View nmdc-schema-v3.2.0-v6.0.3.src.diff
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diff --git a/src/schema/basic_slots.yaml b/src/schema/basic_slots.yaml | |
index 17c8bf3..1fa4bda 100644 | |
--- a/src/schema/basic_slots.yaml | |
+++ b/src/schema/basic_slots.yaml | |
@@ -29,7 +29,7 @@ slots: | |
description: >- | |
A unique identifier for a thing. | |
Must be either a CURIE shorthand for a URI or a complete URI | |
- #required: false # for now we setting this to false until we develop an id template | |
+ #required: false # for now we are setting this to false until we develop an id template |
View nmdc-schema-v3.2.0-v6.0.3.json.diff
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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": "", |
View Taxonomy_Flattening_Search_with_ml_jeffjames.ipynb
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View emsl_fix.csv
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id | action | attribute | value | |
---|---|---|---|---|
emsl:456424 | update | processing_institution | Environmental Molecular Sciences Laboratory |
View nmdc_envo_term_subterms.py
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""" | |
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 |
View fake_biosample.json
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{"biosample_set": [{ | |
"id": "fake3", | |
"env_broad_scale" : { | |
"term" : {"id": "ENVO:01000253"} | |
}, | |
"env_local_scale" : { | |
"term" : {"id": "ENVO:01000621"} | |
}, | |
"env_medium" : { | |
"term" : {"id": "ENVO:01000017"} |
View fake_biosample.json
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{"biosample_set": [{ | |
"id": "fake2", | |
"env_broad_scale" : { | |
"term" : {"id": "ENVO:01000253"} | |
}, | |
"env_local_scale" : { | |
"term" : {"id": "ENVO:01000621"} | |
}, | |
"env_medium" : { | |
"term" : {"id": "ENVO:01000017"} |
View file_type_enum.jsonl
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{ | |
"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\"}}", |
View sensor.py
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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 |
View all_your_zulip_are_belong_to_us.py
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""" | |
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"). | |
""" |
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