turbomam/biosample-xmldb-sqldb issues and pull requests

#42 - sparsity analysis of NCBI Biosamples via relational database created by this repo

Issue - State: closed - Opened by turbomam 5 months ago - 2 comments

#41 - database competency questions

Issue - State: open - Opened by turbomam 6 months ago - 1 comment

#40 - check for capital letters in column names... may require double quotes in queries

Issue - State: open - Opened by turbomam 7 months ago

#39 - More FKs or views

Issue - State: open - Opened by turbomam 7 months ago

#38 - More FTS indices on tables other than NCBI Biosample data

Issue - State: open - Opened by turbomam 7 months ago

#37 - record current DDL

Issue - State: open - Opened by turbomam 7 months ago

#36 - NCBI MIxS class mappings

Issue - State: closed - Opened by turbomam 7 months ago

#35 - what does "either_one_mandatory" mean as a NCBI Package Attribute use value?

Issue - State: open - Opened by turbomam 7 months ago

#34 - Add INSDC missing value table

Issue - State: closed - Opened by turbomam 7 months ago - 2 comments

#33 - Add INSDC country code list

Issue - State: closed - Opened by turbomam 7 months ago - 2 comments

#32 - MIxS combination to NCBI Package mapping

Issue - State: open - Opened by turbomam 7 months ago

#31 - NCBI Package/Attribute use

Issue - State: closed - Opened by turbomam 7 months ago - 1 comment

#30 - add taxonomy data, minimally a list of metagenome ids

Issue - State: closed - Opened by turbomam 7 months ago - 5 comments

#29 - Document process of restoring a SQL dump residing on a NERSC DTN, into a Spin-hosted Postgres container

Pull Request - State: open - Opened by eecavanna 7 months ago

#28 - Document process of retrieving a dump from `dtn01.nersc.gov` and restoring it into a Spin-hosted Postgres server

Issue - State: open - Opened by eecavanna 7 months ago

#27 - Include an alignment between GOLD Biosample IDs and NCBI Biosample IDs

Issue - State: open - Opened by turbomam 7 months ago - 9 comments

#26 - give pivot_harmonized_attributes.py a click CLI and `[tool.poetry.scripts]` entry

Issue - State: closed - Opened by turbomam 8 months ago

#25 - try pre-building the destination pivot table with all harmonized name columns

Issue - State: closed - Opened by turbomam 8 months ago

#25 - try pre-building the destination pivot table with all harmonized name columns

Issue - State: closed - Opened by turbomam 8 months ago

#24 - try AWS

Issue - State: closed - Opened by turbomam 8 months ago - 5 comments

#23 - crashed during pivot_harmonized_attributes.py. Out of RAM (on host?)

Issue - State: closed - Opened by turbomam 8 months ago

#22 - there is a mixture of empty string and NULL values in our Postgres tables

Issue - State: closed - Opened by turbomam 8 months ago

#21 - "/srv/basex/shared-chunks/biosample_set_from_37000001.xml" (Line 20346097): XML document structures must start and end within the same entity.

Issue - State: closed - Opened by turbomam 8 months ago - 3 comments

#20 - Incomplete XQuery results need to be trimmed before `copy`ing into Postgres

Issue - State: closed - Opened by turbomam 8 months ago

#19 - Add fts (full text search) indices for some of the columns in the non_attribute_metadata Postgres table?

Issue - State: closed - Opened by turbomam 8 months ago

#18 - Integrate more data, like a SQL representation of MIxS and the EnvO semantic SQL database

Issue - State: open - Opened by turbomam 8 months ago - 6 comments

#17 - What could we use as a delimiter between concatenated values besides `|||`

Issue - State: open - Opened by turbomam 8 months ago

#16 - Request for PRJNA656268 metadata from Adam Martiny via Montana

Issue - State: open - Opened by turbomam 8 months ago - 2 comments

#15 - Document reasonable Docker settings (CPU, RAM, storage, swap)

Issue - State: open - Opened by turbomam 8 months ago

#14 - Look for parallelization opportunities

Issue - State: open - Opened by turbomam 8 months ago

#13 - Make sure the containers are never CPU or RAM limited

Issue - State: open - Opened by turbomam 8 months ago

#12 - Use host mounts for the BaseX and Postgres data directories

Issue - State: open - Opened by turbomam 8 months ago - 1 comment

#11 - Use this as a starting point for instantiating NMDC Biosamples

Issue - State: open - Opened by turbomam 8 months ago

#10 - Add code, URLs, screenshots etc to "Simon’s half-baked way of looking for relevant metagenomes in SRA"

Issue - State: open - Opened by turbomam 8 months ago - 6 comments

#9 - Explain that NCBI's XML is chunked because there's a cap on the number of nodes in a BaseX database.

Issue - State: closed - Opened by turbomam 8 months ago - 1 comment

#8 - Provide support for writing XQueries

Issue - State: closed - Opened by turbomam 8 months ago

#7 - More documentation for accessing/using the BaseX web interface

Issue - State: closed - Opened by turbomam 8 months ago

#6 - Add support for dumping the Postgres contents in a form that can be easily loaded into another Postgres server

Issue - State: open - Opened by turbomam 8 months ago

#5 - Find a better GH org for this repo

Issue - State: open - Opened by turbomam 8 months ago

#4 - Repair of MIxS triad values (esp. from EnvO)

Issue - State: open - Opened by turbomam 8 months ago

#3 - Repair of MIxS checklist/extension like values

Issue - State: open - Opened by turbomam 8 months ago - 6 comments

#2 - better capture and use of BioProject identifers

Issue - State: open - Opened by turbomam 8 months ago

#1 - improve chaining of `pre-basex-all`, `basex-all` and `postgres-all` targets

Issue - State: closed - Opened by turbomam 8 months ago - 1 comment

GitHub / turbomam/biosample-xmldb-sqldb issues and pull requests