django.db.utils.OperationalError: no such table: main.core_analysistype__old #7
Comments
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It may be an issue of missing some steps during database setup. Can you
double check that you followed the instructions in our documentation (
https://github.com/ubccr/genesysv/blob/master/docs/source/index.rst) step
by step?
Jason
…On Mon, Apr 27, 2020 at 9:14 PM Matthew J. Oldach ***@***.***> wrote:
I'm getting an error trying to install/run genesysv. After following the
installation examples the following code is *partially* working. I'm able
to open but something in the error isn't loading the example data in
properly.
(genesysv) ***@***.***:~/bin/GenESysV$ python manage.py runserver 0.0.0.0:8000
Performing system checks...
System check identified no issues (0 silenced).
April 27, 2020 - 21:03:38
Django version 2.0.5, using settings 'genesysv.settings'
Starting development server at http://0.0.0.0:8000/
Quit the server with CONTROL-C.
I'm able to open local host and login:
[image: Screenshot from 2020-04-27 19-12-42]
<https://user-images.githubusercontent.com/5749465/80435961-30f75980-88bb-11ea-99b3-f81c0100a653.png>
but cannot click on anything (pretty sure the example is the next part).
Trying the example
(genesysv) ***@***.***:~/bin/GenESysV$ python utils/load_vcf.py --vcf test_data/test_4families_annovar.vcf.gz --tmp_dir /tmp --annot annovar --hostname 127.0.0.1 --port 9200 --index test_4families_annovar --study_name test_4families_annovar --dataset_name test_4families_annovar --num_cores 4 --assembly hg19 --ped test_data/test_4families.ped --cleanup
Pid 25941: processed 5000 variants
Pid 25942: processed 5000 variants
Pid 25944: processed 5000 variants
Pid 25943: processed 5000 variants
Pid 25941: processed 10000 variants
Pid 25944: processed 10000 variants
Pid 25942: processed 10000 variants
Pid 25943: processed 10000 variants
Pid 25941: processed 12501 variants
Process 25941 finished ...
Pid 25942: processed 12501 variants
Pid 25944: processed 12498 variants
Process 25942 finished ...
Pid 25943: processed 12501 variants
Process 25943 finished ...
Process 25944 finished ...
Finished parsing vcf file in 11.873375177383423 seconds, now creating ElasticSearch index ...
deleting 'test_4families_annovar' index...
response: '{'acknowledged': True}'
creating 'test_4families_annovar' index...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 590 100 98 100 492 1689 8482 --:--:-- --:--:-- --:--:-- 10000
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 25391 100 28 100 25363 1750 1548k --:--:-- --:--:-- --:--:-- 1549k
Response: '{
"acknowledged" : true,
"shards_acknowledged" : true,
"index" : "test_4families_annovar"
}
{
"acknowledged" : true
}
'
Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_0.json
Took: 3.564603328704834 seconds
Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_1.json
Took: 3.5286946296691895 seconds
Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_2.json
Took: 3.4319169521331787 seconds
Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_3.json
Took: 3.6023032665252686 seconds
Finished creating ES index, parsing time: 11.873375177383423 seconds, indexing time: 14.294233560562134 seconds, vcf: test_data/test_4families_annovar.vcf.gz
Creating Web user interface, please wait ...
Unmapped GUI CLNVAR_nested
Unmapped GUI COSMIC_nested
Unmapped GUI GTEx_nested
Unmapped GUI ICGC_nested
Unmapped GUI RGQ
Unmapped GUI mendelian_diseases
Unmapped GUI RGQ
Unmapped GUI mendelian_diseases
********************************************************************************
Study Name: test_4families_annovar
Dataset Name: test_4families_annovar_hg19
Dataset ES Index Name: test_4families_annovar
Dataset ES Type Name: test_4families_annovar_
Dataset ES Host: 127.0.0.1
Dataset ES Port: 9200
Traceback (most recent call last):
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 85, in _execute
return self.cursor.execute(sql, params)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/sqlite3/base.py", line 303, in execute
return Database.Cursor.execute(self, query, params)
sqlite3.OperationalError: no such table: main.core_analysistype__old
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "utils/load_vcf.py", line 1715, in <module>
make_gui(es, hostname, port, index_name, study, dataset_name, type_name, gui_mapping)
File "/home/mtg/bin/GenESysV/utils/make_gui.py", line 961, in make_gui
dataset_obj.analysis_type.add(*a)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/fields/related_descriptors.py", line 898, in add
self._add_items(self.source_field_name, self.target_field_name, *objs)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/fields/related_descriptors.py", line 1065, in _add_items
for obj_id in new_ids
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/query.py", line 466, in bulk_create
ids = self._batched_insert(objs_without_pk, fields, batch_size)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/query.py", line 1148, in _batched_insert
self._insert(item, fields=fields, using=self.db)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/query.py", line 1125, in _insert
return query.get_compiler(using=using).execute_sql(return_id)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/sql/compiler.py", line 1283, in execute_sql
cursor.execute(sql, params)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 100, in execute
return super().execute(sql, params)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 68, in execute
return self._execute_with_wrappers(sql, params, many=False, executor=self._execute)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 77, in _execute_with_wrappers
return executor(sql, params, many, context)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 85, in _execute
return self.cursor.execute(sql, params)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/utils.py", line 89, in __exit__
raise dj_exc_value.with_traceback(traceback) from exc_value
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 85, in _execute
return self.cursor.execute(sql, params)
File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/sqlite3/base.py", line 303, in execute
return Database.Cursor.execute(self, query, params)
django.db.utils.OperationalError: no such table: main.core_analysistype__old
Not sure what I'm missing.
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Could the error be happening here: I've gone into Then I run Trying this again: It say's:
I'm running |
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Looks like the java can not longer be downloaded from that site. I suggest
that you search the web to find a solution to download and install java 8.
…On Tue, Apr 28, 2020 at 11:41 AM Matthew J. Oldach ***@***.***> wrote:
Could the error be happening here:
(base) ***@***.***:~$ sudo add-apt-repository -y ppa:webupd8team/java
Ign:1 http://dl.google.com/linux/chrome/deb stable InRelease
Hit:2 https://dl.yarnpkg.com/debian stable InRelease
Hit:3 http://dl.google.com/linux/chrome/deb stable Release
Hit:4 http://ca.archive.ubuntu.com/ubuntu eoan InRelease
Hit:5 http://ca.archive.ubuntu.com/ubuntu eoan-updates InRelease
Ign:6 http://ppa.launchpad.net/webupd8team/java/ubuntu eoan InRelease
Hit:7 http://ca.archive.ubuntu.com/ubuntu eoan-backports InRelease
Hit:9 http://security.ubuntu.com/ubuntu eoan-security InRelease
Err:10 http://ppa.launchpad.net/webupd8team/java/ubuntu eoan Release
404 Not Found [IP: 2001:67c:1560:8008::15 80]
Reading package lists... Done
E: The repository 'http://ppa.launchpad.net/webupd8team/java/ubuntu eoan Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration details.
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Okay I've updated to Now I get errors running the Despite having run |
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Looks like you have anaconda3 installed and its on your path: This could be the source of trouble. Can you try to remove it from your env? |
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Hi @jianxinwang I've deactivated This time it looks like the issue is it cannot find So next I exit If I open the python and try to Trying to install pip this way then forces How do I fix this issue? |
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Hi Matt,
I recommend that you start an installation from a clean ubuntu environment
or do a test install on a virtualbox running Ubuntu as guest OS. I found
that elasticsearch is now on version 7 and it came with Java bundled with
it (I found it out using v7.6.2). However, it has some changes that make it
incompatible with v6.3.0 used in our current GenESysV. I'm now in the
process of migrating our code to work under recent versions of
elasticsearch.
Jason
…On Wed, May 20, 2020 at 11:52 AM Matthew J. Oldach ***@***.***> wrote:
Hi @jianxinwang <https://github.com/jianxinwang>
I've deactivated conda and tried again.
(base) ***@***.***:~/bin/GenESysV$ conda deactivate
***@***.***:~/bin/GenESysV$ source venv/bin/activate
This time it looks like the issue is it cannot find elasticsearch -
although I installed it and tested:
(venv) ***@***.***:~$ wget -qO - https://packages.elastic.co/GPG-KEY-elasticsearch | sudo apt-key add -
OK
(venv) ***@***.***:~$ wget https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-6.1.3.deb
--2020-05-20 09:45:35-- https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-6.1.3.deb
Resolving artifacts.elastic.co (artifacts.elastic.co)... 2a04:4e42:d::734, 151.101.54.222
Connecting to artifacts.elastic.co (artifacts.elastic.co)|2a04:4e42:d::734|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 28379628 (27M) [binary/octet-stream]
Saving to: ‘elasticsearch-6.1.3.deb’
elasticsearch-6.1.3.deb 100%[=============================>] 27.06M 6.54MB/s in 4.6s
2020-05-20 09:45:40 (5.94 MB/s) - ‘elasticsearch-6.1.3.deb’ saved [28379628/28379628]
(venv) ***@***.***:~$ sudo dpkg -i elasticsearch-6.1.3.deb
(Reading database ... 249736 files and directories currently installed.)
Preparing to unpack elasticsearch-6.1.3.deb ...
Unpacking elasticsearch (6.1.3) over (6.1.3) ...
Setting up elasticsearch (6.1.3) ...
Processing triggers for systemd (245.4-4ubuntu3) ...
(venv) ***@***.***:~$ sudo su -
***@***.***:~# nano /etc/elasticsearch/jvm.options
***@***.***:~# nano /etc/elasticsearch/elasticsearch.yml
***@***.***:~# systemctl daemon-reload
***@***.***:~# systemctl enable elasticsearch.service
Synchronizing state of elasticsearch.service with SysV service script with /lib/systemd/systemd-sysv-install.
Executing: /lib/systemd/systemd-sysv-install enable elasticsearch
***@***.***:~# systemctl start elasticsearch.service
***@***.***:~# curl 127.0.0.1:9200
{
"name" : "fC5Em3D",
"cluster_name" : "elasticsearch",
"cluster_uuid" : "paQ90Q54TNyBYqaI-A_0GQ",
"version" : {
"number" : "6.1.3",
"build_hash" : "af51318",
"build_date" : "2018-01-26T18:22:55.523Z",
"build_snapshot" : false,
"lucene_version" : "7.1.0",
"minimum_wire_compatibility_version" : "5.6.0",
"minimum_index_compatibility_version" : "5.0.0"
},
"tagline" : "You Know, for Search"
}
So next I exit root (I'm now within the Python3.5 venv and not Conda) and
then try the example:
***@***.***:~# exit
logout
(venv) ***@***.***:~$ cd ~/bin/GenESysV/
(venv) ***@***.***:~/bin/GenESysV$ python utils/load_vcf.py --vcf test_data/test_4families_annovar.vcf.gz --tmp_dir /tmp --annot annovar --hostname 127.0.0.1 --port 9200 --index test_4families_annovar --study_name test_4families_annovar --dataset_name test_4families_annovar --num_cores 4 --assembly hg19 --ped test_data/test_4families.ped --cleanup
Traceback (most recent call last):
File "utils/load_vcf.py", line 21, in <module>
import elasticsearch
ImportError: No module named 'elasticsearch'
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Hi Matt, I have updated our code to make it work on recent versions of Elasticsearch. The installation process had been simplified a bit. Please pull the new code and give it a try. Hopefully this will work out-of-the-box. |
I opened a new issue for a clean Ubuntu 20.04 OS on a VM (above.)
I will continue to troubleshoot this for my computer here. |
|
Pulling the new code I get the following error: |
|
Looks like your elasticserch is not running yet. You need to start it first.
…On Thu, May 28, 2020 at 2:13 PM Matthew J. Oldach ***@***.***> wrote:
Pulling the new code I get the following error:
^C(venv) ***@***.***:~/bin/GenESysV$ python utils/load_vcf.py --vcf test_data/test_4families_annovar.vcf.gz --tmp_dir /tmp --annot annovar --hostname 127.0.0.1 --port 9200 --index test_4families_annovar --study_name test_4families_annovar --dataset_name test_4families_annovar --num_cores 4 --assembly hg19 --ped test_data/test_4families.ped --cleanup
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610e8c88>: Failed to establish a new connection: [Errno 111] Connection refused
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610e8d68>: Failed to establish a new connection: [Errno 111] Connection refused
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610fc0b8>: Failed to establish a new connection: [Errno 111] Connection refused
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610e8e10>: Failed to establish a new connection: [Errno 111] Connection refused
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610e8c88>: Failed to establish a new connection: [Errno 111] Connection refused
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610e8400>: Failed to establish a new connection: [Errno 111] Connection refused
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610e82b0>: Failed to establish a new connection: [Errno 111] Connection refused
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff261156c88>: Failed to establish a new connection: [Errno 111] Connection refused
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610fc160>: Failed to establish a new connection: [Errno 111] Connection refused
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610fcba8>: Failed to establish a new connection: [Errno 111] Connection refused
GET http://127.0.0.1:9200/_cluster/health?wait_for_status=yellow [status:N/A request:0.000s]
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610fcc88>: Failed to establish a new connection: [Errno 111] Connection refused
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 83, in create_connection
raise err
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/connection.py", line 73, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 166, in perform_request
response = self.pool.urlopen(method, url, body, retries=False, headers=request_headers, **kw)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 333, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 686, in reraise
raise value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 357, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/home/mtg/.pyenv/versions/3.6.0/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 166, in connect
conn = self._new_conn()
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7ff2610fcc88>: Failed to establish a new connection: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "utils/load_vcf.py", line 1587, in <module>
es.cluster.health(wait_for_status='yellow')
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/client/utils.py", line 76, in _wrapped
return func(*args, params=params, **kwargs)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/client/cluster.py", line 33, in health
'health', index), params=params)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/transport.py", line 314, in perform_request
status, headers_response, data = connection.perform_request(method, url, params, body, headers=headers, ignore=ignore, timeout=timeout)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/elasticsearch/connection/http_urllib3.py", line 175, in perform_request
raise ConnectionError('N/A', str(e), e)
elasticsearch.exceptions.ConnectionError: ConnectionError(<urllib3.connection.HTTPConnection object at 0x7ff2610fcc88>: Failed to establish a new connection: [Errno 111] Connection refused) caused by: NewConnectionError(<urllib3.connection.HTTPConnection object at 0x7ff2610fcc88>: Failed to establish a new connection: [Errno 111] Connection refused)
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Ahhh okay, right. So I run Then open another window and run the following: |
|
Did you run these two lines? python manage.py makemigrations core These commands create and populate the sqlite tables. |
|
I thought I had but maybe I didn't? Trying again: Able to run the following: now run Close it with |
|
I tried a fresh install on a Ubuntu18.04 box. I can not reproduce the
error, everything worked fine. Did you see any error messages when you
execute these two lines?
pip install wheel
pip install -r requirements.txt
…On Thu, May 28, 2020 at 7:10 PM Matthew J. Oldach ***@***.***> wrote:
I thought I had but maybe I didn't?
Trying again:
(venv) (base) ***@***.***:~/bin/GenESysV$ python manage.py makemigrations core
No changes detected in app 'core'
(venv) (base) ***@***.***:~/bin/GenESysV$ python manage.py migrate
Operations to perform:
Apply all migrations: admin, auth, contenttypes, core, sessions
Running migrations:
No migrations to apply.
Able to run the following:
~/elasticsearch-7.7.0/bin/elasticsearch # then open a new terminal
now run
python manage.py runserver 0.0.0.0:8000
Close it with Ctrl + C and then tried
(venv) (base) ***@***.***:~/bin/GenESysV$ python utils/load_vcf.py --vcf test_data/test_4families_annovar.vcf.gz --tmp_dir /tmp --annot annovar --hostname 127.0.0.1 --port 9200 --index test_4families_annovar --study_name test_4families_annovar --dataset_name test_4families_annovar --num_cores 4 --assembly hg19 --ped test_data/test_4families.ped --cleanup
Pid 161606: processed 5000 variants
Pid 161607: processed 5000 variants
Pid 161605: processed 5000 variants
Pid 161604: processed 5000 variants
Pid 161606: processed 10000 variants
Pid 161604: processed 10000 variants
Pid 161607: processed 10000 variants
Pid 161605: processed 10000 variants
Pid 161606: processed 12501 variants
Pid 161604: processed 12501 variants
Process 161604 finished ...
Pid 161607: processed 12498 variants
Pid 161605: processed 12501 variants
Process 161605 finished ...
Process 161606 finished ...
Process 161607 finished ...
Finished parsing vcf file in 21.185588836669922 seconds, now creating ElasticSearch index ...
deleting 'test_4families_annovar' index...
response: '{'acknowledged': True}'
creating 'test_4families_annovar' index...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 590 100 98 100 492 453 2277 --:--:-- --:--:-- --:--:-- 2731
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 23038 100 28 100 23010 528 423k --:--:-- --:--:-- --:--:-- 424k
Response: '{
"acknowledged" : true,
"shards_acknowledged" : true,
"index" : "test_4families_annovar"
}
{
"acknowledged" : true
}
'
Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_0.json
Took: 5.210810899734497 seconds
Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_1.json
Took: 4.1324498653411865 seconds
Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_2.json
Took: 4.524986743927002 seconds
Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_3.json
Took: 4.066014051437378 seconds
Finished creating ES index, parsing time: 21.185588836669922 seconds, indexing time: 18.4201762676239 seconds, vcf: test_data/test_4families_annovar.vcf.gz
Creating Web user interface, please wait ...
Unmapped GUI CLNVAR_nested
Unmapped GUI COSMIC_nested
Unmapped GUI GTEx_nested
Unmapped GUI ICGC_nested
Unmapped GUI RGQ
Unmapped GUI mendelian_diseases
Unmapped GUI RGQ
Unmapped GUI mendelian_diseases
********************************************************************************
Study Name: test_4families_annovar
Dataset Name: test_4families_annovar_hg19
Dataset ES Index Name: test_4families_annovar
Dataset ES Type Name: test_4families_annovar_
Dataset ES Host: 127.0.0.1
Dataset ES Port: 9200
Traceback (most recent call last):
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/backends/utils.py", line 85, in _execute
return self.cursor.execute(sql, params)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/backends/sqlite3/base.py", line 303, in execute
return Database.Cursor.execute(self, query, params)
sqlite3.OperationalError: no such table: main.core_analysistype__old
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "utils/load_vcf.py", line 1715, in <module>
make_gui(es, hostname, port, index_name, study, dataset_name, type_name, gui_mapping)
File "/home/mtg/bin/GenESysV/utils/make_gui.py", line 959, in make_gui
dataset_obj.analysis_type.add(*a)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/models/fields/related_descriptors.py", line 898, in add
self._add_items(self.source_field_name, self.target_field_name, *objs)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/models/fields/related_descriptors.py", line 1065, in _add_items
for obj_id in new_ids
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/models/query.py", line 466, in bulk_create
ids = self._batched_insert(objs_without_pk, fields, batch_size)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/models/query.py", line 1148, in _batched_insert
self._insert(item, fields=fields, using=self.db)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/models/query.py", line 1125, in _insert
return query.get_compiler(using=using).execute_sql(return_id)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/models/sql/compiler.py", line 1283, in execute_sql
cursor.execute(sql, params)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/backends/utils.py", line 100, in execute
return super().execute(sql, params)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/backends/utils.py", line 68, in execute
return self._execute_with_wrappers(sql, params, many=False, executor=self._execute)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/backends/utils.py", line 77, in _execute_with_wrappers
return executor(sql, params, many, context)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/backends/utils.py", line 85, in _execute
return self.cursor.execute(sql, params)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/utils.py", line 89, in __exit__
raise dj_exc_value.with_traceback(traceback) from exc_value
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/backends/utils.py", line 85, in _execute
return self.cursor.execute(sql, params)
File "/home/mtg/bin/GenESysV/venv/lib/python3.6/site-packages/django/db/backends/sqlite3/base.py", line 303, in execute
return Database.Cursor.execute(self, query, params)
django.db.utils.OperationalError: no such table: main.core_analysistype__old
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I'm using Ubuntu 20.04 not 18.04. When trying to run |
|
Yes, try to comment pkg-resources==0.0.0 out. Can you try ubuntu18.04?
Since we have not tested ubuntu 20.04 yet.
…On Fri, May 29, 2020 at 2:08 PM Matthew J. Oldach ***@***.***> wrote:
I'm using Ubuntu 20.04 not 18.04.
When trying to run pip install -r requirements.txt I get an error from
pkg-resources==0.0.0 which caused the script to stop at that line. I
needed to comment it out with #:
ERROR: Could not find a version that satisfies the requirement pkg-resources==0.0.0 (from -r requirements.txt (line 38)) (from versions: none)
ERROR: No matching distribution found for pkg-resources==0.0.0 (from -r requirements.txt (line 38))
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I reproduce this error in docker container, too. I solve it by upgrade Django from 2.0.5 to 2.1.15 Maybe it's related to this thread https://stackoverflow.com/questions/53637182/django-no-such-table-main-auth-user-old |
|
It is possibly related to Ubuntu. I got the same error if I use Ubuntu 20.
The problem went away when I switched back to Ubuntu 18.
Jason
…On Tue, Jun 15, 2021 at 9:03 AM linnil1 ***@***.***> wrote:
I reproduce this error in docker container, too.
I solve it by upgrade Django from 2.0.5 to 2.1.15
Maybe it's related to this thread
https://stackoverflow.com/questions/53637182/django-no-such-table-main-auth-user-old
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I'm getting an error trying to install/run
genesysv. After following the installation examples the following code is partially working. I'm able to open but something in the error isn't loading the example data in properly.I'm able to open local host and login:
but cannot click on anything (pretty sure the example is the next part).
Trying the example
Not sure what I'm missing.
The text was updated successfully, but these errors were encountered: