[Bug] Phytozome fetch invalid

[alpapan]

$ python -m jcvi.apps.fetch
Usage:
    python -m jcvi.apps.fetch ACTION


Available ACTIONs:
        bisect | Determine the version of the accession by querying entrez
       ensembl | Retrieve genomes and annotations from ensembl
        entrez | Fetch records from entrez using a list of GenBank accessions
     phytozome | Retrieve genomes and annotations from phytozome
    phytozome9 | Retrieve genomes and annotations from phytozome version 9.0 (legacy)
           sra | Retrieve files from SRA via the sra-instant FTP

JCVI utility libraries v1.1.17 [Copyright (c) 2010-2024, Haibao Tang]

$ python -m jcvi.apps.fetch phytozome
Phytozome Login: myusername
Phytozome Password:
--2024-02-15 01:12:29--  http://genome.jgi.doe.gov/ext-api/downloads/get-directory?organism=PhytozomeV12
Resolving genome.jgi.doe.gov (genome.jgi.doe.gov)... 104.18.38.140, 172.64.149.116, 2606:4700:4400::6812:268c, ...
Connecting to genome.jgi.doe.gov (genome.jgi.doe.gov)|104.18.38.140|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://genome.jgi.doe.gov/ext-api/downloads/get-directory?organism=PhytozomeV12 [following]
--2024-02-15 01:12:29--  https://genome.jgi.doe.gov/ext-api/downloads/get-directory?organism=PhytozomeV12
Connecting to genome.jgi.doe.gov (genome.jgi.doe.gov)|104.18.38.140|:443... connected.
HTTP request sent, awaiting response... 307 Temporary Redirect
Location: https://genome.jgi.doe.gov/portal/ext-api/downloads/get-directory?organism=PhytozomeV12 [following]
--2024-02-15 01:12:30--  https://genome.jgi.doe.gov/portal/ext-api/downloads/get-directory?organism=PhytozomeV12
Reusing existing connection to genome.jgi.doe.gov:443.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/xml]
Saving to: '.phytozome_directory_V12.xml'

.phytozome_directory_V12.xml                                [   <=>                                                                                                                          ] 480.05K   548KB/s    in 0.9s

2024-02-15 01:12:33 (548 KB/s) - '.phytozome_directory_V12.xml' saved [491576]

Traceback (most recent call last):
  File "/apps/packages/miniconda/3.1/envs/jcvi/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/apps/packages/miniconda/3.1/envs/jcvi/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/apps/packages/miniconda/3.1/envs/jcvi/lib/python3.9/site-packages/jcvi/apps/fetch.py", line 726, in <module>
    main()
  File "/apps/packages/miniconda/3.1/envs/jcvi/lib/python3.9/site-packages/jcvi/apps/fetch.py", line 136, in main
    p.dispatch(globals())
  File "/apps/packages/miniconda/3.1/envs/jcvi/lib/python3.9/site-packages/jcvi/apps/base.py", line 110, in dispatch
    globals[action](sys.argv[2:])
  File "/apps/packages/miniconda/3.1/envs/jcvi/lib/python3.9/site-packages/jcvi/apps/fetch.py", line 278, in phytozome
    genomes = g.get_genomes()
  File "/apps/packages/miniconda/3.1/envs/jcvi/lib/python3.9/site-packages/jcvi/apps/biomart.py", line 34, in get_genomes
    root = PhytozomePath(next(self.iter(tag="organismDownloads")))
  File "/apps/packages/miniconda/3.1/envs/jcvi/lib/python3.9/site-packages/jcvi/apps/biomart.py", line 69, in __init__
    for child in element.getchildren():
AttributeError: 'xml.etree.ElementTree.Element' object has no attribute 'getchildren'

[tanghaibao]

@alpapan

Thank you for the bug report. I'll take a look when I get back (traveling this week).

Haibao

[tanghaibao]

@alpapan

This is due to older version that you use. Would you please try upgrade jcvi by pip install -U jcvi?
This should fix the issue.

I also found an additional issue that was reported in #619 that Vvinifera (grape) is no longer available for download in Phytozome. Since many people are trying out first from the wiki tutorial (which uses grape as an example; peach is fine though), I'll have to use a different example. But this is a data issue, not code issue.

Haibao

[tanghaibao]

The wiki is temporarily upgraded to reflect the unavailability of grape via direct download. Please use the portal for a manual download of grape.

[alpapan]

Thanks. I used the latest bioconda. Easy fix.