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Merge Camerian's changes from A la carte into master #32

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Merge Camerian's changes from A la carte into master #32

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Commits on Sep 30, 2022

  1. Debugging the webdriver. Chrome seems to have an issue, trying firefo… 

    …x. This failed on the first try (I think it timed out waiting for firefox to launch), and succeeded on the second (once firefox had launched). More work needed.
    @colemathis
    colemathis committed Sep 30, 2022
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  2. Chromedriver working!!

    @colemathis
    colemathis committed Sep 30, 2022
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  3. Updating docs to reflect Chromedriver success

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    colemathis committed Sep 30, 2022
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Commits on Oct 7, 2022

  1. Updating JGI to not take so long, replacing explicit time.sleep with … 

    …a command to wait for the webdriver to confirm page is ready
    @colemathis
    colemathis committed Oct 7, 2022
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  2. Remove egg-info from repo tracking

    @colemathis
    colemathis committed Oct 7, 2022
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Commits on Oct 8, 2022

  1. Update the find_elements_by_tag_name to work with newer versions of s… 

    …elenium
    @colemathis
    colemathis committed Oct 8, 2022
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Commits on Oct 12, 2022

  1. General Debugging and work flow issues

    @colemathis
    colemathis committed Oct 12, 2022
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Commits on Nov 8, 2022

  1. tacked on fxn at end, not yet integrated into Kegg class, for catalog… 

    …uing and documenting transferred EC numbers
    @camerianm
    camerianm committed Nov 8, 2022
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  2. Merge branch 'driver_debug' of https://github.com/ELIFE-ASU/ecg into … 

    …driver_debug
    @camerianm
    camerianm committed Nov 8, 2022
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Commits on Mar 24, 2023

  1. streamlined EC transfer steps and x-referencing of EC-RN ties in KEGG

    @camerianm
    camerianm committed Mar 24, 2023
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  2. Deleted Untitled.ipynb 

    Making room for actual demo NB
    @camerianm
    camerianm authored Mar 24, 2023
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Commits on Apr 19, 2023

  1. removed excess content from enzyme-info scraping; removed metadata sc… 

    …raping as this is now available in bulk download
    @camerianm
    camerianm committed Apr 19, 2023
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  2. notebook demonstrating a la carte taxon-ID enzyme count download

    @camerianm
    camerianm committed Apr 19, 2023
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Commits on Jul 19, 2023

  1. KO edit of jgi data pull

    @camerianm
    camerianm committed Jul 19, 2023
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  2. KO file URLs from KO count and gene counts in metadata CSV file downl… 

    …oaded 03-25-2023; avoids the need to visit main metagenome page during data import
    @camerianm
    camerianm committed Jul 19, 2023
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Commits on Jul 27, 2023

  1. scrape_urls_unsafe_alacarte added to enable use of JGI metadata bulk … 

    …download file in formulating EC and KO urls
    @camerianm
    camerianm committed Jul 27, 2023
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  2. notebook demonstrating a la carte download of EC/KO data when presenc… 

    …e of EC/KO list is known from JGI bulk-download metadata file
    @camerianm
    camerianm committed Jul 27, 2023
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Commits on Nov 14, 2023

  1. download progress indicator

    @camerianm
    camerianm committed Nov 14, 2023
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Commits on Dec 14, 2023

  1. removed excess content

    @camerianm
    camerianm committed Dec 14, 2023
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  2. removed excess file

    @camerianm
    camerianm committed Dec 14, 2023
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  3. working on JGI ECG docs

    @colemathis
    colemathis committed Dec 14, 2023
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  4. Merge branch 'alacarte' of https://github.com/ELIFE-ASU/ecg into alac… 

    …arte
    @colemathis
    colemathis committed Dec 14, 2023
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  5. added IMG/M metadata for Trembath-Reichert et al 2019

    @camerianm
    camerianm committed Dec 14, 2023
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  6. typos in readme

    @colemathis
    colemathis committed Dec 14, 2023
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  7. screenshots of IMG/M process

    @camerianm
    camerianm committed Dec 14, 2023
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  8. Merge branch 'alacarte' of https://github.com/ELIFE-ASU/ecg into alac… 

    …arte
    @camerianm
    camerianm committed Dec 14, 2023
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  9. add images to readme

    @colemathis
    colemathis committed Dec 14, 2023
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  10. filters metadata file to identify eligible samples

    @camerianm
    camerianm committed Dec 14, 2023
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  11. Merge branch 'alacarte' of https://github.com/ELIFE-ASU/ecg into alac… 

    …arte
    @camerianm
    camerianm committed Dec 14, 2023
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  12. expected output from running FormForDownloads.ipynb on example folder

    @camerianm
    camerianm committed Dec 14, 2023
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Commits on Dec 15, 2023

  1. modified FormForDownloads to specify metatranscriptomes or metagenomes

    @camerianm
    camerianm committed Dec 15, 2023
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