About storing edam files in Debian packaging
Hi Matus and Steffen,
I was again stumbling upon totally broken edam yaml files (bowties and
bowtie2 was totally broken, I fixed freecontact and clustalo which had
"topics" instead of "topic" and were breaking UDD import due to this).
To verify how many other edam files might be affected I did some
find . -name "*.edam" -exec yamllint \{\} \; > ../yamllint_result
in the UDD importer dir which is featuring all those files. I have
attached the result here - please note that the packages mentioned
above are fixed meanwhile *syntactically*.
When trying to fix the syntax I also noted that you sometimes are
using input / inputs or output / outputs - so there is no consistent
use of the keywords.
>From my point of view the data quality makes these files pretty useless.
My question is:
1. Are these data really used?
2. What is the plan to use the data?
3. How can we enhance the data quality?
(lintian comes to mind as we are using it for upstream files)
At Debian Med sprint you both asked me to add an additional column in
UDD storing the version of the Ontology. I admit I'm not really
motivated to work on bad quality data with unknown use case. I'd assume
if there would be any consumers of these data they would have thrown
errors. If this is the case, I wonder why you did not contacted the
authors of the edam files to fix these (or just fix these yourself).
Kind regards
Andreas.
--
http://fam-tille.de
./q/qiime.edam
1:1 warning missing document start "---" (document-start)
7:6 error wrong indentation: expected 6 but found 5 (indentation)
9:6 error wrong indentation: expected 6 but found 5 (indentation)
9:15 error too many spaces after colon (colons)
12:6 error wrong indentation: expected 6 but found 5 (indentation)
12:15 error too many spaces after colon (colons)
./a/abacas.edam
1:1 warning missing document start "---" (document-start)
7:6 error wrong indentation: expected 6 but found 5 (indentation)
9:6 error wrong indentation: expected 6 but found 5 (indentation)
9:15 error too many spaces after colon (colons)
12:6 error wrong indentation: expected 6 but found 5 (indentation)
12:15 error too many spaces after colon (colons)
./a/anfo.edam
1:1 warning missing document start "---" (document-start)
7:6 error wrong indentation: expected 6 but found 5 (indentation)
10:6 error wrong indentation: expected 6 but found 5 (indentation)
10:15 error too many spaces after colon (colons)
12:15 error too many spaces after colon (colons)
15:6 error wrong indentation: expected 6 but found 5 (indentation)
15:15 error too many spaces after colon (colons)
17:15 error too many spaces after colon (colons)
18:22 error too few spaces after comma (commas)
18:28 error too few spaces after comma (commas)
19:15 error too many spaces after colon (colons)
./a/ampliconnoise.edam
1:1 warning missing document start "---" (document-start)
7:6 error wrong indentation: expected 6 but found 5 (indentation)
9:6 error wrong indentation: expected 6 but found 5 (indentation)
9:15 error too many spaces after colon (colons)
12:6 error wrong indentation: expected 6 but found 5 (indentation)
12:15 error too many spaces after colon (colons)
./t/tantan.edam
1:1 warning missing document start "---" (document-start)
7:6 error wrong indentation: expected 6 but found 5 (indentation)
9:6 error wrong indentation: expected 6 but found 5 (indentation)
9:15 error too many spaces after colon (colons)
12:6 error wrong indentation: expected 6 but found 5 (indentation)
12:15 error too many spaces after colon (colons)
./h/htslib.tabix.edam
1:1 warning missing document start "---" (document-start)
8:6 error wrong indentation: expected 6 but found 5 (indentation)
10:6 error wrong indentation: expected 6 but found 5 (indentation)
10:15 error too many spaces after colon (colons)
12:15 error too many spaces after colon (colons)
15:6 error wrong indentation: expected 6 but found 5 (indentation)
15:15 error too many spaces after colon (colons)
./k/kissplice.edam
1:1 warning missing document start "---" (document-start)
9:6 error wrong indentation: expected 6 but found 5 (indentation)
13:6 error wrong indentation: expected 6 but found 5 (indentation)
13:15 error too many spaces after colon (colons)
14:24 error too few spaces after comma (commas)
16:6 error wrong indentation: expected 6 but found 5 (indentation)
16:15 error too many spaces after colon (colons)
./m/miniasm.edam
1:1 warning missing document start "---" (document-start)
7:6 error wrong indentation: expected 6 but found 5 (indentation)
9:6 error wrong indentation: expected 6 but found 5 (indentation)
14:6 error wrong indentation: expected 6 but found 5 (indentation)
14:15 error too many spaces after colon (colons)
./m/minimap.edam
1:1 warning missing document start "---" (document-start)
7:6 error wrong indentation: expected 6 but found 5 (indentation)
9:6 error wrong indentation: expected 6 but found 5 (indentation)
9:15 error too many spaces after colon (colons)
12:6 error wrong indentation: expected 6 but found 5 (indentation)
12:15 error too many spaces after colon (colons)
./p/pbsim.edam
1:1 warning missing document start "---" (document-start)
7:6 error wrong indentation: expected 6 but found 5 (indentation)
9:6 error wrong indentation: expected 6 but found 5 (indentation)
9:15 error too many spaces after colon (colons)
12:6 error wrong indentation: expected 6 but found 5 (indentation)
12:15 error too many spaces after colon (colons)
./b/bowtie.edam
1:1 warning missing document start "---" (document-start)
4:10 error syntax error: mapping values are not allowed here
29:81 error line too long (89 > 80 characters) (line-length)
./s/ssake.edam
1:1 warning missing document start "---" (document-start)
7:6 error wrong indentation: expected 6 but found 5 (indentation)
9:6 error wrong indentation: expected 6 but found 5 (indentation)
9:15 error too many spaces after colon (colons)
12:6 error wrong indentation: expected 6 but found 5 (indentation)
12:15 error too many spaces after colon (colons)
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