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guma44 / GEOparse

Python library to access Gene Expression Omnibus Database (GEO)
BSD 3-Clause "New" or "Revised" License
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NCBI GEO FTP has changed their URL structures AGAIN #35

Closed halioui closed 6 years ago

halioui commented 6 years ago

I cannot download the majority of GEO metadata files! I Think that NCBI has changed again the structure of their URLs :(

10-Jan-2018 20:14:50 ERROR utils - Cannot find file ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS301963nnn/GDS301963773/soft/GDS301963773.soft.gz
GDS301963934
10-Jan-2018 20:14:50 INFO GEOparse - Downloading ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS301963nnn/GDS301963934/soft/GDS301963934.soft.gz to XXX/GDS301963934.soft.gz
10-Jan-2018 20:14:50 ERROR utils - Cannot find file ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS301963nnn/GDS301963934/soft/GDS301963934.soft.gz
GDS301385886
10-Jan-2018 20:14:50 INFO GEOparse - Downloading ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS301385nnn/GDS301385886/soft/GDS301385886.soft.gz to XXX/GDS301385886.soft.gz
10-Jan-2018 20:14:50 ERROR utils - Cannot find file ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS301385nnn/GDS301385886/soft/GDS301385886.soft.gz
GDS302278020
10-Jan-2018 20:14:50 INFO GEOparse - Downloading ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS302278nnn/GDS302278020/soft/GDS302278020.soft.gz to XXX/GDS302278020.soft.gz
10-Jan-2018 20:14:50 ERROR utils - Cannot find file ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS302278nnn/GDS302278020/soft/GDS302278020.soft.gz
GDS302478025
10-Jan-2018 20:14:50 INFO GEOparse - Downloading ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS302478nnn/GDS302478025/soft/GDS302478025.soft.gz to XXX/GDS302478025.soft.gz
10-Jan-2018 20:14:50 ERROR utils - Cannot find file ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS302478nnn/GDS302478025/soft/GDS302478025.soft.gz
GDS301172854
10-Jan-2018 20:14:50 INFO GEOparse - Downloading ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS301172nnn/GDS301172854/soft/GDS301172854.soft.gz to XXX/GDS301172854.soft.gz
10-Jan-2018 20:14:51 ERROR utils - Cannot find file ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS301172nnn/GDS301172854/soft/GDS301172854.soft.gz
GDS301192685
10-Jan-2018 20:14:51 INFO GEOparse - Downloading ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS301192nnn/GDS301192685/soft/GDS301192685.soft.gz to XXX/GDS301192685.soft.gz
10-Jan-2018 20:14:51 ERROR utils - Cannot find file ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS301192nnn/GDS301192685/soft/GDS301192685.soft.gz
GDS302483410
10-Jan-2018 20:14:51 INFO GEOparse - Downloading ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS302483nnn/GDS302483410/soft/GDS302483410.soft.gz to XXX/GDS302483410.soft.gz
10-Jan-2018 20:14:51 ERROR utils - Cannot find file ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS302483nnn/GDS302483410/soft/GDS302483410.soft.gz
GDS302048642
10-Jan-2018 20:14:51 INFO GEOparse - Downloading ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS302048nnn/GDS302048642/soft/GDS302048642.soft.gz to XXX/GDS302048642.soft.gz
10-Jan-2018 20:14:51 ERROR utils - Cannot find file ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS302048nnn/GDS302048642/soft/GDS302048642.so
halioui commented 6 years ago

IDS not correct

guma44 commented 6 years ago

OK, that solves the problem :).