Closed agduncan94 closed 4 years ago
ewels
commented
4 years ago This is brilliant stuff, thank you @agduncan94! Just checked the code changes and they look fine - amazingly simple, which is the best kind of fix! ☺️
I'll just wait to test this code myself locally before merging, but I think it looks great..
Phil
ewels
commented
4 years ago Haven't gotten to a computer yet but figured that it couldn't hurt to merge as it's currently broken anyway.
Just had a quick try on my phone and seems to not work with the examples? But maybe I'm being too impatient and haven't waited long enough for the automatic deploy..
ewels
commented
4 years ago Yay, working now! 🎉
Need another PR to remove the notice that it's not working 😅
ewels
commented
4 years ago Thank you!
agduncan94
commented
4 years ago Happy to help! Oh true, I forgot to remove the notice 😆
Hey @ewels I stumbled upon this application when I was failing to download SRA data using prefetch and the SRA toolkit and was looking for an alternative. Hopefully this PR can help fix the issue with the new EBI api.
This is based on issues
There are two parts to this PR. First, there was an issue with the creation of the expXML and rawXML. Instead of using the .html() function followed by trimming, it now just uses the RAW XML directly. From what I understand XML doesn't care about whitespace, though perhaps there is another reason to use the .html() function. This was stopping the results from showing.
The second issue is that EBI changed their API for accessing the ENA. The new endpoint being used can be found on their Swagger page.
The return type of JSON is also passed along to make the code a bit cleaner to read. This was causing the FASTQ downloads tab to be stuck loading.
I will say that I have limited knowledge of this app (I haven't actually used it before trying to fix it), so I hope I didn't break anything. It would be great if others could test this out to make sure it works.