skchronicles
commented
2 years ago Just as a heads up, I was also able to confirm this issue also exists within your Docker image for OpenCRAVAT. It may be worth using python/3.8 as your base image:
user@cn3106:/lscratch/39864423$ SINGULARITY_CACHEDIR=$PWD singularity pull -F docker://karchinlab/opencravat:latest
INFO: Converting OCI blobs to SIF format
INFO: Starting build...
Getting image source signatures
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Writing manifest to image destination
Storing signatures
2022/05/18 10:29:07 info unpack layer: sha256:955615a668ce169f8a1443fc6b6e6215f43fe0babfb4790712a2d3171f34d366
2022/05/18 10:29:09 info unpack layer: sha256:2756ef5f69a5190f4308619e0f446d95f5515eef4a814dbad0bcebbbbc7b25a8
2022/05/18 10:29:09 info unpack layer: sha256:911ea9f2bd51e53a455297e0631e18a72a86d7e2c8e1807176e80f991bde5d64
2022/05/18 10:29:10 info unpack layer: sha256:27b0a22ee906271a6ce9ddd1754fdd7d3b59078e0b57b6cc054c7ed7ac301587
2022/05/18 10:29:12 info unpack layer: sha256:8584d51a9262f9a3a436dea09ba40fa50f85802018f9bd299eee1bf538481077
2022/05/18 10:29:18 info unpack layer: sha256:db63833ee201770b3aa0d7071a972c3a03ae41d11d86061890e385fc2a41545a
2022/05/18 10:29:18 info unpack layer: sha256:670202beded7ea5f23ab5ea78f90eaf00e5f39cd978f6869c1545a725ab6946f
2022/05/18 10:29:19 info unpack layer: sha256:35e5210b09c9f1a52e3255faa346ca29df26389273a434d216abeea4ed01f7b1
2022/05/18 10:29:19 info unpack layer: sha256:b8adb6962ce28cc7a903503a1e1e1b4159aea23a4b32c9a47e8a2ec0c2b1e294
2022/05/18 10:29:19 info unpack layer: sha256:9a00cb98124dbc36c097ef6144b25eb374266d4733aaf3359b1ca29dafd52ef9
2022/05/18 10:29:20 info unpack layer: sha256:3747a1cdb3fa18f8938b8171d3c4dea0b7677db091ae48b488ecb4bc01052e13
2022/05/18 10:29:23 info unpack layer: sha256:13fe569b962f4603d95b43497cd11cc87a8a2edc77af190d6e34a7c9db408382
2022/05/18 10:29:23 info unpack layer: sha256:edbd166503d1d59c91ab1dc862bdf876149847e5594d22e3161e09964fa6c26a
INFO: Creating SIF file...
user@cn3106:/lscratch/39864423$ ll
total 442M
drwxr-xr-x. 5 root root 4.0K May 18 09:23 ..
-rw-rw---- 1 user CCBR 0 May 18 09:37 2.sqlite
-rw-rw---- 1 user CCBR 0 May 18 09:37 1.sqlite
-rw-rw---- 1 user CCBR 0 May 18 09:37 3.sqlite
drwx------ 8 user CCBR 4.0K May 18 10:28 cache
-rwxrwx--- 1 user CCBR 442M May 18 10:29 opencravat_latest.sif
drwx------ 3 user CCBR 4.0K May 18 10:29 .
user@cn3106:/lscratch/39864423$ singularity exec -B $PWD opencravat_latest.sif which oc
/usr/local/bin/oc
user@cn3106:/lscratch/39864423$ singularity exec -B $PWD opencravat_latest.sif oc util mergesqlite 1.sqlite 2.sqlite 3.sqlite -o merged.sqlite
Traceback (most recent call last):
File "/usr/local/bin/oc", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.6/site-packages/cravat/oc.py", line 220, in main
args.func(args)
File "/usr/local/lib/python3.6/site-packages/cravat/cravat_util.py", line 770, in mergesqlite
conn = sqlite3.connect(dbpaths[0])
TypeError: argument 1 must be str, not PosixPath
mryaninsilico
kmoad
Hello there,
I found a bug in the
oc util mergesqlitesubcommand.It seems to fail when OpenCRAVAT is installed with python/3.6. I haven't tested python/3.7 but it seems to work fine in python/3.8.
Description
The
oc util mergesqlitecommand fail with a TypeError in python/3.6.Here is an example:
I looked into this more, and it appears that
Pathreturns a path object in python/3.6:And this causes the
sqlite.connect()method to fail:Solution
The actual fix is pretty stright forward. You could just loop through the paths within a list comprehension and type cast the path objects to strings. There are a few different ways to fix this issue but that seems the most straight forward method.
I haven't had time to test out how this version of python effect the other sub commands. I have a feel some other commands may fail as well. With that being said, it maybe better to fix the problem at its actual cause (line 1113) when setting a type for this option:
You could just use a lambda function to type-cast the Path object to a string:
Please let me know what you think.
Best, @skchronicles