Merge pull request #14973 from guerler/fix_display_application (ef80595c) · Commits · NDIP / Galaxy

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

+2 −2

Original line number	Diff line number	Diff line
		@@ -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=${bgzip_file.qp}&genome=${qp($bgzip_file.dbkey)}&merge=true&name=${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 -->

+3 −2

Original line number	Diff line number	Diff line
		@@ -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

+24 −3

Original line number	Diff line number	Diff line
		@@ -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):

+2 −0

Original line number	Diff line number	Diff line
		@@ -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)
		),