ddbj/submission-excel2xml

Tools for XML submission

submission-excel2xml's Issues

To select 'fastq' for filetype

登録完了メールで以下のようなコメントがついていました。

# fastq ファイルの filetype
fastq ファイルのリード長が一定かどうかに関わらず、
今後は filetype に "fastq" を選択してください。
"generic_fastq" となっている既登録データの修正は不要です。
https://www.ddbj.nig.ac.jp/dra/submission.html#File_Type

dra_metadata.xlsxのfile typeのプルダウンメニューではgeneric_fastqになっているので、
フォーマットの更新をしていただけるとありがたいです。

Errors in the validation

When running validate_dra_meta.rb via docker, the following errors are shown:

== XML validation against SRA xsd ==
warning: failed to load external entity "SRA.submission.xsd"
Schemas parser error : Failed to locate the main schema resource at 'SRA.submission.xsd'.
WXS schema SRA.submission.xsd failed to compile
warning: failed to load external entity "SRA.experiment.xsd"
Schemas parser error : Failed to locate the main schema resource at 'SRA.experiment.xsd'.
WXS schema SRA.experiment.xsd failed to compile
warning: failed to load external entity "SRA.run.xsd"
Schemas parser error : Failed to locate the main schema resource at 'SRA.run.xsd'.
WXS schema SRA.run.xsd failed to compile

I'm afraid that the XSD files are not copied to a docker image.

md5 値に空白混入時にエラー

XML の md5 値に空白が混入している場合、validator でエラーにする

Title が空のときデフォルトの Title を XML に出力する

エクセルの Title が空のときデフォルトの Title を XML に出力する

New display name in Experiment

Thank you for opening this comment;
Could you please reflect in the Excel template the items whose names changed in December 2022?
e.g.) “Spot Type” to “Library Layout”, “Nominal Length” to “Insert Size”, and so on....

No such file to open error upon executing example code

The following error was shown after running the example code

D-way account ID: exampleSubmission number: 0001  
BioProject ID: PRJDB7252
Traceback (most recent call last):
        1: from /usr/local/bin/excel2xml.rb:75:in `<main>'
/usr/local/bin/excel2xml.rb:78:in `rescue in <main>': No such file to open. (RuntimeError)

code used to reproduce:

cd submission-excel2xml
sudo singularity build excel2xml.simg Singularity
singularity exec excel2xml.simg excel2xml.rb -a example -i 0001 -p PRJDB7252 example-0001_dra_metadata.xlsx

Edit:
This problem seems to show up with WSL2

Suggestion to alias format checking

Currently, experiment and run aliases should be in "Experiment-\d+" and "Run-\d+", respectively.
If a user wrote texts in the incorrect format (e.g. Experiment_0001), the system ignore them.
However, in this case, the system does not show any errors and warnings, and produces blank XML files.
For users, it is not easy to recognize why this happens.

Thus, I suggest to put error or warning messages for the incorrect alias texts.