mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 22:06:53 +08:00
Nicola Soranzo
21b44bf348
using the following command: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 . ```
43 lines
2.1 KiB
Python
43 lines
2.1 KiB
Python
# post processing, add sequence and additional annoation info if available
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from six.moves.urllib.parse import urlencode
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from galaxy.datatypes.images import create_applet_tag_peek
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def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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primary_data = next(iter(out_data.values()))
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# default params for LAJ type
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params = {
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"alignfile1": "display?id=%s" % primary_data.id,
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"buttonlabel": "Launch LAJ",
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"title": "LAJ in Galaxy",
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"posturl": "history_add_to?%s" % urlencode({'history_id': primary_data.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': primary_data.dbkey})
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}
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for name, data in inp_data.items():
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if name == "maf_input":
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params["alignfile1"] = "display?id=%s" % data.id
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elif name == "seq_file1" and data.state == data.states.OK and data.has_data():
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params["file1seq1"] = "display?id=%s" % data.id
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elif name == "seq_file2" and data.state == data.states.OK and data.has_data():
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params["file1seq2"] = "display?id=%s" % data.id
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elif name == "exonfile" and data.state == data.states.OK and data.has_data():
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params["exonfile"] = "display?id=%s" % data.id
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elif name == "repeatfile" and data.state == data.states.OK and data.has_data():
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params["repeatfile"] = "display?id=%s" % data.id
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elif name == "annotationfile" and data.state == data.states.OK and data.has_data():
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params["annotationfile"] = "display?id=%s" % data.id
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elif name == "underlayfile" and data.state == data.states.OK and data.has_data():
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params["underlayfile"] = "display?id=%s" % data.id
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elif name == "highlightfile" and data.state == data.states.OK and data.has_data():
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params["highlightfile"] = "display?id=%s" % data.id
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if "file1seq1" not in params and "file1seq2" not in params:
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params["noseq"] = "true"
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class_name = "edu.psu.cse.bio.laj.LajApplet.class"
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archive = "/static/laj/laj.jar"
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primary_data.peek = create_applet_tag_peek(class_name, archive, params)
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app.model.context.add(primary_data)
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app.model.context.flush()
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