diff --git a/meteor/data/zenodo.json b/meteor/data/zenodo.json index c8e3154..bd3861f 100644 --- a/meteor/data/zenodo.json +++ b/meteor/data/zenodo.json @@ -3,11 +3,13 @@ "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" } }, @@ -15,11 +17,13 @@ "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" } }, @@ -27,11 +31,13 @@ "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" } }, @@ -39,11 +45,13 @@ "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" } }, @@ -51,11 +59,13 @@ "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" } }, @@ -63,11 +73,13 @@ "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" } }, @@ -75,11 +87,13 @@ "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" } }, @@ -87,11 +101,13 @@ "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" } }, @@ -99,11 +115,13 @@ "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" } }, @@ -111,11 +129,13 @@ "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" } }, @@ -123,6 +143,7 @@ "file_info": { "catalogue": "https://zenodo.org/records/13693446/files/mock.tar.xz", "filename": "mock.tar.xz", + "reference_date": "2023-03-14", "md5": "f021d007f6c1d0dffc4e94a786fa182c" }, "samples": { diff --git a/meteor/downloader.py b/meteor/downloader.py index cb37358..e81c7da 100644 --- a/meteor/downloader.py +++ b/meteor/downloader.py @@ -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) @@ -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)