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Improve File Name Standardization #332

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ecwood opened this issue Jul 25, 2023 · 2 comments
Closed

Improve File Name Standardization #332

ecwood opened this issue Jul 25, 2023 · 2 comments
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@ecwood
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Erica-look housekeeping

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@ecwood
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ecwood commented Jul 25, 2023

Both of scripts and of output files, we need to improve our file name standardization. This is spun off of #321 and will be worked on in the jsonlines branch.
@ecwood ecwood self-assigned this Jul 25, 2023
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#321 #332 updating filenames for JSON Lines format
b03b2ad
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 repodb extraction should be labeled as such
ddba16b
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 #321 standardize Snakefile
4346127
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#321 #332 cleaning up snakefile names
b0b2303
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 ChEMBL - standardize to kg_jsonl for JSON Lines representation
3ef738c
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 DGIdb - standardize to kg_jsonl for JSON Lines representation
ea8ab0a
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 Report Script - standardize to kg_jsonl for JSON Lines represent…
ac46119 
…ation
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 UniChem - standardize to kg_jsonl for JSON Lines representation
1eadc46
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 centralizing the file names for easier maintenance
9bf1e8f
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 standardize on SEMMEDDB
a6944d7
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 factor out our usual python command, need to do in other places too
9f53310
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 make sure there's log files for all of the rules
7e0eed5
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 centralizing location of filenames for extraction scripts
de4d28c
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 centralize location of filenames for post-etl scripts
8a3c8ec
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 update the filenames that have changed
7707691
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 correcting some typos from update
78a928b
ecwood added a commit that referenced this issue Jul 25, 2023
@ecwood
#332 report script name change
7f7b320
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 factor out name part of file names for easier changing
2a4223e
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 merged kg2 shouldn't be called final
286a3e6
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 Multi Ont - standardize to kg_jsonl for JSON Lines representation
a6799b5
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 SemMedDB - standardize to kg_jsonl for JSON Lines representation
b425236
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 SemMedDB extraction should use tuplelist as one word and jsonl
36309ce
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 updating bash scripts with correct file names
f094382
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 UniProtKB - standardize to kg_jsonl for JSON Lines representation
6bfa52e
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 Ensembl - standardize to kg_jsonl for JSON Lines representation
5720118
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 NCBIGene - standardize to kg_jsonl for JSON Lines representation
58f29ce
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 repoDB - standardize to kg_jsonl for JSON Lines representation
3e07421
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 DrugBank - standardize to kg_jsonl for JSON Lines representation
ee87a9d
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 SMPDB - standardize to kg_jsonl for JSON Lines representation
fce7423
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 HMDB - standardize to kg_jsonl for JSON Lines representation
a7bb6dc
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 GO Annotations - standardize to kg_jsonl for JSON Lines represen…
39c8cbd 
…tation
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 Reactome - standardize to kg_jsonl for JSON Lines representation
34bef3d
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 miRBase - standardize to kg_jsonl for JSON Lines representation
19f622d
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 JensenLab - standardize to kg_jsonl for JSON Lines representation
67be18b
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 DrugCentral - standardize to kg_jsonl for JSON Lines representation
5f85bbe
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 IntAct - standardize to kg_jsonl for JSON Lines representation
cc290ff
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 DisGeNet - standardize to kg_jsonl for JSON Lines representation
ee5a963
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 KEGG - standardize to kg_jsonl for JSON Lines representation
d87e3b5
ecwood added a commit that referenced this issue Jul 26, 2023
@ecwood
#332 file name changes in var file
7f1ccb0
@ecwood
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ecwood commented Aug 28, 2023

I'm going to mark this issue for verification.

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ecwood commented Sep 13, 2023

This was complete as of KG2.8.5pre.

@ecwood ecwood closed this as completed Sep 13, 2023
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