Open flow for IGV viewer

[bnouyou]

Hello,
I have installed a local instance of seqr.
I have loaded the bam paths of my samples, but when I click on 'Show reads', I don't see the viewer.
On the console logs I see that the API GET URL is not accessible : http://<hostname>/api/igv_genomes/s3/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai
So I need to ask my IT to open the flow.

Can I know what is the exact URL for the fasta?

Thank you for your help.

[hanars]

Can you please check the server-side logs for seqr and include those as well

[bnouyou]

These are the docker logs when I click on 'show reads':

{"timestamp": "2024-11-07 14:52:25,556", "severity": "ERROR", "httpRequest": {"requestMethod": "GET", "requestUrl": "http://lx165/api/igv_genomes/s3/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai", "status": 500, "responseSize": 4557, "userAgent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:132.0) Gecko/20100101 Firefox/132.0", "remoteIp": "172.18.9.198", "referer": "http://lx165/variant_search/results/6dc0c6cc6fd765cb3681adcac8979622?page=1&sort=xpos", "protocol": "HTTP/1.1"}, "message": "('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))", "user": "[email protected]", "traceback": "Traceback (most recent call last):\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 710, in urlopen\n    chunked=chunked,\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 386, in _make_request\n    self._validate_conn(conn)\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 1040, in _validate_conn\n    conn.connect()\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connection.py\", line 426, in connect\n    tls_in_tls=tls_in_tls,\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/util/ssl_.py\", line 450, in ssl_wrap_socket\n    sock, context, tls_in_tls, server_hostname=server_hostname\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/util/ssl_.py\", line 493, in _ssl_wrap_socket_impl\n    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)\n  File \"/usr/local/lib/python3.7/ssl.py\", line 423, in wrap_socket\n    session=session\n  File \"/usr/local/lib/python3.7/ssl.py\", line 870, in _create\n    self.do_handshake()\n  File \"/usr/local/lib/python3.7/ssl.py\", line 1139, in do_handshake\n    self._sslobj.do_handshake()\nConnectionResetError: [Errno 104] Connection reset by peer\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n  File \"/opt/venv/lib/python3.7/site-packages/requests/adapters.py\", line 449, in send\n    timeout=timeout\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 786, in urlopen\n    method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/util/retry.py\", line 550, in increment\n    raise six.reraise(type(error), error, _stacktrace)\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/packages/six.py\", line 769, in reraise\n    raise value.with_traceback(tb)\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 710, in urlopen\n    chunked=chunked,\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 386, in _make_request\n    self._validate_conn(conn)\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 1040, in _validate_conn\n    conn.connect()\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connection.py\", line 426, in connect\n    tls_in_tls=tls_in_tls,\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/util/ssl_.py\", line 450, in ssl_wrap_socket\n    sock, context, tls_in_tls, server_hostname=server_hostname\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/util/ssl_.py\", line 493, in _ssl_wrap_socket_impl\n    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)\n  File \"/usr/local/lib/python3.7/ssl.py\", line 423, in wrap_socket\n    session=session\n  File \"/usr/local/lib/python3.7/ssl.py\", line 870, in _create\n    self.do_handshake()\n  File \"/usr/local/lib/python3.7/ssl.py\", line 1139, in do_handshake\n    self._sslobj.do_handshake()\nurllib3.exceptions.ProtocolError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n  File \"/opt/venv/lib/python3.7/site-packages/django/core/handlers/base.py\", line 181, in _get_response\n    response = wrapped_callback(request, *callback_args, **callback_kwargs)\n  File \"/seqr/seqr/views/apis/igv_api.py\", line 217, in igv_genomes_proxy\n    genome_response = requests.get(f'{CLOUD_STORAGE_URLS[cloud_host]}/{file_path}', headers=headers)\n  File \"/opt/venv/lib/python3.7/site-packages/requests/api.py\", line 76, in get\n    return request('get', url, params=params, **kwargs)\n  File \"/opt/venv/lib/python3.7/site-packages/requests/api.py\", line 61, in request\n    return session.request(method=method, url=url, **kwargs)\n  File \"/opt/venv/lib/python3.7/site-packages/requests/sessions.py\", line 542, in request\n    resp = self.send(prep, **send_kwargs)\n  File \"/opt/venv/lib/python3.7/site-packages/requests/sessions.py\", line 655, in send\n    r = adapter.send(request, **kwargs)\n  File \"/opt/venv/lib/python3.7/site-packages/requests/adapters.py\", line 498, in send\n    raise ConnectionError(err, request=request)\nrequests.exceptions.ConnectionError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))\n", "@type": "type.googleapis.com/google.devtools.clouderrorreporting.v1beta1.ReportedErrorEvent"}
{"timestamp": "2024-11-07 14:52:25,556", "severity": "ERROR", "message": "Internal Server Error: /api/igv_genomes/s3/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai", "@type": "type.googleapis.com/google.devtools.clouderrorreporting.v1beta1.ReportedErrorEvent"}
{"timestamp": "2024-11-07 14:52:31,223", "severity": "ERROR", "httpRequest": {"requestMethod": "GET", "requestUrl": "http://lx165/api/igv_genomes/s3/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai", "status": 500, "responseSize": 4557, "userAgent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:132.0) Gecko/20100101 Firefox/132.0", "remoteIp": "172.18.9.198", "referer": "http://lx165/variant_search/results/6dc0c6cc6fd765cb3681adcac8979622?page=1&sort=xpos", "protocol": "HTTP/1.1"}, "message": "('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))", "user": "[email protected]", "traceback": "Traceback (most recent call last):\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 710, in urlopen\n    chunked=chunked,\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 386, in _make_request\n    self._validate_conn(conn)\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 1040, in _validate_conn\n    conn.connect()\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connection.py\", line 426, in connect\n    tls_in_tls=tls_in_tls,\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/util/ssl_.py\", line 450, in ssl_wrap_socket\n    sock, context, tls_in_tls, server_hostname=server_hostname\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/util/ssl_.py\", line 493, in _ssl_wrap_socket_impl\n    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)\n  File \"/usr/local/lib/python3.7/ssl.py\", line 423, in wrap_socket\n    session=session\n  File \"/usr/local/lib/python3.7/ssl.py\", line 870, in _create\n    self.do_handshake()\n  File \"/usr/local/lib/python3.7/ssl.py\", line 1139, in do_handshake\n    self._sslobj.do_handshake()\nConnectionResetError: [Errno 104] Connection reset by peer\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n  File \"/opt/venv/lib/python3.7/site-packages/requests/adapters.py\", line 449, in send\n    timeout=timeout\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 786, in urlopen\n    method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/util/retry.py\", line 550, in increment\n    raise six.reraise(type(error), error, _stacktrace)\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/packages/six.py\", line 769, in reraise\n    raise value.with_traceback(tb)\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 710, in urlopen\n    chunked=chunked,\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 386, in _make_request\n    self._validate_conn(conn)\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connectionpool.py\", line 1040, in _validate_conn\n    conn.connect()\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/connection.py\", line 426, in connect\n    tls_in_tls=tls_in_tls,\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/util/ssl_.py\", line 450, in ssl_wrap_socket\n    sock, context, tls_in_tls, server_hostname=server_hostname\n  File \"/opt/venv/lib/python3.7/site-packages/urllib3/util/ssl_.py\", line 493, in _ssl_wrap_socket_impl\n    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)\n  File \"/usr/local/lib/python3.7/ssl.py\", line 423, in wrap_socket\n    session=session\n  File \"/usr/local/lib/python3.7/ssl.py\", line 870, in _create\n    self.do_handshake()\n  File \"/usr/local/lib/python3.7/ssl.py\", line 1139, in do_handshake\n    self._sslobj.do_handshake()\nurllib3.exceptions.ProtocolError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n  File \"/opt/venv/lib/python3.7/site-packages/django/core/handlers/base.py\", line 181, in _get_response\n    response = wrapped_callback(request, *callback_args, **callback_kwargs)\n  File \"/seqr/seqr/views/apis/igv_api.py\", line 217, in igv_genomes_proxy\n    genome_response = requests.get(f'{CLOUD_STORAGE_URLS[cloud_host]}/{file_path}', headers=headers)\n  File \"/opt/venv/lib/python3.7/site-packages/requests/api.py\", line 76, in get\n    return request('get', url, params=params, **kwargs)\n  File \"/opt/venv/lib/python3.7/site-packages/requests/api.py\", line 61, in request\n    return session.request(method=method, url=url, **kwargs)\n  File \"/opt/venv/lib/python3.7/site-packages/requests/sessions.py\", line 542, in request\n    resp = self.send(prep, **send_kwargs)\n  File \"/opt/venv/lib/python3.7/site-packages/requests/sessions.py\", line 655, in send\n    r = adapter.send(request, **kwargs)\n  File \"/opt/venv/lib/python3.7/site-packages/requests/adapters.py\", line 498, in send\n    raise ConnectionError(err, request=request)\nrequests.exceptions.ConnectionError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))\n", "@type": "type.googleapis.com/google.devtools.clouderrorreporting.v1beta1.ReportedErrorEvent"}
{"timestamp": "2024-11-07 14:52:31,224", "severity": "ERROR", "message": "Internal Server Error: /api/igv_genomes/s3/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai", "@type": "type.googleapis.com/google.devtools.clouderrorreporting.v1beta1.ReportedErrorEvent"}

[hanars]

the most likely case here is that you have seqr running in an environment that does nto allow it full access to the rest of the internet. This may be due to where you are running seqr and how you may have configured a firewall. if that is the case, you would need to adjust the deployment/ firewalls on your end

[bnouyou]

Yes that's it. I need to ask my IT team to allow some flows. So I would like to know the URL behind /api/igv_genomes/s3/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai .
I would like to know if it's https://s3.amazonaws.com ?
Thank you for your help.

[hanars]

The reason I am not giving you specific URLs is because seqr is unable to run without full internet access. If you unblock just s3 you will just run into a different issue a couple steps later when you try to load a different part of the IGV reference from a different source. Running seqr without full internet access is unsupported and we do not document or commit to maintaining a whitelist of required sites to access.
The seqr team has very limited bandwidth to provide support and we simply do not have the resources to help people who are using seqr in unsupported ways. If you have to run seqr in an environment without full access to the internet, you will run into many issues like this and our team can not help you with them. I hope you and your team are able to figure out how to adjust your firewalls accordingly, but I strongly recommend simply removing the firewall entirely. I am sorry we can not be more helpful.