Mercurial > repos > iuc > pangolin

annotate fetch_latest_pangolearn.py @ 1:de3ceb419d91 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
author iuc
date Sun, 25 Apr 2021 20:16:28 +0000
parents
children 3eb349ea33a6
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de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
parents:
diff changeset
1 #!/usr/bin/env python
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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2
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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3 import json
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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4 import os
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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5 import tarfile
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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6
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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7 # rely on the fact that pangolin itself uses the requests module
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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8 import requests
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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9
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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10 response = requests.get(
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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11 "https://api.github.com/repos/cov-lineages/pangoLEARN/releases/latest"
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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12 )
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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13 if response.status_code == 200:
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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14 details = json.loads(response.text)
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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15 response = requests.get(details["tarball_url"])
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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16 if response.status_code == 200:
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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17 with open("pangolearn.tgz", "wb") as handle:
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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18 handle.write(response.content)
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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19 tf = tarfile.open("pangolearn.tgz")
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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20 pl_path = tf.next().name
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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21 tf.extractall()
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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22 tf.close()
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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23 os.rename(os.path.join(pl_path, "pangoLEARN"), "datadir")
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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24 else:
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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25 response.raise_for_status()
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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26 else:
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
iuc
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27 response.raise_for_status()