turbomam biosample-xmldb-sqldb issues

turbomam / biosample-xmldb-sqldb

Tools for loading NCBI Biosample into an XML database and then transforming that into a SQL database

MIT License

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

#42 turbomam closed 2 months ago
2
database competency questions

#41 turbomam opened 4 months ago
1
check for capital letters in column names... may require double quotes in queries

#40 turbomam opened 4 months ago
0
More FKs or views

#39 turbomam opened 4 months ago
0
More FTS indices on tables other than NCBI Biosample data

#38 turbomam opened 4 months ago
0
record current DDL

#37 turbomam opened 4 months ago
0
NCBI MIxS class mappings

#36 turbomam closed 4 months ago
0
what does "either_one_mandatory" mean as a NCBI Package Attribute use value?

#35 turbomam opened 4 months ago
0
Add INSDC missing value table

#34 turbomam closed 4 months ago
2
Add INSDC country code list

#33 turbomam closed 4 months ago
2
MIxS combination to NCBI Package mapping

#32 turbomam opened 4 months ago
0
NCBI Package/Attribute use

#31 turbomam closed 4 months ago
1
add taxonomy data, minimally a list of metagenome ids

#30 turbomam closed 4 months ago
5
Document process of restoring a SQL dump residing on a NERSC DTN, into a Spin-hosted Postgres container

#29 eecavanna opened 5 months ago
0
Document process of retrieving a dump from `dtn01.nersc.gov` and restoring it into a Spin-hosted Postgres server

#28 eecavanna opened 5 months ago
0
Include an alignment between GOLD Biosample IDs and NCBI Biosample IDs

#27 turbomam opened 5 months ago
9
give pivot_harmonized_attributes.py a click CLI and `[tool.poetry.scripts]` entry

#26 turbomam closed 5 months ago
0
try pre-building the destination pivot table with all harmonized name columns

#25 turbomam closed 5 months ago
0
try AWS

#24 turbomam closed 5 months ago
5
crashed during pivot_harmonized_attributes.py. Out of RAM (on host?)

#23 turbomam closed 5 months ago
0
there is a mixture of empty string and NULL values in our Postgres tables

#22 turbomam closed 5 months ago
0
"/srv/basex/shared-chunks/biosample_set_from_37000001.xml" (Line 20346097): XML document structures must start and end within the same entity.

#21 turbomam closed 5 months ago
3
Incomplete XQuery results need to be trimmed before `copy`ing into Postgres

#20 turbomam closed 5 months ago
0
Add fts (full text search) indices for some of the columns in the non_attribute_metadata Postgres table?

#19 turbomam closed 5 months ago
0
Integrate more data, like a SQL representation of MIxS and the EnvO semantic SQL database

#18 turbomam opened 5 months ago
6
What could we use as a delimiter between concatenated values besides `|||`

#17 turbomam opened 5 months ago
0
Request for PRJNA656268 metadata from Adam Martiny via Montana

#16 turbomam opened 5 months ago
2
Document reasonable Docker settings (CPU, RAM, storage, swap)

#15 turbomam opened 5 months ago
0
Look for parallelization opportunities

#14 turbomam opened 5 months ago
0
Make sure the containers are never CPU or RAM limited

#13 turbomam opened 5 months ago
0
Use host mounts for the BaseX and Postgres data directories

#12 turbomam opened 5 months ago
1
Use this as a starting point for instantiating NMDC Biosamples

#11 turbomam opened 5 months ago
0
Add code, URLs, screenshots etc to "Simon’s half-baked way of looking for relevant metagenomes in SRA"

#10 turbomam opened 5 months ago
6
Explain that NCBI's XML is chunked because there's a cap on the number of nodes in a BaseX database.

#9 turbomam closed 5 months ago
1
Provide support for writing XQueries

#8 turbomam closed 5 months ago
0
More documentation for accessing/using the BaseX web interface

#7 turbomam closed 5 months ago
0
Add support for dumping the Postgres contents in a form that can be easily loaded into another Postgres server

#6 turbomam opened 5 months ago
0
Find a better GH org for this repo

#5 turbomam opened 5 months ago
0
Repair of MIxS triad values (esp. from EnvO)

#4 turbomam opened 5 months ago
0
Repair of MIxS checklist/extension like values

#3 turbomam opened 5 months ago
6
better capture and use of BioProject identifers

#2 turbomam opened 5 months ago
0
improve chaining of `pre-basex-all`, `basex-all` and `postgres-all` targets

#1 turbomam closed 5 months ago
1