Ebi: ability to extend a submission #1489
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…nto ebi-improvements-add
| # The sample.xml file needs to be generated if and only if there are | ||
| # samples in the current submission that do NOT have an | ||
| # ebi_sample_accession | ||
| new_samples = { |
There was a problem hiding this comment.
Should this be the prep template and not the sample template?
There was a problem hiding this comment.
No, the ebi_sample_accessions are stored in the sample template.
|
The failures here are expected - will fix the interface in an oncoming PR |
| @@ -362,8 +372,10 @@ def generate_sample_xml(self): | |||
| 'xmlns:xsi': self.xmlns_xsi, | |||
| "xsi:noNamespaceSchemaLocation": self.xsi_noNSL % "sample"}) | |||
|
|
|||
| for sample_name, sample_info in sorted(viewitems(self.samples)): | |||
| sample_info = dict(sample_info) | |||
| samples = samples if samples is not None else viewkeys(self.samples) | |||
There was a problem hiding this comment.
This is a rather subjective comment, but this line doesn't need to be a one-liner, it should jus be an if statement:
if samples is not None:
samples = viewkeys(self.samples)There was a problem hiding this comment.
You're correct, although the correct if is:
if not samples:
samples = viewkeys(self.samples)
|
👍 |
Merged
|
comments addressed |
|
I don't see any outstanding issues |
ElDeveloper
added a commit
that referenced
this pull request
Oct 8, 2015
Ebi: ability to extend a submission
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR modifies the EBI code to be able to extend an existent EBI submission with new samples, experiments and/or runs.