{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/oncotator/issues/355","repository_url":"https://api.github.com/repos/broadinstitute/oncotator","labels_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/355/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/355/comments","events_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/355/events","html_url":"https://github.com/broadinstitute/oncotator/issues/355","id":176008728,"number":355,"title":"Cache filename too long?","user":{"login":"lebolo","id":2286572,"avatar_url":"https://avatars.githubusercontent.com/u/2286572?v=3","gravatar_id":"","url":"https://api.github.com/users/lebolo","html_url":"https://github.com/lebolo","followers_url":"https://api.github.com/users/lebolo/followers","following_url":"https://api.github.com/users/lebolo/following{/other_user}","gists_url":"https://api.github.com/users/lebolo/gists{/gist_id}","starred_url":"https://api.github.com/users/lebolo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lebolo/subscriptions","organizations_url":"https://api.github.com/users/lebolo/orgs","repos_url":"https://api.github.com/users/lebolo/repos","events_url":"https://api.github.com/users/lebolo/events{/privacy}","received_events_url":"https://api.github.com/users/lebolo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-09-09T13:24:28Z","updated_at":"2016-10-18T14:20:08Z","closed_at":null,"body":"I'm using oncotator v1.9.0.0 and am trying to speed up the process by creating a file cache for subsequent VCF to MAF processing. I get the error pasted below.  I **think** the problem is that Linux has a filename length limit of 255 characters and the filename for this mutation is 299 characters. Before this mutation, the longest filename I see is 255 characters: \r\n\r\n`12_57870602_57870602_GGAGGGGGGGCAGGGAGGATCTTGGCCTTCACAAAGAAATGGGAGATTCACATGGGGGTCGTCCAGGAGCTGCGGCAGAGGTCGAGGGGCCTGCAAGGCT_AGCCTTGCAGGCCCCTCGACCTCTGCCGCAGCTCCTGGACGACCCCCATGTGAATCTCCCATTTCTTTGTGAAGGCCAAGATCCTCCCTGCCCCCCCTCC_16348fb8e83ab2e686dfc2a90986f498`.\r\n\r\n**Any thoughts on how I can fix this without modifying oncotator code?**\r\n\r\nJust in case, this is what my command line looks like:\r\n\r\n```\r\noncotator\r\n  --input_format=VCF\r\n  --db-dir /path/to/trimmed.cache\r\n  -c /path/to/tx_exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt\r\n  -u file:///path/to/oncotator.cache\r\n  --log_name foo.log\r\n  foo.vcf\r\n  output.maf\r\n  hg19\r\n```\r\n\r\n# Error\r\n\r\n```\r\n2016-09-09 10:12:28,501 ERROR [oncotator.output.TcgaMafOutputRenderer:333] Traceback (most recent call last):\r\n  File \"build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py\", line 321, in renderMutations\r\n    for m in mutations:\r\n  File \"build/bdist.linux-x86_64/egg/oncotator/Annotator.py\", line 448, in _applyManualAnnotations\r\n    for m in mutations:\r\n  File \"build/bdist.linux-x86_64/egg/oncotator/Annotator.py\", line 456, in _applyDefaultAnnotations\r\n    for m in mutations:\r\n  File \"build/bdist.linux-x86_64/egg/oncotator/Annotator.py\", line 523, in _annotate_mutations_using_datasources\r\n    self._cacheManager.store_annotations_in_cache(m)\r\n  File \"build/bdist.linux-x86_64/egg/oncotator/cache/CacheManager.py\", line 85, in store_annotations_in_cache\r\n    self._store_basic_annotations_in_cache(cache_key, annotations)\r\n  File \"build/bdist.linux-x86_64/egg/oncotator/cache/CacheManager.py\", line 91, in _store_basic_annotations_in_cache\r\n    self.get_cache().store_into_cache(key, annotations)\r\n  File \"build/bdist.linux-x86_64/egg/oncotator/cache/ShoveCache.py\", line 71, in store_into_cache\r\n    self.db[key] = value\r\n  File \"/opt/conda/lib/python2.7/site-packages/shove-0.6.6-py2.7.egg/shove/core.py\", line 44, in __setitem__\r\n    self.sync()\r\n  File \"/opt/conda/lib/python2.7/site-packages/shove-0.6.6-py2.7.egg/shove/core.py\", line 74, in sync\r\n    self._store.update(self._buffer)\r\n  File \"/opt/conda/lib/python2.7/_abcoll.py\", line 566, in update\r\n    self[key] = other[key]\r\n  File \"/opt/conda/lib/python2.7/site-packages/shove-0.6.6-py2.7.egg/shove/base.py\", line 123, in __setitem__\r\n    raise KeyError(key)\r\nKeyError: '12_62775059_62775301_ATTTATTATAAGTAATTATTTTGAAATTTGGGAAATGAATAGTTGAGTACATCATTTGAGTGTTTATTTGACCAGTTATTAGTGCAAGAAACCATCATTTAAATGTTCTCTGTGTTATAGCAAATCAATTTGTTTCTCTCTTCATATTAATGTGTTTTAAGAAAAATTCATTATGATTACTTTTACTTGAAAATATATTTTATTTTTTGCAGTGTTTGAGCAACACACCTCCACTTACTGAGT_-_16348fb8e83ab2e686dfc2a90986f498'\r\n\r\n2016-09-09 10:12:28,501 ERROR [oncotator.output.TcgaMafOutputRenderer:334] Error at mutation 1746159 ['12', 62775059, 62775301, 'ATTTATTATAAGTAATTATTTTGAAATTTGGGAAATGAA  TAGTTGAGTACATCATTTGAGTGTTTATTTGACCAGTTATTAGTGCAAGAAACCATCATTTAAATGTTCTCTGTGTTATAGCAAATCAATTTGTTTCTCTCTTCATATTAATGTGTTTTAAGAAAAATTCATTATGATTACTTTTACTTGAAAATATATTTTATTTTT  TGCAGTGTTTGAGCAACACACCTCCACTTACTGAGT', '-']:\r\n2016-09-09 10:12:28,501 ERROR [oncotator.output.TcgaMafOutputRenderer:335] Incomplete: rendered 1746159 mutations.\r\nTraceback (most recent call last):\r\n  File \"/opt/conda/bin/oncotator\", line 11, in <module>\r\n    load_entry_point('Oncotator==1.9.0.0', 'console_scripts', 'oncotator')()\r\n  File \"build/bdist.linux-x86_64/egg/oncotator/Oncotator.py\", line 309, in main\r\n  File \"build/bdist.linux-x86_64/egg/oncotator/Annotator.py\", line 437, in annotate\r\n  File \"build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py\", line 337, in renderMutations\r\nKeyError: '12_62775059_62775301_ATTTATTATAAGTAATTATTTTGAAATTTGGGAAATGAATAGTTGAGTACATCATTTGAGTGTTTATTTGACCAGTTATTAGTGCAAGAAACCATCATTTAAATGTTCTCTGTGTTATAGCAAATCAATTTGTTTC  TCTCTTCATATTAATGTGTTTTAAGAAAAATTCATTATGATTACTTTTACTTGAAAATATATTTTATTTTTTGCAGTGTTTGAGCAACACACCTCCACTTACTGAGT_-_16348fb8e83ab2e686dfc2a90986f498'\r\n```"},"comment":{"url":"https://api.github.com/repos/broadinstitute/oncotator/issues/comments/254522212","html_url":"https://github.com/broadinstitute/oncotator/issues/355#issuecomment-254522212","issue_url":"https://api.github.com/repos/broadinstitute/oncotator/issues/355","id":254522212,"user":{"login":"lebolo","id":2286572,"avatar_url":"https://avatars.githubusercontent.com/u/2286572?v=3","gravatar_id":"","url":"https://api.github.com/users/lebolo","html_url":"https://github.com/lebolo","followers_url":"https://api.github.com/users/lebolo/followers","following_url":"https://api.github.com/users/lebolo/following{/other_user}","gists_url":"https://api.github.com/users/lebolo/gists{/gist_id}","starred_url":"https://api.github.com/users/lebolo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lebolo/subscriptions","organizations_url":"https://api.github.com/users/lebolo/orgs","repos_url":"https://api.github.com/users/lebolo/repos","events_url":"https://api.github.com/users/lebolo/events{/privacy}","received_events_url":"https://api.github.com/users/lebolo/received_events","type":"User","site_admin":false},"created_at":"2016-10-18T14:20:08Z","updated_at":"2016-10-18T14:20:08Z","body":"`trimmed.cache` is a proper datasource directory. If I remove the caching option, Oncotator successfully runs through the whole VCF using this configuration. The spaces are an artifact of my copy-pasting, it's a valid VCF throughout."}}
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