pombase / pombase-chado-json Goto Github PK

Dependabot can't resolve your Rust dependency files.

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The error Dependabot encountered was:

error: failed to parse manifest at `/home/dependabot/dependabot-updater/dependabot_tmp_dir/Cargo.toml`

Caused by:
  editions are unstable

Caused by:
  feature `edition` is required

this Cargo does not support nightly features, but if you
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Create a table for each top level key in the current JSON file. Create two columns: ID and json_blob. Use compression.

Then change the server code to query SQLite instead of holding everything in memory - big job.

Current top level keys:

• alleles
• annotation_details
• children_by_termid
• chromosomes
• gene_expression_measurements
• gene_name_gene_map
• gene_query_data_map
• gene_subsets
• gene_summaries
• genes
• genotypes
• interactors_of_genes
• other_features
• references
• term_subsets
• term_summaries
• termid_genes
• termid_genotype_annotation
• terms
• transcripts

Exception, because it is not a map:

• seq_feature_page_features

In the mini-curation feed on the front page there are publications that are still in progress like:

• https://www.pombase.org/reference/PMID:31941401
• https://www.pombase.org/reference/PMID:20967237

@ValWood

Instead of failing when a user tries a query.

This also helps a Babraham issue: sometimes the database isn't available the first time a container is started.

Replace the Perl code.

They look like this in the contig files like: /db_xref="SPD:50/50G04"

We should store just the annotation IDs in the terms and genes. There is a lot of duplication in the JSON file especially for term because we including annotation from descendent on term pages.

The same annotation ID appears twice in the annotations array for one of the terms in the SPBC776.02c JSON. This duplicate is discarded by the web code but we should find out what the cause is:

 {
    "term": "FYPO:0005450",
    "is_not": false,
    "annotations": [
      237667,
      237667
    ],
    "summary": [
      {
        "genotype_uniquenames": [
          "dis1-288-unknown-unknown-expression-not_assayed__dis2-11-unknown-unknown-expression-not_assayed__dis2delta__dis3-54-P509L-amino_acid_mutation-expression-not_assayed__ppa1delta__ppe1delta__sds21delta"
        ]
      }
    ]
  },

The gene details need to be added to genes_by_uniquename.

eg. https://www.pombase.org/gene/SPBC725.16 for "binds promoter of cdc22" the identifier in Chado is "SPAC1F7.05-promoter"

pombase/website#904

Currently if JSON file generation fails we end up with broken web site. We need to monitor the process and only update the site if the load looks good and JSON generation works.

We'll only update the "beta" site from the nightly load.

Dependabot can't resolve your Rust dependency files.

As a result, Dependabot couldn't update your dependencies.

The error Dependabot encountered was:

error: failed to parse manifest at `/home/dependabot/dependabot-updater//dependabot_tmp_dir/Cargo.toml`

Caused by:
  editions are unstable

Caused by:
  feature `edition` is required

this Cargo does not support nightly features, but if you
switch to nightly channel you can add
`cargo-features = ["edition"]` to enable this feature

If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.

You can mention @dependabot in the comments below to contact the Dependabot team.

We need to write out the files that aren't static so we can update the FTP site each night.

So we can add a message on the allele pages saying that the allele is obsolete / has no annotation.