Ecosyste.ms: Issues

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GitHub / turbomam/biosample-basex issues and pull requests

#41 - samples with missing Bioproject ids

Issue - State: open - Opened by realmarcin about 2 years ago

#41 - samples with missing Bioproject ids

Issue - State: open - Opened by realmarcin about 2 years ago

#38 - do we have minimal metadata rules for inclusion in NMDC

Issue - State: open - Opened by turbomam almost 3 years ago

#38 - do we have minimal metadata rules for inclusion in NMDC

Issue - State: open - Opened by turbomam almost 3 years ago

#37 - subset whole database on a few repaired env packages for Data Good

Issue - State: closed - Opened by turbomam almost 3 years ago - 7 comments

#37 - subset whole database on a few repaired env packages for Data Good

Issue - State: closed - Opened by turbomam almost 3 years ago - 7 comments

#36 - I don't have permission to move this to INCATools

Issue - State: closed - Opened by turbomam almost 3 years ago

#36 - I don't have permission to move this to INCATools

Issue - State: closed - Opened by turbomam almost 3 years ago

#35 - are there any column that are really numerical?

Issue - State: closed - Opened by turbomam almost 3 years ago

#35 - are there any column that are really numerical?

Issue - State: closed - Opened by turbomam almost 3 years ago

#33 - add a units table like the wide repaired?

Issue - State: open - Opened by turbomam almost 3 years ago

#33 - add a units table like the wide repaired?

Issue - State: open - Opened by turbomam almost 3 years ago

#32 - include ENVO semantic SQL tables in biosample SQLite

Issue - State: closed - Opened by turbomam almost 3 years ago

#32 - include ENVO semantic SQL tables in biosample SQLite

Issue - State: closed - Opened by turbomam almost 3 years ago

#31 - get exp types and descriptions from BioProject

Issue - State: open - Opened by turbomam almost 3 years ago

#31 - get exp types and descriptions from BioProject

Issue - State: open - Opened by turbomam almost 3 years ago

#30 - per Chris call repaired table `biosample` and the raw table `biosample_raw`

Issue - State: open - Opened by turbomam almost 3 years ago - 1 comment

#30 - per Chris call repaired table `biosample` and the raw table `biosample_raw`

Issue - State: open - Opened by turbomam almost 3 years ago - 1 comment

#28 - zip reports from ha_highlights.py

Issue - State: closed - Opened by turbomam almost 3 years ago - 3 comments

#28 - zip reports from ha_highlights.py

Issue - State: closed - Opened by turbomam almost 3 years ago - 3 comments

#27 - make desired columns an argument to ha_highlights.py

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#27 - make desired columns an argument to ha_highlights.py

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#26 - Write README or other documentation

Issue - State: open - Opened by turbomam almost 3 years ago

#26 - Write README or other documentation

Issue - State: open - Opened by turbomam almost 3 years ago

#25 - Biosample fields to summarize for Montana

Issue - State: closed - Opened by turbomam almost 3 years ago - 4 comments

#24 - make clean will nuke target/env_package_repair_curated.tsv

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#24 - make clean will nuke target/env_package_repair_curated.tsv

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#23 - cori requires module load python

Issue - State: closed - Opened by turbomam almost 3 years ago - 2 comments

#23 - cori requires module load python

Issue - State: closed - Opened by turbomam almost 3 years ago - 2 comments

#21 - recreate non-attribute + harmonized attribute view

Issue - State: closed - Opened by turbomam almost 3 years ago - 2 comments

#21 - recreate non-attribute + harmonized attribute view

Issue - State: closed - Opened by turbomam almost 3 years ago - 2 comments

#20 - env_package repair: examine various taxon fields too?

Issue - State: open - Opened by turbomam almost 3 years ago

#20 - env_package repair: examine various taxon fields too?

Issue - State: open - Opened by turbomam almost 3 years ago

#19 - write directly to SQLite

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#19 - write directly to SQLite

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#18 - switch to $d deletion for biosample_set_under

Issue - State: closed - Opened by turbomam almost 3 years ago - 2 comments

#18 - switch to $d deletion for biosample_set_under

Issue - State: closed - Opened by turbomam almost 3 years ago - 2 comments

#17 - use .env for Makefile parameters

Issue - State: closed - Opened by turbomam almost 3 years ago - 2 comments

#17 - use .env for Makefile parameters

Issue - State: closed - Opened by turbomam almost 3 years ago - 2 comments

#16 - Special handling for Keywords portion of paragraph element?

Issue - State: open - Opened by turbomam almost 3 years ago

#16 - Special handling for Keywords portion of paragraph element?

Issue - State: open - Opened by turbomam almost 3 years ago

#15 - Are there enough DOIs to justify a column in SQLite?

Issue - State: open - Opened by turbomam almost 3 years ago

#15 - Are there enough DOIs to justify a column in SQLite?

Issue - State: open - Opened by turbomam almost 3 years ago

#14 - Elephant in room: biosample_set.xml too big for one BaseX database now

Issue - State: closed - Opened by turbomam almost 3 years ago - 2 comments

#14 - Elephant in room: biosample_set.xml too big for one BaseX database now

Issue - State: closed - Opened by turbomam almost 3 years ago - 2 comments

#13 - Changes to biosample_non_harmonized_attributes_wide.xq query

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#13 - Changes to biosample_non_harmonized_attributes_wide.xq query

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#12 - Rename SQLite tables?

Issue - State: closed - Opened by turbomam almost 3 years ago

#12 - Rename SQLite tables?

Issue - State: closed - Opened by turbomam almost 3 years ago

#11 - Rename SQLite database file?

Issue - State: closed - Opened by turbomam almost 3 years ago

#11 - Rename SQLite database file?

Issue - State: closed - Opened by turbomam almost 3 years ago

#10 - Add normalized 'env_package's to SQLite?

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#10 - Add normalized 'env_package's to SQLite?

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#9 - Use basex command 'info index' to display paths summary

Issue - State: closed - Opened by turbomam almost 3 years ago

#9 - Use basex command 'info index' to display paths summary

Issue - State: closed - Opened by turbomam almost 3 years ago

#8 - Are triple pipe ||| delimiters justified?

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#8 - Are triple pipe ||| delimiters justified?

Issue - State: closed - Opened by turbomam almost 3 years ago - 1 comment

#7 - Issue 1 cori

Pull Request - State: closed - Opened by turbomam about 3 years ago

#7 - Issue 1 cori

Pull Request - State: closed - Opened by turbomam about 3 years ago

#6 - Issue #1 cori

Pull Request - State: closed - Opened by turbomam about 3 years ago

#6 - Issue #1 cori

Pull Request - State: closed - Opened by turbomam about 3 years ago

#5 - fencepost errors in chunk_harmonized_attributes_long.xq

Issue - State: closed - Opened by turbomam about 3 years ago - 1 comment

#5 - fencepost errors in chunk_harmonized_attributes_long.xq

Issue - State: closed - Opened by turbomam about 3 years ago - 1 comment

#4 - log of xqueries that are really part of make process

Issue - State: closed - Opened by turbomam about 3 years ago

#4 - log of xqueries that are really part of make process

Issue - State: closed - Opened by turbomam about 3 years ago

#2 - distinguish raw id from "BIOSAMPLE:" + id

Issue - State: closed - Opened by turbomam about 3 years ago

#1 - set up for production on large memory machines like NERSC cori

Issue - State: open - Opened by turbomam about 3 years ago - 5 comments