Mercurial > repos > sanbi-uwc > build_ctb_gene
changeset 32:9e33d452ad8c draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit cca5de2166bbc2fbbab368415853e085d474b6b2
| author | sanbi-uwc |
|---|---|
| date | Tue, 24 May 2016 04:19:03 -0400 |
| parents | bcf4f741b94f |
| children | f9ad7d3cd333 |
| files | build_ctb_gene.py |
| diffstat | 1 files changed, 11 insertions(+), 11 deletions(-) [+] |
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--- a/build_ctb_gene.py Mon May 23 09:20:36 2016 -0400 +++ b/build_ctb_gene.py Tue May 24 04:19:03 2016 -0400 @@ -37,8 +37,8 @@ self.docker_instance_name = "build_ctb_gene_" + str(random.randrange(0, 1000, 2)) def build_ctb_gene(self): - # cmdline_str = "build_ctb_gene goterms {}".format(self.args.input_file) - cmdline_str = "touch /tmp/foo.bar" + cmdline_str = "build_ctb_gene goterms {}".format(self.args.input_file) + #cmdline_str = "touch /tmp/foo.bar" cmdline_str = self.newSplit(cmdline_str) build_ctb_run = False try: @@ -46,12 +46,12 @@ build_ctb_run = True except CalledProcessError: print("Error running the build_ctb_gene goterms", file=sys.stderr) - if build_ctb_run: - self.copy_output_file_to_dataset() - print("Building a new DB, current time: %s" % str(datetime.date.today())) - # print("Noe4j Database Name: http://%s:%s@%s:%s/db/data/" % ( - # self.args.username, self.args.password, self.args.url, self.args.port)) - print("GFF File - Input: %s" % str(self.args.input_file)) + if build_ctb_run: + self.copy_output_file_to_dataset() + print("Building a new DB, current time: %s" % str(datetime.date.today())) + # print("Noe4j Database Name: http://%s:%s@%s:%s/db/data/" % ( + # self.args.username, self.args.password, self.args.url, self.args.port)) + print("GFF File - Input: %s" % str(self.args.input_file)) def newSplit(self, value): lex = shlex.shlex(value) @@ -110,12 +110,12 @@ cmd_str = "docker inspect --format='{{(index (index .NetworkSettings.Ports \"7474/tcp\") 0).HostPort}}' %s" % ctb_gene_runner.docker_instance_name # TODO: randomise the ports/names/mount_point and use the autokill image - export_cmd = 'export NEO4J_REST_URL=http://localhost:{}/db/data/'.format( + neo4j_url = 'http://localhost:{}/db/data/'.format( inspect_docker(cmd_str)[:-1]) try: - os.system(export_cmd) + os.environ["NEO4J_REST_URL"] = neo4j_url except (OSError, ValueError), e: - print("Error exporting the NEO4J db environmental values", e) + print("Error setting the NEO4J db environmental values", e) # make the output directory if not os.path.exists(args.outputdir):