Hi All,
I intended to resume download of files (synapse -p ${token} get -r syn51365301) which was paused for larger disk space. I ran the command-line without problem but it refused to start now,
The error message is as as follows,
Traceback (most recent call last):
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/bin/synapse", line 8, in
sys.exit(main())
^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/__main__.py", line 1841, in main
syn = synapseclient.Synapse(
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/client.py", line 257, in __init__
self.setEndpoints(
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/client.py", line 373, in setEndpoints
response = self._requests_session.get(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 602, in get
return self.request("GET", url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 575, in request
prep = self.prepare_request(req)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 486, in prepare_request
p.prepare(
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/models.py", line 368, in prepare
self.prepare_url(url, params)
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/models.py", line 439, in prepare_url
raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL '/repo/v1': No scheme supplied. Perhaps you meant https:///repo/v1?
Any idea why this happens? Initially, I used pip to install but I used the GitHub clone with similar message -- I am wondering it might be to do with change of our computer systems/version of software.
Thank you so much,
Jing Hua Zhao
Created by Jing Hua Zhao jhz Hi @bfauble,
I could tell immediately that is the cause of the problem -- I was lost with where to put the URL.
I thought I never use .synapseConfig but username/passwd & Token, however I do have it with the endpoints all missing the prefix.
Now the error message is gone and hopefully the download can be furnished upon data access is granted,
Once again great thanks to you and also to @thomas.yu for help and insights.
Best regards,
Jing Hua
Hi @jhz ,
Would you be able to check if you have a `.synapseConfig` file present at `~/.synapseConfig` - I suspect that you are defining the `repoEndpoint` in that file incorrectly. If you are using the production syanpse endpoints you can either not have an `[endpoints]` section in that file - or define it as:
```
[endpoints]
repoEndpoint=https://repo-prod.prod.sagebase.org/repo/v1
authEndpoint=https://repo-prod.prod.sagebase.org/auth/v1
fileHandleEndpoint=https://repo-prod.prod.sagebase.org/file/v1
```
The error actually remains so would need another spell to figure it out.
Strangely, it works for one of our IT staff; I loaded the same module as with .bashrc from .snapshot in June I remain have the same issue. I understand they identified some issue with storage and will need to wait until tomorrow afternoon to see it has any impact after the planned maintenance. HI @jhz
Please review this with your IT team: https://help.synapse.org/docs/Synapse-Infrastructure.2835382273.html. It appears to be an issue of login -- our system had a power outrage and back after two weeks; maybe IT has done something to make the identity different. Here are the three sessions I had:
$ **synapse -p ${token} get -r syn51365301**
Traceback (most recent call last):
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/bin/synapse", line 33, in
sys.exit(load_entry_point('synapseclient==3.1.1', 'console_scripts', 'synapse')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/__main__.py", line 1841, in main
syn = synapseclient.Synapse(
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/client.py", line 257, in __init__
self.setEndpoints(
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/client.py", line 373, in setEndpoints
response = self._requests_session.get(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 602, in get
return self.request("GET", url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 575, in request
prep = self.prepare_request(req)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 486, in prepare_request
p.prepare(
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/models.py", line 368, in prepare
self.prepare_url(url, params)
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/models.py", line 439, in prepare_url
raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL '/repo/v1': No scheme supplied. Perhaps you meant https:///repo/v1?
$ **synapse login -p ${token}**
Traceback (most recent call last):
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/bin/synapse", line 33, in
sys.exit(load_entry_point('synapseclient==3.1.1', 'console_scripts', 'synapse')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/__main__.py", line 1841, in main
syn = synapseclient.Synapse(
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/client.py", line 257, in __init__
self.setEndpoints(
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/client.py", line 373, in setEndpoints
response = self._requests_session.get(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 602, in get
return self.request("GET", url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 575, in request
prep = self.prepare_request(req)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 486, in prepare_request
p.prepare(
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/models.py", line 368, in prepare
self.prepare_url(url, params)
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/models.py", line 439, in prepare_url
raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL '/repo/v1': No scheme supplied. Perhaps you meant https:///repo/v1?
$ **synapse login -u jhz -p ${token}**
Traceback (most recent call last):
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/bin/synapse", line 33, in
sys.exit(load_entry_point('synapseclient==3.1.1', 'console_scripts', 'synapse')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/__main__.py", line 1841, in main
syn = synapseclient.Synapse(
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/client.py", line 257, in __init__
self.setEndpoints(
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/synapseclient/client.py", line 373, in setEndpoints
response = self._requests_session.get(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 602, in get
return self.request("GET", url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 575, in request
prep = self.prepare_request(req)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/sessions.py", line 486, in prepare_request
p.prepare(
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/models.py", line 368, in prepare
self.prepare_url(url, params)
File "/usr/local/Cluster-Apps/ceuadmin/snakemake/7.19.1/lib/python3.11/site-packages/requests/models.py", line 439, in prepare_url
raise MissingSchema(
requests.exceptions.MissingSchema: Invalid URL '/repo/v1': No scheme supplied. Perhaps you meant https:///repo/v1?
Hi @jhz,
Sorry you're running into troubles! Some questions:
1. Is this on a completely new deployment of an environment?
2. Are you able to run `synapse login` or that `synapse get` and paste the results here?
Using pip or GitHub to install shouldn't impact it.
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