Mercurial > repos > galaxyp > unipept
changeset 7:b329d34f5eed draft default tip
planemo upload for repository https://unipept.ugent.be/apidocs commit 3c558355ee4f859d4356a05e79f8777fdfbede87
| author | galaxyp |
|---|---|
| date | Fri, 14 Nov 2025 21:04:50 +0000 |
| parents | ee99ebe711a8 |
| children | |
| files | unipept.py unipept.xml |
| diffstat | 2 files changed, 18 insertions(+), 13 deletions(-) [+] |
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--- a/unipept.py Fri Apr 25 20:57:51 2025 +0000 +++ b/unipept.py Fri Nov 14 21:04:50 2025 +0000 @@ -199,16 +199,16 @@ def get_node(id, name, rank, child, seq): if id not in id_to_node: - data = {'count': 0, 'self_count': 0, 'valid_taxon': 1, 'rank': rank, 'sequences': []} - node = {'id': id, 'name': name, 'children': [], 'kids': [], 'data': data} + extra = {'valid_taxon': 1, 'rank': rank, 'sequences': []} + node = {'id': id, 'name': name, 'children': [], 'kids': [], 'count': 0, 'selfCount': 0, 'extra': extra} id_to_node[id] = node else: node = id_to_node[id] - node['data']['count'] += 1 - if seq is not None and seq not in node['data']['sequences']: - node['data']['sequences'].append(seq) + node['count'] += 1 + if seq is not None and seq not in node['extra']['sequences']: + node['extra']['sequences'].append(seq) if child is None: - node['data']['self_count'] += 1 + node['selfCount'] += 1 elif child['id'] not in node['kids']: node['kids'].append(child['id']) node['children'].append(child) @@ -249,16 +249,16 @@ def get_node(id, name, child, seq): if id not in id_to_node: - data = {'count': 0, 'self_count': 0, 'sequences': []} - node = {'id': id, 'name': name, 'children': [], 'kids': [], 'data': data} + extra = {'sequences': []} + node = {'id': id, 'name': name, 'children': [], 'kids': [], 'count': 0, 'selfCount': 0, 'extra': extra} id_to_node[id] = node else: node = id_to_node[id] - node['data']['count'] += 1 - if seq is not None and seq not in node['data']['sequences']: - node['data']['sequences'].append(seq) + node['count'] += 1 + if seq is not None and seq not in node['extra']['sequences']: + node['extra']['sequences'].append(seq) if child is None: - node['data']['self_count'] += 1 + node['selfCount'] += 1 elif child['id'] not in node['kids']: node['kids'].append(child['id']) node['children'].append(child)
--- a/unipept.xml Fri Apr 25 20:57:51 2025 +0000 +++ b/unipept.xml Fri Nov 14 21:04:50 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="unipept" name="Unipept" version="6.2.4+galaxy0" profile="22.05"> +<tool id="unipept" name="Unipept" version="6.2.4+galaxy1" profile="25.0"> <description>retrieve taxonomy for peptides</description> <macros> <xml name="equate_il"> @@ -619,6 +619,11 @@ type: Optional, type of the InterPro entry. Included when the extra parameter is set to true. name: Optional, name of the InterPro entry. Included when the extra parameter is set to true. + **Note on Output JSON** + + In Unipept Galaxy Version 6.2.4+galaxy1 the structure of output Taxonomy and EC JSON files was changed to conform to non-backwards compatible changes in unipept-visualizations versions >= 2.0, utilized by the Unipept Taxonomy Viewer visualization tool in Galaxy versions >= 25.0. + + Documentation of this structure may be found here: https://github.com/unipept/unipept-visualizations/wiki/DataNode **Attributions**