mskcc/beagle_cli

Beagle API Command Line Utility

beagle_cli's Issues

updates in lims not reflected in voyager.

A cmoid change that is in the lims has not yet registered in voyager. The two igo ids 08039_CV_1 and 08039_CN_11 both had the sample id s_C_4HX0K5_M001_d and mapped to the following two fastq pairs:

s_C_4HX0K5_M001_d	idt	/igo/delivery/FASTQ/PITT_0522_AHJV3KBBXY/Project_08039_CV/Sample_P-0027816-T02-WES_IGO_08039_CV_1/P-0027816-T02-WES_IGO_08039_CV_1_S6_R1_001.fastq.gz	/igo/delivery/FASTQ/PITT_0522_AHJV3KBBXY/Project_08039_CV/Sample_P-0027816-T02-WES_IGO_08039_CV_1/P-0027816-T02-WES_IGO_08039_CV_1_S6_R2_001.fastq.gz	2
s_C_4HX0K5_M001_d	idt	/ifs/archive/GCL/hiseq/FASTQ/PITT_0495_BHHYJGBBXY_A1/Project_08039_CN/Sample_P-0027816-T02-WES_IGO_08039_CN_11/P-0027816-T02-WES_IGO_08039_CN_11_S21_R1_001.fastq.gz	/ifs/archive/GCL/hiseq/FASTQ/PITT_0495_BHHYJGBBXY_A1/Project_08039_CN/Sample_P-0027816-T02-WES_IGO_08039_CN_11/P-0027816-T02-WES_IGO_08039_CN_11_S21_R2_001.fastq.gz	2

However, the fastq pairs related to 08039_CN_11 change cmo id, and is now known as s_C_UE1MR5_M001_d. this can be seen in the lims. after updating both requests with the following command:

singularity exec beagle_0.0.1.sif beaglecli import-requests --request-ids=08039_CN,08039_CV --redelivery=True

the changes are still not reflected in the voyager database.

Add command to redact samples

deregister script needs to delete Sample Object record, too

Add command to update partial metadata

error submitting tempo-mpgen job

I got this error, after it was working all day today

$ /opt/local/singularity/3.3.0/bin/singularity exec ~/beagle-mpgen/beagle_0.0.1.sif beaglecli tempo-mpgen
Running Tempo MPGen
ERROR: bad response from server.
<Response [500]>
Internal Server Error
{"normals_override": [], "tumors_override": []}
None

repeating the command gives the same error.

Beagle client library that can be imported from other Python programs

Methods and attributes for communicating with Beagle can be moved out of the main beaglecli file into a separate client module, so that they could be imported from other Python programs and services in order to communicate with Beagle. This would be really useful for things like the Config for handling the auth tokens, the API endpoint addresses, and the functions that run the basic Get, Create, Update, Delete methods for different endpoints. Also consider some Django-inspired wrappers such as get_or_create and update_or_create to make it easier to use, along with things like validation of the existence of Files, etc., in Beagle before trying to run operations on them.

ACCESS Linker should pull latest runs regardless of pipeline version

ACCESS Linker will first find the latest version of the pipeline, and then pull the latest runs associated with that pipeline. If latest version of the pipeline does not have any runs but an older version does, they will not be found unless they're explicitly requested. By default, we should return the latest runs available.

add capability for non-interactive login

currently to authenticate beaglecli i have to run and enter Username and Password interactively. Is there any way to pass in this information in a file for automatic usage?

Add sample redaction through cli

Low priority; for now redactions are possible through the admin panel

Something like

./beaglecli sample redact <sampleId>

# for example
./beagecli sample redact 08944_B_1

Add beagle_cli option to input/output download json given a list of run ids

beaglecli crashes immediately if it cannot connect to Beagle

beaglecli crashes immediately upon starting if it cannot connect to a Beagle instance. This prevents you from seeing the 'help' page with beaglecli -h;

$ beaglecli -h
Traceback (most recent call last):
  File "/home/kellys5/projects/beagle-dev/beagle-dev4/conda/lib/python3.7/site-packages/urllib3/connection.py", line 159, in _new_conn
    (self._dns_host, self.port), self.timeout, **extra_kw)
  File "/home/kellys5/projects/beagle-dev/beagle-dev4/conda/lib/python3.7/site-packages/urllib3/util/connection.py", line 80, in create_connection
    raise err
  File "/home/kellys5/projects/beagle-dev/beagle-dev4/conda/lib/python3.7/site-packages/urllib3/util/connection.py", line 70, in create_connection
    sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused

During handling of the above exception, another exception occurred:
....
....

It would be more helpful to allow bealgecli to delay trying to establish a connection to a Beagle instance until it actually needs one, so you can at least see the 'help' page in offline mode.