How to set up customized ip address?
iiiir opened this issue · 5 comments
I am using the docker version on my macbook at it worked:
$ docker run -it -p 5000:5000 --rm -v pwd
:/data cumulusprod/cirrocumulus cirro launch /data/pbmc3k.h5ad --host 0.0.0.0
Change IP to 127.0.0.1 will run but cannot open the link. Says "This page isn’t working":
$ docker run -it -p 5000:5000 --rm -v pwd
:/data cumulusprod/cirrocumulus cirro launch /data/pbmc3k.h5ad --host 127.0.0.1
And changing the ip address to my macbook's ip address with not run:
$ docker run -it -p 5000:5000 --rm -v pwd
:/data cumulusprod/cirrocumulus cirro launch /data/pbmc3k.h5ad --host [ip adress of my macbook]
...
OSError: [Errno 99] Cannot assign requested address
Question:
How can i set up with my ip address, or hostname?
Thanks,
Another question:
I was able to run the app with miniconda, but it cannot find files.
$ cirro launch pbmc3k.h5ad --host [host ip addr] --port 8080
[01/Aug/2020 21:46:08] "GET /api/filters?id=pbmc3k.h5ad HTTP/1.1" 200 -
[2020-08-01 21:46:08,763] ERROR in app: Exception on /api/schema [GET]
Traceback (most recent call last):
File "/apps/python/Miniconda/lib/python3.7/site-packages/flask/app.py", line 2447, in wsgi_app
response = self.full_dispatch_request()
File "/apps/python/Miniconda/lib/python3.7/site-packages/flask/app.py", line 1952, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/apps/python/Miniconda/lib/python3.7/site-packages/flask/app.py", line 1821, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/apps/python/Miniconda/lib/python3.7/site-packages/flask/_compat.py", line 39, in reraise
raise value
File "/apps/python/Miniconda/lib/python3.7/site-packages/flask/app.py", line 1950, in full_dispatch_request
rv = self.dispatch_request()
File "/apps/python/Miniconda/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request
return self.view_functionsrule.endpoint
File "/apps/python/Miniconda/lib/python3.7/site-packages/cirrocumulus/api.py", line 127, in handle_schema
return to_json(get_schema_and_dataset()[0])
File "/apps/python/Miniconda/lib/python3.7/site-packages/cirrocumulus/api.py", line 119, in get_schema_and_dataset
schema = dataset_api.schema(dataset)
File "/apps/python/Miniconda/lib/python3.7/site-packages/cirrocumulus/dataset_api.py", line 46, in schema
value = provider.schema(self.fs_adapter.get_fs(path), path)
File "/apps/python/Miniconda/lib/python3.7/site-packages/cirrocumulus/anndata_dataset.py", line 57, in schema
return SimpleData.schema(self.get_data(path))
File "/apps/python/Miniconda/lib/python3.7/site-packages/cirrocumulus/anndata_dataset.py", line 50, in get_data
adata = self.read_adata(path)
File "/apps/python/Miniconda/lib/python3.7/site-packages/cirrocumulus/anndata_dataset.py", line 33, in read_adata
return anndata.read(path, backed=self.backed)
File "/apps/python/Miniconda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 447, in read_h5ad
constructor_args = _read_args_from_h5ad(filename=filename, chunk_size=chunk_size)
File "/apps/python/Miniconda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 486, in _read_args_from_h5ad
_read_key_value_from_h5(f, d, key, chunk_size=chunk_size)
File "/apps/python/Miniconda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 510, in _read_key_value_from_h5
_read_key_value_from_h5(f, d[key_write], key + '/' + k, k, chunk_size)
File "/apps/python/Miniconda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 510, in _read_key_value_from_h5
_read_key_value_from_h5(f, d[key_write], key + '/' + k, k, chunk_size)
File "/apps/python/Miniconda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 544, in _read_key_value_from_h5
key, value = postprocess_reading(key, value)
File "/apps/python/Miniconda/lib/python3.7/site-packages/anndata/readwrite/read.py", line 541, in postprocess_reading
value = value.astype(new_dtype)
ValueError: invalid shape in fixed-type tuple.
[ip adress] - - [01/Aug/2020 21:46:08] "GET /api/schema?id=pbmc3k.h5ad HTTP/1.1" 500 -
@iiiir Thanks a lot for your interest in Cirrocumulus. @joshua-gould will look into your issue tomorrow.
Best,
Bo
Can you please confirm that the path to your h5ad file is correct?
@joshua-gould , If you are referring to my second post yes i can conform the path is correct. I was running under the same folder -- also tried full path which gave same error. HOWEVER, the run was in a conda environment, which I am not sure if the path should be specified otherwise.
The reason i use conda is because some dependent libraries cannot be installed as I am not admin for the cluster. e.g. cython and pandas (I do not have permission to uninstall older versions of cython).
I was able to run the command successfully with regular python environment (without conda), on my personal macbook.
Sorry for the delay in my response. Were you able to resolve these issues?