Merge branch 'release_22.05' into dev

lib/galaxy/datatypes/display_applications/configs/igv/vcf.xml

@@ -13,7 +13,7 @@
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${redirect_url}</url>
         <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" allow_cors="true" mimetype="application/octet-stream"/>
-        <param type="data" name="tabix_file" metadata="tabix_index" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" allow_cors="true" mimetype="application/octet-stream"/>
+        <param type="data" name="tabix_file" metadata="tabix_index" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" allow_cors="true" mimetype="application/octet-stream" />
         <param type="template" name="site_organism" strip="True" >
             #if ($dataset.dbkey in $site_dbkeys)
                 $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ]
@@ -95,7 +95,7 @@
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgzip_file.qp}&amp;genome=${qp($bgzip_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
         <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" mimetype="application/octet-stream"/>
-        <param type="data" name="tabix_file" metadata="tabix_index" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="vcf_bgzip" mimetype="application/octet-stream"/>
+        <param type="data" name="tabix_file" metadata="tabix_index" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" mimetype="application/octet-stream" />
     </dynamic_links>
 </display>
 <!-- Dan Blankenberg -->

lib/galaxy/datatypes/display_applications/parameters.py

@@ -100,6 +100,8 @@ class DisplayApplicationDataParameter(DisplayApplicationParameter):
         assert data, "Base dataset could not be found in values provided to DisplayApplicationDataParameter"
         if isinstance(data, DisplayDataValueWrapper):
             data = data.value
+        if data.state != data.states.OK:
+            return None
         if self.metadata:
             rval = getattr(data.metadata, self.metadata, None)
             assert rval, f'Unknown metadata name "{self.metadata}" provided for dataset type "{data.ext}".'
@@ -109,8 +111,7 @@ class DisplayApplicationDataParameter(DisplayApplicationParameter):
                 rval = data.get_converted_files_by_type(ext)
                 if rval:
                     return rval
-
-            direct_match, target_ext, converted_dataset = data.find_conversion_destination(self.formats)
+            direct_match, target_ext, _ = data.find_conversion_destination(self.formats)
             assert direct_match or target_ext is not None, f"No conversion path found for data param: {self.name}"
             return None
         return data

lib/galaxy/util/commands.py

@@ -174,7 +174,7 @@ def new_clean_env():
     Returns a minimal environment to use when invoking a subprocess
     """
     env = {}
-    for k in ("HOME", "PATH", "TMPDIR"):
+    for k in ("HOME", "LC_CTYPE", "PATH", "TMPDIR"):
         if k in os.environ:
             env[k] = os.environ[k]
     if "TMPDIR" not in env:
@@ -183,7 +183,8 @@ def new_clean_env():
     # This is needed e.g. for Python < 3.7 where
     # `locale.getpreferredencoding()` (also used by open() to determine the
     # default file encoding) would return `ANSI_X3.4-1968` without this.
-    env["LC_CTYPE"] = "C.UTF-8"
+    if not env.get("LC_CTYPE", "").endswith("UTF-8"):
+        env["LC_CTYPE"] = "C.UTF-8"
     return env
 
 

lib/galaxy/web/framework/base.py

@@ -530,20 +530,41 @@ def send_file(start_response, trans, body):
         body = [b""]
     # Fall back on sending the file in chunks
     else:
-        body = iterate_file(body)
+        trans.response.headers["accept-ranges"] = "bytes"
+        start = None
+        end = None
+        if trans.request.range:
+            start = trans.request.range.start
+            end = trans.request.range.end
+            file_size = trans.response.headers["content-length"]
+            trans.response.headers["content-length"] = str(end - start)
+            trans.response.headers["content-range"] = f"bytes {start}-{end - 1}/{file_size}"
+            trans.response.status = 206
+        body = iterate_file(body, start, end)
     start_response(trans.response.wsgi_status(), trans.response.wsgi_headeritems())
     return body
 
 
-def iterate_file(fh):
+def iterate_file(fh, start=None, stop=None):
     """
     Progressively return chunks from `file`.
     """
+    length = None
+    if start:
+        fh.seek(start)
+    if stop:
+        length = stop - start
     while 1:
-        chunk = fh.read(CHUNK_SIZE)
+        read_size = CHUNK_SIZE
+        if length:
+            read_size = min(CHUNK_SIZE, length)
+            length -= read_size
+        chunk = fh.read(read_size)
         if not chunk:
             break
         yield chunk
+        if length is not None and length == 0:
+            break
 
 
 def flatten(seq):

packages/tool_util/HISTORY.rst

@@ -3,6 +3,11 @@ History
 
 .. to_doc
 
+22.1.5 (2022-11-14)
+-------------------
+
+* Set test status to success on expected failure
+
 22.1.4 (2022-10-28)
 -------------------
 

test/unit/util/test_commands.py

@@ -0,0 +1,20 @@
+import os
+
+from galaxy.util.commands import new_clean_env
+
+
+def test_new_clean_env() -> None:
+    saved_environ = os.environ.copy()
+    os.environ["FOO"] = "foo"
+    os.environ.pop("TMPDIR", None)
+    try:
+        clean_env = new_clean_env()
+    finally:
+        os.environ.clear()
+        os.environ.update(saved_environ)
+    assert "FOO" not in clean_env
+    for k in ("HOME", "PATH"):
+        if k in saved_environ:
+            assert clean_env[k] == saved_environ[k]
+    assert clean_env["LC_CTYPE"].endswith("UTF-8")
+    assert clean_env["TMPDIR"]

test/unit/webapps/test_send_file.py

@@ -7,6 +7,7 @@ from fastapi.testclient import TestClient
 
 from galaxy.util.bunch import Bunch
 from galaxy.web.framework.base import (
+    Request,
     Response,
     send_file,
 )
@@ -18,6 +19,7 @@ def setup_fastAPI(fh, nginx_x_accel_redirect_base=None, apache_xsendfile=None):
     def wsgi_application(env, start_response):
         trans = Bunch(
             response=Response(),
+            request=Request(env),
             app=Bunch(
                 config=Bunch(nginx_x_accel_redirect_base=nginx_x_accel_redirect_base, apache_xsendfile=apache_xsendfile)
             ),