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Add reference date
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@aghozlane
aghozlane committed Nov 29, 2024
1 parent f051251 commit d75cc19
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21 changes: 21 additions & 0 deletions meteor/data/zenodo.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,126 +3,147 @@
"file_info": {
"catalogue": "https://zenodo.org/records/14181283/files/fc_1_3_gut.tar.xz",
"filename": "fc_1_3_gut.tar.xz",
"reference_date": "2024-11-18",
"md5": "7d49c3a0e565e3e74a2e6bb67886d4c2"
},
"taxonomy_info": {
"catalogue": "https://zenodo.org/records/14181283/files/fc_1_3_gut_taxo.tar.xz",
"filename": "fc_1_3_gut_taxo.tar.xz",
"reference_date": "2024-11-18",
"md5": "50942ab4f4f0aae43d7f3dd19df041d8"
}
},
"chicken_caecal": {
"file_info": {
"catalogue": "https://zenodo.org/records/14181300/files/gg_13_6_caecal.tar.xz",
"filename": "gg_13_6_caecal.tar.xz",
"reference_date": "2024-11-18",
"md5": "8e35a94d01aaded8fb322b7e22e0441f"
},
"taxonomy_info": {
"catalogue": "https://zenodo.org/records/14181300/files/gg_13_6_caecal_taxo.tar.xz",
"filename": "gg_13_6_caecal_taxo.tar.xz",
"reference_date": "2024-11-18",
"md5": "10b2e0e208cba88e4b635f5a317f94a2"
}
},
"dog_gut": {
"file_info": {
"catalogue": "https://zenodo.org/records/14180833/files/clf_1_0_gut.tar.xz",
"filename": "clf_1_0_gut.tar.xz",
"reference_date": "2024-11-18",
"md5": "e3a0b9c30461f2d478c77be7c3cdc529"
},
"taxonomy_info": {
"catalogue": "https://zenodo.org/records/14180833/files/clf_1_0_gut_taxo.tar.xz",
"filename": "clf_1_0_gut_taxo.tar.xz",
"reference_date": "2024-11-18",
"md5": "8b1b709c741eed98ccc0c5fcdfa299ab"
}
},
"human_gut": {
"file_info": {
"catalogue": "https://zenodo.org/records/14181329/files/hs_10_4_gut.tar.xz",
"filename": "hs_10_4_gut.tar.xz",
"reference_date": "2024-11-18",
"md5": "dd295f2ac27d68389a4a7ebc8f5b4125"
},
"taxonomy_info": {
"catalogue": "https://zenodo.org/records/14181329/files/hs_10_4_gut_taxo.tar.xz",
"filename": "hs_10_4_gut_taxo.tar.xz",
"reference_date": "2024-11-18",
"md5": "730b62479d835af5b217f0d9eda4ce2d"
}
},
"human_oral": {
"file_info": {
"catalogue": "https://zenodo.org/records/14181351/files/hs_8_4_oral.tar.xz",
"filename": "hs_8_4_oral.tar.xz",
"reference_date": "2024-11-18",
"md5": "5b4d832b226c69766e6b35be229a9aa4"
},
"taxonomy_info": {
"catalogue": "https://zenodo.org/records/14181351/files/hs_8_4_oral_taxo.tar.xz",
"filename": "hs_8_4_oral_taxo.tar.xz",
"reference_date": "2024-11-18",
"md5": "10565aafc059b663cbf1f7297a56047b"
}
},
"human_skin": {
"file_info": {
"catalogue": "https://zenodo.org/records/14181341/files/hs_2_9_skin.tar.xz",
"filename": "hs_2_9_skin.tar.xz",
"reference_date": "2024-11-18",
"md5": "4860182792a44058ffa671217c71d789"
},
"taxonomy_info": {
"catalogue": "https://zenodo.org/records/14181341/files/hs_2_9_skin_taxo.tar.xz",
"filename": "hs_2_9_skin_taxo.tar.xz",
"reference_date": "2024-11-18",
"md5": "68a011b4f319b118cda9b05b637dbc19"
}
},
"mouse_gut": {
"file_info": {
"catalogue": "https://zenodo.org/records/14184128/files/mm_5_0_gut.tar.xz",
"filename": "mm_5_0_gut.tar.xz",
"reference_date": "2024-11-19",
"md5": "029bd928c4d5b00462bcc12950857f54"
},
"taxonomy_info": {
"catalogue": "https://zenodo.org/records/14184128/files/mm_5_0_gut_taxo.tar.xz",
"filename": "mm_5_0_gut_taxo.tar.xz",
"reference_date": "2024-11-19",
"md5": "cd404b109553cc01cb93ead46a85b07b"
}
},
"rabbit_gut": {
"file_info": {
"catalogue": "https://zenodo.org/records/14184141/files/oc_5_7_gut.tar.xz",
"filename": "oc_5_7_gut.tar.xz",
"reference_date": "2024-11-19",
"md5": "071d2ac2bcb90545edc2104cc2aa6aef"
},
"taxonomy_info": {
"catalogue": "https://zenodo.org/records/14184141/files/oc_5_7_gut_taxo.tar.xz",
"filename": "oc_5_7_gut_taxo.tar.xz",
"reference_date": "2024-11-19",
"md5": "f2fea0c805acc7f527e32bacfc93d59a"
}
},
"rat_gut": {
"file_info": {
"catalogue": "https://zenodo.org/records/14184150/files/rn_5_9_gut.tar.xz",
"filename": "rn_5_9_gut.tar.xz",
"reference_date": "2024-11-19",
"md5": "6b860f2ca7826a5f8473c30337635cd2"
},
"taxonomy_info": {
"catalogue": "https://zenodo.org/records/14184150/files/rn_5_9_gut_taxo.tar.xz",
"filename": "rn_5_9_gut_taxo.tar.xz",
"reference_date": "2024-11-19",
"md5": "131df23bfb7758c539c012bd8726eeb5"
}
},
"pig_gut": {
"file_info": {
"complete": "https://zenodo.org/records/14184158/files/ssc_9_3_gut.tar.xz",
"filename": "ssc_9_3_gut.tar.xz",
"reference_date": "2024-11-19",
"md5": "9b0df528d4c74662393b4c7358f69121"
},
"taxonomy_info": {
"taxo": "https://zenodo.org/records/14184158/files/ssc_9_3_gut_taxo.tar.xz",
"filename": "ssc_9_3_gut_taxo.tar.xz",
"reference_date": "2024-11-19",
"md5": "8cbdb0bb7cbbdcd90981ed9d7fc4ad38"
}
},
"test": {
"file_info": {
"catalogue": "https://zenodo.org/records/13693446/files/mock.tar.xz",
"filename": "mock.tar.xz",
"reference_date": "2023-03-14",
"md5": "f021d007f6c1d0dffc4e94a786fa182c"
},
"samples": {
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3 changes: 1 addition & 2 deletions meteor/downloader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ def execute(self) -> None:
/ self.catalogues_config[self.choice][self.data_type]["filename"]
)
urlretrieve(url, filename=catalogue, reporthook=self.show_progress)
# print(flush=True)
self.progress_bar.close()
if self.choice == Downloader.TEST_CATALOGUE:
for sample in self.catalogues_config[self.choice]["samples"]:
logging.info("Download %s fastq file", sample)
Expand All @@ -141,7 +141,6 @@ def execute(self) -> None:
url_fastq, filename=fastq_test, reporthook=self.show_progress
)
self.progress_bar.close()
print(flush=True)
assert md5fastq_expect == self.getmd5(fastq_test)
if self.check_md5:
assert md5_expect == self.getmd5(catalogue)
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