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Af 146 configargparse #444

Merged
merged 99 commits into from Jan 24, 2019
Merged

Af 146 configargparse #444

merged 99 commits into from Jan 24, 2019

Commits on Nov 23, 2018

  1. move some things to harmonized config

    @afaulconbridge
    afaulconbridge committed Nov 23, 2018
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  2. removed unused config options

    @afaulconbridge
    afaulconbridge committed Nov 23, 2018
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  3. temporarily re-add envparse to allow intermediate testing

    @afaulconbridge
    afaulconbridge committed Nov 23, 2018
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  4. remove lingering config option

    @afaulconbridge
    afaulconbridge committed Nov 23, 2018
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  5. remove unneeded import

    @afaulconbridge
    afaulconbridge committed Nov 23, 2018
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  6. add default redis host and port

    @afaulconbridge
    afaulconbridge committed Nov 23, 2018
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  7. cleanup redis commands and tests

    @afaulconbridge
    afaulconbridge committed Nov 23, 2018
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  8. formatting fix

    @afaulconbridge
    afaulconbridge committed Nov 23, 2018
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  9. logging fixes

    @afaulconbridge
    afaulconbridge committed Nov 23, 2018
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  10. remove unused tempfiles

    @afaulconbridge
    afaulconbridge committed Nov 23, 2018
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Commits on Nov 26, 2018

  1. merge from master

    @afaulconbridge
    afaulconbridge committed Nov 26, 2018
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  2. merge from master

    @afaulconbridge
    afaulconbridge committed Nov 26, 2018
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Commits on Nov 27, 2018

  1. resolve conflicts properly

    @afaulconbridge
    afaulconbridge committed Nov 27, 2018
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  2. remove unused config

    @afaulconbridge
    afaulconbridge committed Nov 27, 2018
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  3. remove more unused config

    @afaulconbridge
    afaulconbridge committed Nov 27, 2018
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  4. remove invalid documentation

    @afaulconbridge
    afaulconbridge committed Nov 27, 2018
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Commits on Dec 5, 2018

  1. merge from master

    @afaulconbridge
    afaulconbridge committed Dec 5, 2018
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  2. added extra args from master

    @afaulconbridge
    afaulconbridge committed Dec 5, 2018
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Commits on Dec 7, 2018

  1. revert some changes to restore functionallity

    @afaulconbridge
    afaulconbridge committed Dec 7, 2018
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  2. fixes to arguments

    @afaulconbridge
    afaulconbridge committed Dec 7, 2018
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  3. disable queue tests as it interacts poorly with lookuptables test

    @afaulconbridge
    afaulconbridge committed Dec 7, 2018
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  4. remove some settings, reformat cfg

    @afaulconbridge
    afaulconbridge committed Dec 7, 2018
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Commits on Dec 11, 2018

  1. cleanup

    @afaulconbridge
    afaulconbridge committed Dec 11, 2018
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  2. cleanup

    @afaulconbridge
    afaulconbridge committed Dec 11, 2018
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  3. fix logging configuration control

    @afaulconbridge
    afaulconbridge committed Dec 11, 2018
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  4. move reactome pathways to config file

    @afaulconbridge
    afaulconbridge committed Dec 11, 2018
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  5. Merge branch 'master' into af-146-configargparse

    @afaulconbridge
    afaulconbridge committed Dec 11, 2018
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Commits on Dec 12, 2018

  1. Merge branch 'master' into af-146-configargparse

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  2. update num workers docs

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  3. merge from af-371-reactome-updates

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  4. Merge branch 'af-372-hgnc-urlzsource' into af-146-configargparse

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  5. Merge branch 'af-373-orthologs-urlzsource' into af-146-configargparse

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  6. fix missed merge

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  7. re-add required import

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  8. merge from master

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  9. Merge branch 'master' into af-146-configargparse

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  10. hgnc plugin, and wider plugin config

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  11. correctly use known args

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  12. correctly use known args again

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  13. add otholog plugin config

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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  14. merge from master

    @afaulconbridge
    afaulconbridge committed Dec 12, 2018
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Commits on Dec 14, 2018

  1. remove old ortholog and use new config

    @afaulconbridge
    afaulconbridge committed Dec 14, 2018
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Commits on Dec 19, 2018

  1. update plugin argument handling, adapt mousephenotypes

    @afaulconbridge
    afaulconbridge committed Dec 19, 2018
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Commits on Dec 20, 2018

  1. disable partial redis reconfig

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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  2. cleanup

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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  3. Merge branch 'master' into af-146-configargparse

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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  4. move uniprot uri

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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  5. add default uniprot config

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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  6. update cancer biomarkers plugin

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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  7. update chemical probes

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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  8. update hallmark config

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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  9. tractability plugin

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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  10. update ensembl filename

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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  11. fix tractability ref

    @afaulconbridge
    afaulconbridge committed Dec 20, 2018
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Commits on Dec 21, 2018

  1. move index name and document type constants

    @afaulconbridge
    afaulconbridge committed Dec 21, 2018
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  2. tissue curation and translation

    @afaulconbridge
    afaulconbridge committed Dec 21, 2018
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Commits on Jan 9, 2019

  1. Reactome module and setting update. Unit test updated

    Cinzia Malangone committed Jan 9, 2019
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Commits on Jan 10, 2019

  1. merge from master

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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  2. fix merge issues with reactome

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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  3. remove unused functions

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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  4. remove unused code

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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  5. remove ontology_config.ini

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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  6. merge from master

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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  7. fix typos in hpa args

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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  8. merge from master

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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  9. merge from master

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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  10. lookup helper uri handling fixes

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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  11. Merge branch 'master' into af-146-configargparse

    @afaulconbridge
    afaulconbridge committed Jan 10, 2019
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Commits on Jan 11, 2019

  1. syntax fix

    @afaulconbridge
    afaulconbridge committed Jan 11, 2019
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Commits on Jan 14, 2019

  1. chembl api configuration

    @afaulconbridge
    afaulconbridge committed Jan 14, 2019
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  2. fix disease phenotype

    @afaulconbridge
    afaulconbridge committed Jan 14, 2019
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  3. eco scores handling

    @afaulconbridge
    afaulconbridge committed Jan 14, 2019
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  4. remove evidene_sources.txt

    @afaulconbridge
    afaulconbridge committed Jan 14, 2019
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  5. Merge branch 'master' into af-146-configargparse

    @afaulconbridge
    afaulconbridge committed Jan 14, 2019
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  6. fix chembl in search

    @afaulconbridge
    afaulconbridge committed Jan 14, 2019
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Commits on Jan 17, 2019

  1. move gene plugin to configuration file

    @afaulconbridge
    afaulconbridge committed Jan 17, 2019
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  2. move HPA configuration

    @afaulconbridge
    afaulconbridge committed Jan 17, 2019
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  3. move validator config

    @afaulconbridge
    afaulconbridge committed Jan 17, 2019
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  4. move elasticsearch config

    @afaulconbridge
    afaulconbridge committed Jan 17, 2019
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  5. remove broken tests

    @afaulconbridge
    afaulconbridge committed Jan 17, 2019
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Commits on Jan 18, 2019

  1. improve input files and logging configuration

    @afaulconbridge
    afaulconbridge committed Jan 18, 2019
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  2. merge from master

    @afaulconbridge
    afaulconbridge committed Jan 18, 2019
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  3. remove excess checking and downloading

    @afaulconbridge
    afaulconbridge committed Jan 18, 2019
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  4. split data and ops config

    @afaulconbridge
    afaulconbridge committed Jan 18, 2019
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  5. create log dir on travis

    @afaulconbridge
    afaulconbridge committed Jan 18, 2019
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Commits on Jan 21, 2019

  1. more data options

    @afaulconbridge
    afaulconbridge committed Jan 21, 2019
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Commits on Jan 22, 2019

  1. merge from aster

    @afaulconbridge
    afaulconbridge committed Jan 22, 2019
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  2. merge from af-esquery-cleanup

    @afaulconbridge
    afaulconbridge committed Jan 22, 2019
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  3. remove empty file

    @afaulconbridge
    afaulconbridge committed Jan 22, 2019
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  4. cleanup merge

    @afaulconbridge
    afaulconbridge committed Jan 22, 2019
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  5. fix ops config, hpa es

    @afaulconbridge
    afaulconbridge committed Jan 22, 2019
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  6. fix typo

    @afaulconbridge
    afaulconbridge committed Jan 22, 2019
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  7. tweak makefile es prfix handling

    @afaulconbridge
    afaulconbridge committed Jan 22, 2019
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  8. add default data config filename

    @afaulconbridge
    afaulconbridge committed Jan 22, 2019
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  9. remove chembl from lookuphelper

    @afaulconbridge
    afaulconbridge committed Jan 22, 2019
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  10. travis fixing

    @afaulconbridge
    afaulconbridge committed Jan 22, 2019
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Commits on Jan 23, 2019

  1. search and evidence fixes

    @afaulconbridge
    afaulconbridge committed Jan 23, 2019
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Commits on Jan 24, 2019

  1. bug fix

    @afaulconbridge
    afaulconbridge committed Jan 24, 2019
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  2. Merge branch 'master' into af-146-configargparse

    @afaulconbridge
    afaulconbridge committed Jan 24, 2019
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