Link to GO data needs to be updated

ncatlett commented 11 years ago

Most recent manually QC'd GO obo-xml file is located here - http://archive.geneontology.org/latest-full/

The link/filename includes date, which will change with each monthly release, so link is broken

ncatlett commented 11 years ago

needs to be updated in both configuration.py and changelog_config.py

digitallance commented 11 years ago

Added automatic check for the current latest-full go_YYYYMM-termdb.obo-xml.gz file since it uses a changing YYYYMM filename component for each new release.

added function get_latest_GO_filename(url) to common.py to fetch latest file URL from archive.geneontology.org
modified parsers.py and change log_config.py to use latest_GO_filename() function before downloading resource file
modified configuration.py to remove the resource file name from URL to GO latest-full as the full file URL is obtained by the get_latest_GO_filename() function.

ncatlett commented 11 years ago

now getting error with GOBP parser:

Traceback (most recent call last): File "./gp_baseline.py", line 104, in <module> for x in parser.parse(): File "/home/ncatlett/resource-generator/parsers.py", line 651, in parse root = etree.parse(go, parser) File "lxml.etree.pyx", line 3201, in lxml.etree.parse (src/lxml/lxml.etree.c:65033) File "parser.pxi", line 1593, in lxml.etree._parseDocument (src/lxml/lxml.etree.c:93438) File "parser.pxi", line 1624, in lxml.etree._parseFilelikeDocument (src/lxml/lxml.etree.c:93781) File "parser.pxi", line 1506, in lxml.etree._parseDocFromFilelike (src/lxml/lxml.etree.c:92636) File "parser.pxi", line 1069, in lxml.etree._BaseParser._parseDocFromFilelike (src/lxml/lxml.etree.c:89658) File "parser.pxi", line 577, in lxml.etree._ParserContext._handleParseResultDoc (src/lxml/lxml.etree.c:84831) File "parser.pxi", line 672, in lxml.etree._handleParseResult (src/lxml/lxml.etree.c:85901) File "lxml.etree.pyx", line 294, in lxml.etree._ExceptionContext._raise_if_stored (src/lxml/lxml.etree.c:9387) File "parser.pxi", line 372, in lxml.etree._FileReaderContext.copyToBuffer (src/lxml/lxml.etree.c:82877) File "/usr/local/lib/python3.3/gzip.py", line 365, in read self._read(readsize) File "/usr/local/lib/python3.3/gzip.py", line 439, in _read self._read_gzip_header() File "/usr/local/lib/python3.3/gzip.py", line 289, in _read_gzip_header raise IOError('Not a gzipped file') OSError: Not a gzipped file

OpenBEL / resource-generator

Link to GO data needs to be updated #11