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dwinston / nmdc-schema-v3.2.0-v6.0.3.json.diff
Last active August 12, 2022 14:30
<github.com:microbiomedata/nmdc-schema>: git diff v3.2.0 v6.0.3 -- jsonschema/nmdc.schema.json
diff --git a/jsonschema/nmdc.schema.json b/jsonschema/nmdc.schema.json
index 3a18b59..1efa788 100644
--- a/jsonschema/nmdc.schema.json
+++ b/jsonschema/nmdc.schema.json
@@ -53,6 +53,28 @@
"title": "Agent",
"type": "object"
},
+ "AnalysisTypeEnum": {
+ "description": "",
@dwinston
dwinston / Taxonomy_Flattening_Search_with_ml_jeffjames.ipynb
Created July 10, 2022 13:30 — forked from jrjames83/Taxonomy_Flattening_Search_with_ml_jeffjames.ipynb
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@dwinston
dwinston / emsl_fix.csv
Created July 6, 2022 21:21
id action attribute value
emsl:456424 update processing_institution Environmental Molecular Sciences Laboratory
@dwinston
dwinston / nmdc_envo_term_subterms.py
Created April 15, 2022 18:43
build a subsumption map scoped to ENVO terms in use by NMDC biosamples
"""
Build a subsumption map scoped to ENVO terms in use by NMDC biosamples
"""
from collections import defaultdict
import json
from rdflib import Graph
from rdflib.namespace import Namespace
from tqdm import tqdm
@dwinston
dwinston / fake_biosample.json
Created November 18, 2021 13:41
{"biosample_set": [{
"id": "fake3",
"env_broad_scale" : {
"term" : {"id": "ENVO:01000253"}
},
"env_local_scale" : {
"term" : {"id": "ENVO:01000621"}
},
"env_medium" : {
"term" : {"id": "ENVO:01000017"}
@dwinston
dwinston / fake_biosample.json
Last active November 17, 2021 19:24
{"biosample_set": [{
"id": "fake2",
"env_broad_scale" : {
"term" : {"id": "ENVO:01000253"}
},
"env_local_scale" : {
"term" : {"id": "ENVO:01000621"}
},
"env_medium" : {
"term" : {"id": "ENVO:01000017"}
@dwinston
dwinston / file_type_enum.jsonl
Created October 13, 2021 20:08
{
"name" : "FT ICR-MS analysis results",
"description" : "FT ICR-MS-based metabolite assignment results table",
"filter" : "{\"url\": {\"$regex\": \"nom\\\\/results\"}, \"description\": {\"$regex\": \"FT ICR-MS\"}}",
"id" : "nmdc:sys045mx19"
}
{
"name" : "GC-MS Metabolomics Results",
"description" : "GC-MS-based metabolite assignment results table",
"filter" : "{\"url\": {\"$regex\": \"metabolomics\\\\/results\"}}",
@dwinston
dwinston / sensor.py
Created June 23, 2021 14:45
dagster resource in a sensor via preset definition run config
from dagster import (
ModeDefinition, PresetDefinition, resource, StringSource,
build_init_resource_context, RunRequest, sensor,
)
class ApiClient:
def __init__(self, base_url: str, site_id: str, client_id: str, client_secret: str):
self.base_url = base_url
self.site_id = site_id
self.client_id = client_id
@dwinston
dwinston / all_your_zulip_are_belong_to_us.py
Last active February 26, 2021 15:57
get all Zulip messages sent by non-bot users to public streams
"""
A script developed to get all Zulip messages sent by non-bot users to public streams.
Need to pip install pymongo tqdm zulip, and run a local MongoDB server.
But you can also adapt the script to append to an in-memory Python list, and not need MongoDB or pymongo.
I found that the total volume of data in my case (see in-script comments) was 700MB uncompressed.
Developed at the Recurse Center (https://www.recurse.com/) in order to apply PageRank to Zulip entities.
Licensed as <https://opensource.org/licenses/MIT>(year=2021, copyright_holder="Donny Winston").
"""
@dwinston
dwinston / machine.js
Created October 16, 2020 18:58
Generated by XState Viz: https://xstate.js.org/viz
// Available variables:
// - Machine
// - interpret
// - assign
// - send
// - sendParent
// - spawn
// - raise
// - actions