[WIP] Biotools #1891
[WIP] Biotools #1891
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To add a little bit of information here. |
| :rtype: string | ||
| """ | ||
| try: | ||
| return "/".join(tool_id.replace('repos', 'view', 1).split('/')[0:-2]) |
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Galaxy versions > 16.01 return a tool_shed_repository entry for toolshed tools that looks like this:
"tool_shed_repository": {"owner": "devteam", "changeset_revision": "e359ce20fbd9", "name": "fastq_quality_boxplot", "tool_shed": "toolshed.g2.bx.psu.edu"}
This is probably better suited for constructing a link, given that a toolshed may well be reachable at <http://server_url/abc/toolshed>
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Sure, this does look really interesting. One thing that I would discuss is the use of tool_id ... it's a bit unfortunate that the same tool_id may not be sufficient to unambiguously identify the origin of a tool. AFAIK we'd need a combo of toolshed/owner/name/changeset_revision. |
lib/galaxy/datatypes/data.py
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| edam_format = "format_1915" | ||
| edam_data = "data_0006" |
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@nsoranzo feel free to PR against this branch. I can merge it afaik.
| 'datatypes', | ||
| path_prefix='/api', | ||
| collection={ 'sniffers': 'GET', 'mapping': 'GET', 'converters': 'GET', 'edam_data': 'GET' }, | ||
| parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) |
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I think that instead of invoking again webapp.mapper.resource() here, you should just add 'edam_data': 'GET' at line 303.
| else: | ||
| return description[0].upper() + description[1:size] + '.' | ||
| except IndexError: | ||
| raise description |
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This will cause a TypeError if description is "".
| 'dataDescription': data_json['name'] | ||
| }) | ||
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| def inputs_extract_repeat(repeat_json): |
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Is there not already a function in Galaxy that traverses all params and extracting data-params.
If not this should probably end up in some utils file to be reused by other modules.
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This has been rebased now that #2387 is merged. |
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@galaxybot test this |
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@hmenager What's the status of this? Shall we hack on it next week? |
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