jan 2021 00:13:17 -0500
Subject: [PATCH 05/17] Close some files

...and cross your fingers: no tests.
---
 lib/galaxy/visualization/genomes.py | 146 ++++++++++++++--------------
 1 file changed, 75 insertions(+), 71 deletions(-)

diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 23483a500b3..a88a886c796 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -124,69 +124,70 @@ class Genome:
         if not self.len_file:
             raise MissingDataError(f'len_file not set for {self.key}')
 
-        len_file_enumerate = enumerate(open(self.len_file))
-        chroms = {}
-        prev_chroms = False
-        start_index = 0
-        if chrom:
-            # Use starting chrom to start list.
-            found = False
-            count = 0
-            for line_num, line in len_file_enumerate:
-                if line.startswith("#"):
-                    continue
-                name, len = line.split("\t")
-                if found:
-                    chroms[name] = int(len)
-                    count += 1
-                elif name == chrom:
-                    # Found starting chrom.
-                    chroms[name] = int(len)
-                    count += 1
-                    found = True
-                    start_index = line_num
-                    if line_num != 0:
-                        prev_chroms = True
-                if count >= num:
-                    break
-        else:
-            # Use low to start list.
-            high = low + int(num)
-            prev_chroms = (low != 0)
-            start_index = low
+        with open(self.len_file) as f:
+            len_file_enumerate = enumerate(f)
+            chroms = {}
+            prev_chroms = False
+            start_index = 0
+            if chrom:
+                # Use starting chrom to start list.
+                found = False
+                count = 0
+                for line_num, line in len_file_enumerate:
+                    if line.startswith("#"):
+                        continue
+                    name, len = line.split("\t")
+                    if found:
+                        chroms[name] = int(len)
+                        count += 1
+                    elif name == chrom:
+                        # Found starting chrom.
+                        chroms[name] = int(len)
+                        count += 1
+                        found = True
+                        start_index = line_num
+                        if line_num != 0:
+                            prev_chroms = True
+                    if count >= num:
+                        break
+            else:
+                # Use low to start list.
+                high = low + int(num)
+                prev_chroms = (low != 0)
+                start_index = low
 
-            # Read chrom data from len file.
-            for line_num, line in len_file_enumerate:
-                if line_num < low:
-                    continue
-                if line_num >= high:
-                    break
-                if line.startswith("#"):
-                    continue
-                # LEN files have format:
-                #   <chrom_name><tab><chrom_length>
-                fields = line.split("\t")
-                chroms[fields[0]] = int(fields[1])
+                # Read chrom data from len file.
+                for line_num, line in len_file_enumerate:
+                    if line_num < low:
+                        continue
+                    if line_num >= high:
+                        break
+                    if line.startswith("#"):
+                        continue
+                    # LEN files have format:
+                    #   <chrom_name><tab><chrom_length>
+                    fields = line.split("\t")
+                    chroms[fields[0]] = int(fields[1])
 
-        # Set flag to indicate whether there are more chroms after list.
-        next_chroms = False
-        try:
-            next(len_file_enumerate)
-            next_chroms = True
-        except StopIteration:
-            # No more chroms to read.
-            pass
+            # Set flag to indicate whether there are more chroms after list.
+            next_chroms = False
+            try:
+                next(len_file_enumerate)
+                next_chroms = True
+            except StopIteration:
+                # No more chroms to read.
+                pass
 
-        to_sort = [{'chrom': chrm, 'len': length} for chrm, length in chroms.items()]
-        to_sort.sort(key=lambda _: split_by_number(_['chrom']))
-        return {
-            'id': self.key,
-            'reference': self.twobit_file is not None,
-            'chrom_info': to_sort,
-            'prev_chroms': prev_chroms,
-            'next_chroms': next_chroms,
-            'start_index': start_index
-        }
+            to_sort = [{'chrom': chrm, 'len': length} for chrm, length in chroms.items()]
+            to_sort.sort(key=lambda _: split_by_number(_['chrom']))
+            return {
+                'id': self.key,
+                'reference': self.twobit_file is not None,
+                'chrom_info': to_sort,
+                'prev_chroms': prev_chroms,
+                'next_chroms': next_chroms,
+                'start_index': start_index
+            }
 
 
 class Genomes:
@@ -215,13 +216,15 @@ class Genomes:
         if twobit_table is None:
             # Add genome data (twobit files) to genomes, directly from twobit.loc
             try:
-                for line in open(os.path.join(self.app.config.tool_data_path, "twobit.loc")):
-                    if line.startswith("#"):
-                        continue
-                    val = line.split()
-                    if len(val) == 2:
-                        key, path = val
-                        twobit_fields[key] = path
+                twobit_path = os.path.join(self.app.config.tool_data_path, "twobit.loc")
+                with open(twobit_path) as f:
+                    for line in f:
+                        if line.startswith("#"):
+                            continue
+                        val = line.split()
+                        if len(val) == 2:
+                            key, path = val
+                            twobit_fields[key] = path
             except OSError:
                 # Thrown if twobit.loc does not exist.
                 log.exception("Error reading twobit.loc")
@@ -394,9 +397,10 @@ class Genomes:
 
         # Read and return reference data.
         try:
-            twobit = TwoBitFile(open(twobit_file_name, 'rb'))
-            if chrom in twobit:
-                seq_data = twobit[chrom].get(int(low), int(high))
-                return GenomeRegion(chrom=chrom, start=low, end=high, sequence=seq_data)
+            with open(twobit_file_name, 'rb') as f:
+                twobit = TwoBitFile(f)
+                if chrom in twobit:
+                    seq_data = twobit[chrom].get(int(low), int(high))
+                    return GenomeRegion(chrom=chrom, start=low, end=high, sequence=seq_data)
         except OSError:
             return None

From f135af6efe303f604c9df98eca1806f9c9d5a5b3 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 29 Jan 2021 02:40:22 -0500
Subject: [PATCH 06/17] Add integration tests to cover essential cases

---
 lib/galaxy/visualization/genomes.py |  6 +--
 lib/galaxy_test/api/test_genomes.py | 24 ----------
 test/integration/test_genomes.py    | 69 +++++++++++++++++++++++++++++
 3 files changed, 72 insertions(+), 27 deletions(-)
 delete mode 100644 lib/galaxy_test/api/test_genomes.py
 create mode 100644 test/integration/test_genomes.py

diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index a88a886c796..b342c78ad9a 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -90,6 +90,9 @@ class Genome:
         """
         Returns representation of self as a dictionary.
         """
+        # if there's no len_file, there's nothing to return
+        if not self.len_file:
+            raise MissingDataError(f'len_file not set for {self.key}')
 
         def check_int(s):
             if s.isdigit():
@@ -121,9 +124,6 @@ class Genome:
         #   (b) whether there are previous, next chroms;
         #   (c) index of start chrom.
         #
-        if not self.len_file:
-            raise MissingDataError(f'len_file not set for {self.key}')
-
         with open(self.len_file) as f:
             len_file_enumerate = enumerate(f)
             chroms = {}
diff --git a/lib/galaxy_test/api/test_genomes.py b/lib/galaxy_test/api/test_genomes.py
deleted file mode 100644
index b50af8b8bfe..00000000000
--- a/lib/galaxy_test/api/test_genomes.py
+++ /dev/null
@@ -1,24 +0,0 @@
-from galaxy.exceptions import (
-    MissingDataError,
-    ObjectNotFound,
-)
-from ._framework import ApiTestCase
-
-
-class GenomesApiTestCase(ApiTestCase):
-
-    def test_index(self):
-        response = self._get('genomes')
-        self._assert_status_code_is(response, 200)
-        assert response.json()[0][0] == 'unspecified (?)'
-
-    def test_show_invalid(self):
-        response = self._get('genomes/invalid')
-        self._assert_status_code_is(response, 404)
-        assert response.json()['err_code'] == ObjectNotFound.err_code.code
-
-    def test_show_missing_data(self):
-        # 'anoGam3' is a valid id, but its anoGam3.len file will be missing on a new instance
-        response = self._get('genomes/anoGam3')
-        self._assert_status_code_is(response, 500)
-        assert response.json()['err_code'] == MissingDataError.err_code.code
diff --git a/test/integration/test_genomes.py b/test/integration/test_genomes.py
new file mode 100644
index 00000000000..01bfa2b9549
--- /dev/null
+++ b/test/integration/test_genomes.py
@@ -0,0 +1,69 @@
+from galaxy.exceptions import (
+    MissingDataError,
+    ObjectNotFound,
+)
+from galaxy.visualization.genomes import Genome
+from galaxy_test.driver import integration_util
+
+
+class MockGenome:
+    MOCK = {'a': 1, 'b': 2}
+
+    def to_dict(*args, **kwgs):
+        return MockGenome.MOCK
+
+
+class GenomesTestCase(integration_util.IntegrationTestCase):
+
+    def test_index(self):
+        gen1, gen2 = 1, 2
+        try:
+            orig = self._app.genomes.get_dbkeys
+            self._app.genomes.get_dbkeys = lambda *args, **kwgs: [gen1, gen2]
+            response = self._get('genomes')
+            self._assert_status_code_is(response, 200)
+            assert response.json() == [gen1, gen2]
+        except Exception as e:
+            raise e
+        finally:
+            self._app.genomes.get_dbkeys = orig
+
+    def test_show_valid(self):
+        mock_key, mock_genome = 'foo', MockGenome()
+        try:
+            orig = self._app.genomes.genomes
+            self._app.genomes.genomes = {mock_key: mock_genome}
+            response = self._get(f'genomes/{mock_key}')
+            self._assert_status_code_is(response, 200)
+            assert response.json() == MockGenome.MOCK
+        except Exception as e:
+            raise e
+        finally:
+            self._app.genomes.genomes = orig
+
+    def test_show_valid_missing(self):
+        # Will call the real to_dict(), which should raise an error because foo has no len_file.
+        mock_key, genome = 'foo', Genome('a', 'desc')
+        try:
+            orig = self._app.genomes.genomes
+            self._app.genomes.genomes = {mock_key: genome}
+            response = self._get(f'genomes/{mock_key}')
+            self._assert_status_code_is(response, 500)
+            assert response.json()['err_code'] == MissingDataError.err_code.code
+        except Exception as e:
+            raise e
+        finally:
+            self._app.genomes.genomes = orig
+
+    def test_show_invalid(self):
+        mock_key, mock_genome = 'foo', MockGenome()
+        try:
+            orig = self._app.genomes.genomes
+            self._app.genomes.genomes = {mock_key: mock_genome}
+            response = self._get('genomes/invalid')
+            self._assert_status_code_is(response, 404)
+            assert response.json()['err_code'] == ObjectNotFound.err_code.code
+        except Exception as e:
+            raise e
+        finally:
+            self._app.genomes.genomes = orig

From bfcb473888a88a7689533f3bbccbbe3f8efc09ad Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 29 Jan 2021 17:30:33 -0500
Subject: [PATCH 07/17] Config test instance instead of mocking

---
 test/integration/test_genomes.py | 108 +++++++++++++++++--------------
 1 file changed, 58 insertions(+), 50 deletions(-)

diff --git a/test/integration/test_genomes.py b/test/integration/test_genomes.py
index 01bfa2b9549..fbc66efca8e 100644
--- a/test/integration/test_genomes.py
+++ b/test/integration/test_genomes.py
@@ -1,69 +1,77 @@
+import os
+
 from galaxy.exceptions import (
     MissingDataError,
     ObjectNotFound,
 )
-from galaxy.visualization.genomes import Genome
 from galaxy_test.driver import integration_util
 
+BUILDS_DATA = (
+    '?\tunspecified (?)',
+    'hg_test\tdescription of hg_test',
+    'hg_test_nolen\tdescription of hg_test_nolen',
+)
 
-class MockGenome:
-    MOCK = {'a': 1, 'b': 2}
+LEN_DATA = (
+    'chr1\t248956422',
+    'chr2\t242193529',
+    'chr3\t198295559',
+)
 
-    def to_dict(*args, **kwgs):
-        return MockGenome.MOCK
+
+def get_key(has_len_file=True):
+    pos = 1 if has_len_file else 2
+    return BUILDS_DATA[pos].split('\t')[0]
 
 
 class GenomesTestCase(integration_util.IntegrationTestCase):
 
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        genomes_dir = cls.temp_config_dir("test_genomes")
+        os.makedirs(genomes_dir)
+        cls._setup_builds_file(config, genomes_dir)
+        cls._setup_len_file(config, genomes_dir)
+
+    @classmethod
+    def _setup_builds_file(cls, config, genomes_dir):
+        """Create builds file + set config option."""
+        builds_file_path = os.path.join(genomes_dir, 'builds.txt')
+        config['builds_file_path'] = builds_file_path
+        with open(builds_file_path, 'w') as f:
+            f.write('\n'.join(BUILDS_DATA))
+
+    @classmethod
+    def _setup_len_file(cls, config, genomes_dir):
+        """Create len file + set config option."""
+        config['len_file_path'] = genomes_dir  # the config option is a dir
+        key = get_key()
+        len_file_path = os.path.join(genomes_dir, f'{key}.len')
+        with open(len_file_path, 'w') as f:
+            f.write('\n'.join(LEN_DATA))
+
     def test_index(self):
-        gen1, gen2 = 1, 2
-        try:
-            orig = self._app.genomes.get_dbkeys
-            self._app.genomes.get_dbkeys = lambda *args, **kwgs: [gen1, gen2]
-            response = self._get('genomes')
-            self._assert_status_code_is(response, 200)
-            assert response.json() == [gen1, gen2]
-        except Exception as e:
-            raise e
-        finally:
-            self._app.genomes.get_dbkeys = orig
+        response = self._get('genomes')
+        self._assert_status_code_is(response, 200)
+        rval = response.json()
+        expected_data = [item.split('\t')[::-1] for item in BUILDS_DATA]
+        assert rval == expected_data
 
     def test_show_valid(self):
-        mock_key, mock_genome = 'foo', MockGenome()
-        try:
-            orig = self._app.genomes.genomes
-            self._app.genomes.genomes = {mock_key: mock_genome}
-            response = self._get(f'genomes/{mock_key}')
-            self._assert_status_code_is(response, 200)
-            assert response.json() == MockGenome.MOCK
-        except Exception as e:
-            raise e
-        finally:
-            self._app.genomes.genomes = orig
+        key = get_key()
+        response = self._get(f'genomes/{key}')
+        self._assert_status_code_is(response, 200)
+        rval = response.json()
+        assert rval['id'] == key
+        assert len(rval['chrom_info']) == len(LEN_DATA)
 
     def test_show_valid_missing(self):
-        # Will call the real to_dict(), which should raise an error because foo has no len_file.
-        mock_key, genome = 'foo', Genome('a', 'desc')
-        try:
-            orig = self._app.genomes.genomes
-            self._app.genomes.genomes = {mock_key: genome}
-            response = self._get(f'genomes/{mock_key}')
-            self._assert_status_code_is(response, 500)
-            assert response.json()['err_code'] == MissingDataError.err_code.code
-        except Exception as e:
-            raise e
-        finally:
-            self._app.genomes.genomes = orig
+        key = get_key(has_len_file=False)
+        response = self._get(f'genomes/{key}')
+        self._assert_status_code_is(response, 500)
+        assert response.json()['err_code'] == MissingDataError.err_code.code
 
     def test_show_invalid(self):
-        mock_key, mock_genome = 'foo', MockGenome()
-        try:
-            orig = self._app.genomes.genomes
-            self._app.genomes.genomes = {mock_key: mock_genome}
-            response = self._get('genomes/invalid')
-            self._assert_status_code_is(response, 404)
-            assert response.json()['err_code'] == ObjectNotFound.err_code.code
-        except Exception as e:
-            raise e
-        finally:
-            self._app.genomes.genomes = orig
+        response = self._get('genomes/invalid')
+        self._assert_status_code_is(response, 404)
+        assert response.json()['err_code'] == ObjectNotFound.err_code.code

From 626c0f7d107f907c6b548b000d02dcd662e66311 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 1 Feb 2021 14:09:36 -0500
Subject: [PATCH 08/17] Remove unused `reference` keyword from endpoint

Added in https://github.com/galaxyproject/galaxy/pull/2939 but
apparently not used.
---
 lib/galaxy/webapps/galaxy/api/genomes.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/genomes.py b/lib/galaxy/webapps/galaxy/api/genomes.py
index 453a53e0b49..6c505333f15 100644
--- a/lib/galaxy/webapps/galaxy/api/genomes.py
+++ b/lib/galaxy/webapps/galaxy/api/genomes.py
@@ -73,7 +73,5 @@ class GenomesController(BaseAPIController):
         want a raw return, not json
         """
         id = get_id(id, kwd.get('format', None))
-        reference = is_true(kwd.get('reference', False))
-        assert reference
         region = self.app.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
         return region.sequence

From 561cd9971905a799fe26d94f9959d23ded7111f7 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 1 Feb 2021 22:05:06 -0500
Subject: [PATCH 09/17] Improve error handling; modify exception

ReferenceDataError is more appropriate than MissingDataError
---
 lib/galaxy/exceptions/__init__.py      |  4 ++--
 lib/galaxy/exceptions/error_codes.json |  4 ++--
 lib/galaxy/visualization/genomes.py    | 13 ++++++++-----
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/exceptions/__init__.py b/lib/galaxy/exceptions/__init__.py
index 34c02448e14..c79d1f9c8c6 100644
--- a/lib/galaxy/exceptions/__init__.py
+++ b/lib/galaxy/exceptions/__init__.py
@@ -221,9 +221,9 @@ class InvalidFileFormatError(MessageException):
     err_code = error_codes_by_name['INVALID_FILE_FORMAT']
 
 
-class MissingDataError(MessageException):
+class ReferenceDataError(MessageException):
     status_code = 500
-    err_code = error_codes_by_name['MISSING_DATA_ERROR']
+    err_code = error_codes_by_name['REFERENCE_DATA_ERROR']
 
 
 # non-web exceptions
diff --git a/lib/galaxy/exceptions/error_codes.json b/lib/galaxy/exceptions/error_codes.json
index 054f8ee999c..4a746065df1 100644
--- a/lib/galaxy/exceptions/error_codes.json
+++ b/lib/galaxy/exceptions/error_codes.json
@@ -160,9 +160,9 @@
     "message": "File format not supported for this operation."
    },
    {
-    "name": "MISSING_DATA_ERROR",
+    "name": "REFERENCE_DATA_ERROR",
     "code": 500006,
-    "message": "Data required for program execution is missing."
+    "message": "Reference data required for program execution failed to load."
    },
    {
     "name": "NOT_IMPLEMENTED",
diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index b342c78ad9a..1da998bb0df 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -7,7 +7,7 @@ from json import loads
 from bx.seq.twobit import TwoBitFile
 
 from galaxy.exceptions import (
-    MissingDataError,
+    ReferenceDataError,
     ObjectNotFound,
 )
 from galaxy.util.bunch import Bunch
@@ -92,7 +92,7 @@ class Genome:
         """
         # if there's no len_file, there's nothing to return
         if not self.len_file:
-            raise MissingDataError(f'len_file not set for {self.key}')
+            raise ReferenceDataError(f'len_file not set for {self.key}')
 
         def check_int(s):
             if s.isdigit():
@@ -375,7 +375,7 @@ class Genomes:
             dbkey_user = trans.user
 
         if not self.has_reference_data(dbkey, dbkey_user):
-            return None
+            raise ReferenceDataError(f"No reference data for {dbkey}")
 
         #
         # Get twobit file with reference data.
@@ -395,6 +395,9 @@ class Genomes:
                 twobit_dataset = fasta_dataset.get_converted_dataset(trans, 'twobit')
                 twobit_file_name = twobit_dataset.file_name
 
+        return self._get_reference_data()
+
+    def _get_reference_data():
         # Read and return reference data.
         try:
             with open(twobit_file_name, 'rb') as f:
@@ -402,5 +405,5 @@ class Genomes:
                 if chrom in twobit:
                     seq_data = twobit[chrom].get(int(low), int(high))
                     return GenomeRegion(chrom=chrom, start=low, end=high, sequence=seq_data)
-        except OSError:
-            return None
+        except OSError as e:
+            raise e()

From 5a3eab3fd18afca73ef2b34e358baa7aadd73cbf Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 1 Feb 2021 22:20:20 -0500
Subject: [PATCH 10/17] Add tests for sequences and indexes endpoints

---
 test/integration/test_genomes.py | 40 +++++++++++++++++++++++++++++---
 1 file changed, 37 insertions(+), 3 deletions(-)

diff --git a/test/integration/test_genomes.py b/test/integration/test_genomes.py
index fbc66efca8e..50556ebee0b 100644
--- a/test/integration/test_genomes.py
+++ b/test/integration/test_genomes.py
@@ -1,8 +1,10 @@
 import os
+import tempfile
+from unittest.mock import patch
 
 from galaxy.exceptions import (
-    MissingDataError,
     ObjectNotFound,
+    ReferenceDataError,
 )
 from galaxy_test.driver import integration_util
 
@@ -65,13 +67,45 @@ class GenomesTestCase(integration_util.IntegrationTestCase):
         assert rval['id'] == key
         assert len(rval['chrom_info']) == len(LEN_DATA)
 
-    def test_show_valid_missing(self):
+    def test_show_valid_no_refdata(self):
         key = get_key(has_len_file=False)
         response = self._get(f'genomes/{key}')
         self._assert_status_code_is(response, 500)
-        assert response.json()['err_code'] == MissingDataError.err_code.code
+        assert response.json()['err_code'] == ReferenceDataError.err_code.code
 
     def test_show_invalid(self):
         response = self._get('genomes/invalid')
         self._assert_status_code_is(response, 404)
         assert response.json()['err_code'] == ObjectNotFound.err_code.code
+
+    def test_sequences(self):
+
+        class RefDataMock:
+            sequence = 'test-value'
+
+        key = get_key()
+        with patch.object(self._app.genomes, 'has_reference_data', return_value=True), \
+                patch.object(self._app.genomes, '_get_reference_data', return_value=RefDataMock()):
+            response = self._get(f'genomes/{key}/sequences')
+            self._assert_status_code_is(response, 200)
+            assert response.content == bytes(RefDataMock.sequence, 'utf-8')
+
+    def test_sequences_no_data(self):
+        key = get_key()
+        with patch.object(self._app.genomes, 'has_reference_data', return_value=False):
+            response = self._get(f'genomes/{key}/sequences')
+            self._assert_status_code_is(response, 500)
+            assert response.json()['err_code'] == ReferenceDataError.err_code.code
+
+    def test_indexes(self):
+        mock_key, mock_content, index_type, suffix = 'mykey', 'mydata', 'fasta_indexes', '.fai'
+        # write some data to a tempfile
+        with tempfile.NamedTemporaryFile(dir=self._tempdir, suffix=suffix, mode="w", delete=False) as tf:
+            tf.write(mock_content)
+        # make a mock containing the path to the tempfile
+        tmpfile_path = tf.name[:-len(suffix)]  # chop off the extention
+        mock_data = [[mock_key, tmpfile_path]]
+        with patch.object(self._app.tool_data_tables.data_tables[index_type], 'data', new=mock_data):
+            response = self._get(f'genomes/{mock_key}/indexes?type={index_type}')
+            self._assert_status_code_is(response, 200)
+            assert response.content == bytes(mock_content, 'utf-8')

From f184fa90fbc51a301e87698da8642972cc0d54a5 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 1 Feb 2021 22:35:02 -0500
Subject: [PATCH 11/17] Add proper error handling to endpoint, refactor

This is the first step in refactoring this endpoint (now that it's
covered by a test, we can finally do that).
---
 lib/galaxy/visualization/genomes.py      |  6 ++---
 lib/galaxy/webapps/galaxy/api/genomes.py | 30 ++++++++++++++++++++----
 2 files changed, 28 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 1da998bb0df..41cd442ae66 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -7,8 +7,8 @@ from json import loads
 from bx.seq.twobit import TwoBitFile
 
 from galaxy.exceptions import (
-    ReferenceDataError,
     ObjectNotFound,
+    ReferenceDataError,
 )
 from galaxy.util.bunch import Bunch
 
@@ -395,9 +395,9 @@ class Genomes:
                 twobit_dataset = fasta_dataset.get_converted_dataset(trans, 'twobit')
                 twobit_file_name = twobit_dataset.file_name
 
-        return self._get_reference_data()
+        return self._get_reference_data(twobit_file_name, chrom, low, high)
 
-    def _get_reference_data():
+    def _get_reference_data(twobit_file_name, chrom, low, high):
         # Read and return reference data.
         try:
             with open(twobit_file_name, 'rb') as f:
diff --git a/lib/galaxy/webapps/galaxy/api/genomes.py b/lib/galaxy/webapps/galaxy/api/genomes.py
index 6c505333f15..c370ee98298 100644
--- a/lib/galaxy/webapps/galaxy/api/genomes.py
+++ b/lib/galaxy/webapps/galaxy/api/genomes.py
@@ -1,3 +1,7 @@
+from galaxy.exceptions import (
+    ReferenceDataError,
+    RequestParameterInvalidException,
+)
 from galaxy.web import (
     expose_api_anonymous,
     expose_api_raw_anonymous,
@@ -54,15 +58,31 @@ class GenomesController(BaseAPIController):
         Returns all available indexes for a genome id for type={table name}
         For instance, /api/genomes/hg19/indexes?type=fasta_indexes
         """
-        index_extensions = {'fasta_indexes': '.fai'}
         id = get_id(id, kwd.get('format', None))
         index_type = kwd.get('type', None)
+        index_filename = self._get_index_filename(id, index_type)
+        try:
+            fh = open(index_filename, mode='r')
+        except OSError:
+            raise ReferenceDataError(f'Failed to load index file for {id}')
+        else:
+            return fh.read()
+
+    def _get_index_filename(self, id, index_type):
+        index_extensions = {'fasta_indexes': '.fai'}
+        if index_type not in index_extensions:
+            raise RequestParameterInvalidException(f'Invalid index type: {index_type}')
 
         tbl_entries = self.app.tool_data_tables.data_tables[index_type].data
-        index_file_name = [x[-1] for x in tbl_entries if id in x].pop()
-
-        if_open = open(index_file_name + index_extensions[index_type], mode='r')
-        return if_open.read()
+        try:
+            paths = [x[-1] for x in tbl_entries if id in x]
+            index_file_name = paths.pop()
+        except TypeError:
+            raise ReferenceDataError('Data tables not found for {index_type}')
+        except IndexError:
+            raise ReferenceDataError('Data tables not found for {index_type} for {id}')
+        else:
+            return index_file_name + index_extensions[index_type]
 
     @expose_api_raw_anonymous
     def sequences(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd):

From 5876d6d503381206bb690fcdbc983b8420a75477 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Tue, 2 Feb 2021 15:49:57 -0500
Subject: [PATCH 12/17] Do not expunge_all

Causes DetachedInstanceError
when accessing trans.get_user().preferences
(See https://docs.sqlalchemy.org/en/13/errors.html#error-bhk3)
---
 lib/galaxy/webapps/galaxy/api/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/__init__.py b/lib/galaxy/webapps/galaxy/api/__init__.py
index 4665a075b70..027bf619b0a 100644
--- a/lib/galaxy/webapps/galaxy/api/__init__.py
+++ b/lib/galaxy/webapps/galaxy/api/__init__.py
@@ -77,7 +77,7 @@ def get_user(galaxy_session: Optional[model.GalaxySession] = Depends(get_session
 def get_trans(app: UniverseApplication = Depends(get_app), user: Optional[User] = Depends(get_user),
               galaxy_session: Optional[model.GalaxySession] = Depends(get_session),
               ) -> SessionRequestContext:
-    app.model.session.expunge_all()
+    # app.model.session.expunge_all()
     return SessionRequestContext(app=app, user=user, galaxy_session=galaxy_session)
 
 

From bda6c048daea54e8d2193f6001d3076b66fe306e Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 5 Feb 2021 15:01:35 -0500
Subject: [PATCH 13/17] Remove unused **kwd parameter

---
 lib/galaxy/visualization/genomes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 41cd442ae66..507747eac15 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -256,7 +256,7 @@ class Genomes:
             rval = self.genomes[dbkey]
         return rval
 
-    def get_dbkeys(self, trans, chrom_info=False, **kwd):
+    def get_dbkeys(self, trans, chrom_info=False):
         """ Returns all known dbkeys. If chrom_info is True, only dbkeys with
             chromosome lengths are returned. """
         self.check_and_reload()

From d1729c2d8b8cc43c2fafe1562ad06322d5f360c6 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 5 Feb 2021 15:21:29 -0500
Subject: [PATCH 14/17] Simplify method call: we need user, not trans

---
 lib/galaxy/visualization/genomes.py                    | 9 +++------
 lib/galaxy/webapps/galaxy/controllers/visualization.py | 5 +++--
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 507747eac15..8c8e265cb39 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -256,18 +256,15 @@ class Genomes:
             rval = self.genomes[dbkey]
         return rval
 
-    def get_dbkeys(self, trans, chrom_info=False):
+    def get_dbkeys(self, user, chrom_info=False):
         """ Returns all known dbkeys. If chrom_info is True, only dbkeys with
             chromosome lengths are returned. """
         self.check_and_reload()
         dbkeys = []
 
         # Add user's custom keys to dbkeys.
-        user_keys_dict = {}
-        user = trans.get_user()
-        if user:
-            if 'dbkeys' in user.preferences:
-                user_keys_dict = loads(user.preferences['dbkeys'])
+        if user and 'dbkeys' in user.preferences:
+            user_keys_dict = loads(user.preferences['dbkeys'])
             dbkeys.extend([(attributes['name'], key) for key, attributes in user_keys_dict.items()])
 
         # Add app keys to dbkeys.
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index e4a1056a560..ea8e4857a69 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -541,6 +541,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         id = kwd.get('id')
         if not id:
             return self.message_exception(trans, 'No visualization id received for editing.')
+        trans_user = trans.get_user()
         v = self.get_visualization(trans, id, check_ownership=True)
         if trans.request.method == 'GET':
             if v.slug is None:
@@ -562,7 +563,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
                     'type': 'select',
                     'optional': True,
                     'value': v.dbkey,
-                    'options': trans.app.genomes.get_dbkeys(trans, chrom_info=True),
+                    'options': trans.app.genomes.get_dbkeys(trans_user, chrom_info=True),
                     'help': 'Parameter to associate your visualization with a database key.'
                 }, {
                     'name': 'annotation',
@@ -590,7 +591,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
                 v.dbkey = v_dbkey
                 if v_annotation:
                     v_annotation = sanitize_html(v_annotation)
-                    self.add_item_annotation(trans.sa_session, trans.get_user(), v, v_annotation)
+                    self.add_item_annotation(trans.sa_session, trans_user, v, v_annotation)
                 trans.sa_session.add(v)
                 trans.sa_session.flush()
             return {'message': 'Attributes of \'%s\' successfully saved.' % v.title, 'status': 'success'}

From f8efaa87500d163b6ae675a02557b2ef0352a612 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 8 Feb 2021 16:06:18 -0500
Subject: [PATCH 15/17] Add fastaapi controller, manager, typing; refactor

---
 lib/galaxy/managers/genomes.py           |  78 +++++++++
 lib/galaxy/webapps/galaxy/api/genomes.py | 211 ++++++++++++++++++-----
 lib/galaxy/webapps/galaxy/fast_app.py    |   4 +
 3 files changed, 246 insertions(+), 47 deletions(-)
 create mode 100644 lib/galaxy/managers/genomes.py

diff --git a/lib/galaxy/managers/genomes.py b/lib/galaxy/managers/genomes.py
new file mode 100644
index 00000000000..623f6f4f1dd
--- /dev/null
+++ b/lib/galaxy/managers/genomes.py
@@ -0,0 +1,78 @@
+from typing import (
+    Any,
+    List,
+)
+
+from galaxy import model as m
+from galaxy.exceptions import (
+    ReferenceDataError,
+    RequestParameterInvalidException,
+)
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.structured_app import StructuredApp
+
+
+class GenomesManager:
+
+    def __init__(self, app: StructuredApp):
+        self._app = app
+        self.genomes = app.genomes
+
+    def get_dbkeys(self, user: m.User, chrom_info: bool) -> List[List[str]]:
+        return self.genomes.get_dbkeys(user, chrom_info)
+
+    def get_genome(
+        self,
+        trans: ProvidesUserContext,
+        id: str,
+        num: int,
+        chrom: str,
+        low: int,
+        high: int,
+        reference: bool
+    ) -> Any:
+        if reference:
+            region = self.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
+            return {'dataset_type': 'refseq', 'data': region.sequence}
+        else:
+            return self.genomes.chroms(trans, dbkey=id, num=num, chrom=chrom, low=low)
+
+    def get_sequence(
+        self,
+        trans: ProvidesUserContext,
+        id: str,
+        chrom: str,
+        low: int,
+        high: int
+    ) -> Any:
+        region = self.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
+        return region.sequence
+
+    def get_indexes(self, id: str, index_type: str) -> Any:
+        index_extensions = {'fasta_indexes': '.fai'}
+        if index_type not in index_extensions:
+            raise RequestParameterInvalidException(f'Invalid index type: {index_type}')
+
+        tbl_entries = self._app.tool_data_tables.data_tables[index_type].data
+        ext = index_extensions[index_type]
+        index_filename = self._get_index_filename(id, tbl_entries, ext, index_type)
+
+        try:
+            fh = open(index_filename, mode='r')
+        except OSError:
+            raise ReferenceDataError(f'Failed to load index file for {id}')
+        else:
+            return fh.read()
+        finally:
+            fh.close()
+
+    def _get_index_filename(self, id, tbl_entries, ext, index_type):
+        try:
+            paths = [x[-1] for x in tbl_entries if id in x]
+            file_name = paths.pop()
+        except TypeError:
+            raise ReferenceDataError('Data tables not found for {index_type}')
+        except IndexError:
+            raise ReferenceDataError('Data tables not found for {index_type} for {id}')
+        else:
+            return f"{file_name}{ext}"
diff --git a/lib/galaxy/webapps/galaxy/api/genomes.py b/lib/galaxy/webapps/galaxy/api/genomes.py
index c370ee98298..28f738824e4 100644
--- a/lib/galaxy/webapps/galaxy/api/genomes.py
+++ b/lib/galaxy/webapps/galaxy/api/genomes.py
@@ -1,33 +1,183 @@
-from galaxy.exceptions import (
-    ReferenceDataError,
-    RequestParameterInvalidException,
+from typing import (
+    Any,
+    List,
 )
+
+from fastapi import (
+    Depends,
+    Path,
+    Query,
+)
+from fastapi.responses import Response
+from fastapi_utils.cbv import cbv
+from fastapi_utils.inferring_router import InferringRouter as APIRouter
+
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.managers.genomes import GenomesManager
+from galaxy.structured_app import StructuredApp
 from galaxy.web import (
     expose_api_anonymous,
     expose_api_raw_anonymous,
 )
 from galaxy.web.framework.helpers import is_true
 from galaxy.webapps.base.controller import BaseAPIController
+from . import (
+    get_app,
+    get_trans,
+)
+
+router = APIRouter(tags=['genomes'])
+
+IdPathParam: str = Path(
+    ...,
+    title='Genome ID',
+    description='Genome ID'
+)
+
+ChromInfoQueryParam: bool = Query(
+    None,
+    title='ChromInfo',
+    description='If true, return genome keys with chromosome lengths'
+)
+
+NumQueryParam: int = Query(
+    None,
+    title='Number',
+    description='Limits size of returned data',
+)
+
+ChromQueryParam: Any = Query(
+    None,
+    title='Chrom',
+    description='Limits size of returned data',
+)
+
+LowQueryParam: int = Query(
+    None,
+    title='Low',
+    description='Limits size of returned data',
+)
+
+HighQueryParam: int = Query(
+    None,
+    title='High',
+    description='Limits size of returned data',
+)
+
+FormatQueryParam: str = Query(
+    None,
+    title='Format',
+    description='Format'
+)
+
+ReferenceQueryParam: bool = Query(
+    None,
+    title='Reference',
+    description='If true, return reference data'
+)
+
+IndexTypeQueryParam: str = Query(
+    'fasta_indexes',  # currently this is the only supported index type
+    title='Index type',
+    description='Index type'
+)
+
+
+def get_genomes_manager(app: StructuredApp = Depends(get_app)) -> GenomesManager:
+    return GenomesManager(app)
 
 
 def get_id(base, format):
     if format:
         return f"{base}.{format}"
-    else:
-        return base
+    return base
+
+
+@cbv(router)
+class FastAPIGenomes:
+    manager: GenomesManager = Depends(get_genomes_manager)
+
+    @router.get(
+        '/api/genomes',
+        summary='Return a list of installed genomes',
+        response_description='Installed genomes'
+    )
+    def index(
+        self,
+        trans: ProvidesUserContext = Depends(get_trans),
+        chrom_info: bool = ChromInfoQueryParam
+    ) -> List[List[str]]:
+        return self.manager.get_dbkeys(trans.user, chrom_info)
+
+    @router.get(
+        '/api/genomes/{id}',
+        summary='Return information about build <id>',
+        response_description='Information about genome build <id>'
+    )
+    def show(
+        self,
+        trans: ProvidesUserContext = Depends(get_trans),
+        id: str = IdPathParam,
+        reference: bool = ReferenceQueryParam,
+        num: int = NumQueryParam,
+        chrom: str = ChromQueryParam,
+        low: int = LowQueryParam,
+        high: int = HighQueryParam,
+        format: str = FormatQueryParam,
+    ) -> Any:
+        id = get_id(id, format)
+        return self.manager.get_genome(trans, id, num, chrom, low, high, reference)
+
+    @router.get(
+        '/api/genomes/{id}/indexes',
+        summary='Return all available indexes for a genome id for provided type',
+        response_description='Indexes for a genome id for provided type'
+    )
+    def indexes(
+        self,
+        id: str = IdPathParam,
+        type: str = IndexTypeQueryParam,
+        format: str = FormatQueryParam,
+    ) -> Any:
+        id = get_id(id, format)
+        rval = self.manager.get_indexes(id, type)
+        return Response(rval)
+
+    @router.get(
+        '/api/genomes/{id}/sequences',
+        summary='Return raw sequence data',
+        response_description='Raw sequence data'
+    )
+    def sequences(
+        self,
+        trans: ProvidesUserContext = Depends(get_trans),
+        id: str = IdPathParam,
+        reference: bool = ReferenceQueryParam,
+        chrom: str = ChromQueryParam,
+        low: int = LowQueryParam,
+        high: int = HighQueryParam,
+        format: str = FormatQueryParam,
+    ) -> Any:
+        id = get_id(id, format)
+        rval = self.manager.get_sequence(trans, id, chrom, low, high)
+        return Response(rval)
 
 
 class GenomesController(BaseAPIController):
     """
     RESTful controller for interactions with genome data.
     """
+    def __init__(self, app: StructuredApp):
+        super().__init__(app)
+        self.manager = GenomesManager(app)
 
     @expose_api_anonymous
     def index(self, trans, **kwd):
         """
         GET /api/genomes: returns a list of installed genomes
         """
-        return self.app.genomes.get_dbkeys(trans, **kwd)
+        chrom_info = kwd.get('chrom_info')
+        return self.manager.get_dbkeys(trans.user, chrom_info)
 
     @expose_api_anonymous
     def show(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd):
@@ -36,19 +186,9 @@ class GenomesController(BaseAPIController):
 
         Returns information about build <id>
         """
-
-        # Process kwds.
-        id = get_id(id, kwd.get('format', None))
+        id = get_id(id, kwd.get('format'))
         reference = is_true(kwd.get('reference', False))
-
-        # Return info.
-        rval = None
-        if reference:
-            region = self.app.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
-            rval = {'dataset_type': 'refseq', 'data': region.sequence}
-        else:
-            rval = self.app.genomes.chroms(trans, dbkey=id, num=num, chrom=chrom, low=low)
-        return rval
+        return self.manager.get_genome(trans, id, num, chrom, low, high, reference)
 
     @expose_api_raw_anonymous
     def indexes(self, trans, id, **kwd):
@@ -58,40 +198,17 @@ class GenomesController(BaseAPIController):
         Returns all available indexes for a genome id for type={table name}
         For instance, /api/genomes/hg19/indexes?type=fasta_indexes
         """
-        id = get_id(id, kwd.get('format', None))
-        index_type = kwd.get('type', None)
-        index_filename = self._get_index_filename(id, index_type)
-        try:
-            fh = open(index_filename, mode='r')
-        except OSError:
-            raise ReferenceDataError(f'Failed to load index file for {id}')
-        else:
-            return fh.read()
-
-    def _get_index_filename(self, id, index_type):
-        index_extensions = {'fasta_indexes': '.fai'}
-        if index_type not in index_extensions:
-            raise RequestParameterInvalidException(f'Invalid index type: {index_type}')
-
-        tbl_entries = self.app.tool_data_tables.data_tables[index_type].data
-        try:
-            paths = [x[-1] for x in tbl_entries if id in x]
-            index_file_name = paths.pop()
-        except TypeError:
-            raise ReferenceDataError('Data tables not found for {index_type}')
-        except IndexError:
-            raise ReferenceDataError('Data tables not found for {index_type} for {id}')
-        else:
-            return index_file_name + index_extensions[index_type]
+        id = get_id(id, kwd.get('format'))
+        index_type = kwd.get('type')
+        return self.manager.get_indexes(id, index_type)
 
     @expose_api_raw_anonymous
-    def sequences(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd):
+    def sequences(self, trans, id, chrom=None, low=None, high=None, **kwd):
         """
         GET /api/genomes/{id}/sequences
 
         This is a wrapper for accepting sequence requests that
         want a raw return, not json
         """
-        id = get_id(id, kwd.get('format', None))
-        region = self.app.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
-        return region.sequence
+        id = get_id(id, kwd.get('format'))
+        return self.manager.get_sequence(trans, id, chrom, low, high)
diff --git a/lib/galaxy/webapps/galaxy/fast_app.py b/lib/galaxy/webapps/galaxy/fast_app.py
index d5bd24f7130..d46204354d1 100644
--- a/lib/galaxy/webapps/galaxy/fast_app.py
+++ b/lib/galaxy/webapps/galaxy/fast_app.py
@@ -24,6 +24,10 @@ api_tags_metadata = [
         "name": "datatypes",
         "description": "Operations with supported data types.",
     },
+    {
+        "name": "genomes",
+        "description": "Operations with genome data.",
+    },
     {
         "name": "licenses",
         "description": "Operations with [SPDX licenses](https://spdx.org/licenses/).",

From e3c9969be73bebe77e24ec25106f53c13a217eab Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 10 Feb 2021 15:54:07 -0500
Subject: [PATCH 16/17] Remove comment

---
 lib/galaxy/webapps/galaxy/api/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/__init__.py b/lib/galaxy/webapps/galaxy/api/__init__.py
index 027bf619b0a..02e2669397a 100644
--- a/lib/galaxy/webapps/galaxy/api/__init__.py
+++ b/lib/galaxy/webapps/galaxy/api/__init__.py
@@ -77,7 +77,6 @@ def get_user(galaxy_session: Optional[model.GalaxySession] = Depends(get_session
 def get_trans(app: UniverseApplication = Depends(get_app), user: Optional[User] = Depends(get_user),
               galaxy_session: Optional[model.GalaxySession] = Depends(get_session),
               ) -> SessionRequestContext:
-    # app.model.session.expunge_all()
     return SessionRequestContext(app=app, user=user, galaxy_session=galaxy_session)
 
 

From 16a420c9660819a3f7c15e7775bd470f42b80d1e Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Thu, 11 Feb 2021 10:40:45 -0500
Subject: [PATCH 17/17] Use context manager to open file

---
 lib/galaxy/managers/genomes.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/managers/genomes.py b/lib/galaxy/managers/genomes.py
index 623f6f4f1dd..f0970982756 100644
--- a/lib/galaxy/managers/genomes.py
+++ b/lib/galaxy/managers/genomes.py
@@ -56,15 +56,11 @@ class GenomesManager:
         tbl_entries = self._app.tool_data_tables.data_tables[index_type].data
         ext = index_extensions[index_type]
         index_filename = self._get_index_filename(id, tbl_entries, ext, index_type)
-
         try:
-            fh = open(index_filename, mode='r')
+            with open(index_filename, mode='r') as f:
+                return f.read()
         except OSError:
             raise ReferenceDataError(f'Failed to load index file for {id}')
-        else:
-            return fh.read()
-        finally:
-            fh.close()
 
     def _get_index_filename(self, id, tbl_entries, ext, index_type):
         try: