From 197d2908dc424d822e72983528f6d29b1523fdbd Mon Sep 17 00:00:00 2001
From: Gavin <gaprice@lbl.gov>
Date: Fri, 3 Nov 2023 14:07:56 -0700
Subject: [PATCH 1/2] Add genome_attribs histogram endpoint

---
 Pipfile                                       |    1 +
 Pipfile.lock                                  | 1494 +++++++++--------
 src/service/data_products/common_models.py    |   22 +
 .../data_products/genome_attributes.py        |  262 ++-
 4 files changed, 991 insertions(+), 788 deletions(-)

diff --git a/Pipfile b/Pipfile
index 3475f91a9..3a66b6b42 100644
--- a/Pipfile
+++ b/Pipfile
@@ -28,6 +28,7 @@ PyYAML = "==6.0.1"
 # abandonware
 urllib3 = "==1.26.17"
 python-dateutil = "==2.8.2"
+numpy = "==1.26.1"
 
 [dev-packages]
 pytest = "==7.4.2"
diff --git a/Pipfile.lock b/Pipfile.lock
index d68c8c4e4..ae329447d 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "67d50c5c8b10a419f753d12802d4e8364710db7512d11fb7896e72ccfb486d3f"
+            "sha256": "95108c647f859bdeeccb62703ce6a8dd301ad52215e10a256f3a5ea8fe382586"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -135,11 +135,11 @@
         },
         "annotated-types": {
             "hashes": [
-                "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802",
-                "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"
+                "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43",
+                "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"
             ],
-            "markers": "python_version >= '3.7'",
-            "version": "==0.5.0"
+            "markers": "python_version >= '3.8'",
+            "version": "==0.6.0"
         },
         "anyio": {
             "hashes": [
@@ -264,99 +264,99 @@
         },
         "charset-normalizer": {
             "hashes": [
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@@ -482,43 +482,44 @@
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@@ -724,41 +725,41 @@
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@@ -801,60 +802,60 @@
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@@ -2292,90 +2352,90 @@
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-                "sha256:fff7d17d30b2cd45afd654b3fc117755c5d84506ed25fda386494e4e0a3416e1"
+                "sha256:014e7049dd019a6663747ca7dae328943e14f7261f7c1381045dfc26a04fa330",
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+                "sha256:10a379fb60f1b2406ae57b8899bacfe20567918c8e9d2d545e1b93628fcf2050",
+                "sha256:128b1485753106c54af481789cdfea12b90a228afca0b11fb3828309a907e10e",
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+                "sha256:256c503a75bd71cf7fb9ebf889e7e222d49c6036a48aad5a619f98a0adf0e0d7",
+                "sha256:2703a9f8f5767986b4f51c259ff452cc837c5a83c8ed5f5361f6e49933743b2f",
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+                "sha256:2973f113e079fb98515722cd728e1820282721ec9fd52830e4b73cabdbf1eb28",
+                "sha256:2ca0ba501898b2ec31e6c3acf90c31910944f01d454ad8e489213a156ccf1bda",
+                "sha256:2d2be5c9c3488fa8a70f83ed925940f488eac2837a996708d98a0e54a861f212",
+                "sha256:2f8c04277d879146eacda920476e93d520eff8bec6c022ac108cfa6280d84348",
+                "sha256:325701ae7b56daa5b0692305b7cb505ca50f80a1288abb32ff420a8a209b01ca",
+                "sha256:3729b8db02063da50eeb3db88a27670d85953afb9a7f14c213ac9e3dca93034b",
+                "sha256:3919708594b86d0f5cdc713eb6fccd3f9b9532af09ea7a5d843c933825ef56c4",
+                "sha256:39a1cd5d383b37285641d5a7a86be85274466ae336a61b51117155936529f9b3",
+                "sha256:3ec6c20385c5a58e16b1ea60c5e4993ea060540671d7d12664f385f2fb32fe79",
+                "sha256:47aa128be2e66abd9d1a9b0437c62499d812d291f17b55185cb4aa33a5f710a4",
+                "sha256:49f2af6cf82509b15093ce3569229e0d53c90ad8ae2eef940652d4cf1f81e045",
+                "sha256:4a0269811661ba93c472c8a60ea82640e838c2eb148d252720a09b5123f2c2fe",
+                "sha256:518c90bdd6e842c446d01a766b9136fec5ec6cc94f3b8c3f8b4a332786ee6b64",
+                "sha256:5717a308a703dda2886a5796a07489c698b442f5e409cf7dc2ac93de8d61d764",
+                "sha256:5802acc012bbb4bce4dff92973dff76482f30ef35dd4cb8ab5b0e06aa8f08c80",
+                "sha256:5e63146dbdb1eac207464f6e0cfcdb640c9c5ff0f57b754fa96fe252314a1dc6",
+                "sha256:6695d7136a435c1305b261a9ddb9b3ecec9863e05aab3935b96038145fd3a977",
+                "sha256:680fa0fc719e1a3dcb81130858368f51d83667d431924d0bcf249644bce8f303",
+                "sha256:6b18276f14b4b6d92e707ab6db19b938e112bd2f1dc3f9f1a628df58e4fd3f0d",
+                "sha256:6bafea6061d63059d8bc2ffc545e2f049221c8a4457d236c5cd6a66678673eab",
+                "sha256:6d6a1b1361f118e7fefa17ae3114e77f10ee1b228b20d50c47c9f351346180c8",
+                "sha256:747c84f4e690fbe6999c90ac97246c95d31460d890510e4a3fa61b7d2b87aa34",
+                "sha256:79f41576b3022c2fe9780ae3e44202b2438128a25284a8ddfa038f0785d87019",
+                "sha256:7b0e6361754ac596cd16bfc6ed49f69ffcd9b60b7bc4bcd3ea65c6a83475e4ff",
+                "sha256:7e3b0127b260d4abae7b62203c4c7ef0874c901b55155692353db19de4b18bc4",
+                "sha256:7fc2bb8a74dcfcdd32f89528e38dcbf70a3a6594963d60dc9595e3b35b66e414",
+                "sha256:806e094e9e85d8badc978af8c95b69c556077f11844655cb8cd2d1758769e521",
+                "sha256:81dd1308bd5630d2bb5980f00aa163b986b133f1e9ed66c66ce2a5bc3572e891",
+                "sha256:82e620842e12e8cb4050d2643a81c8149361cd82c0a920fa5a15dc4ca8a4000f",
+                "sha256:85f2cdc400ee87f5952ebf2a117488f2525a3fb2e23863a8efe3e4ee9e54e4d1",
+                "sha256:8ab6bcc8e424e07c1d4ba6df96f7fb963bcb48f590b9456de9ebd03b88084fe8",
+                "sha256:8adf014f2779992eba3b513e060d06f075f0ab2fb3ad956f413a102312f65cdf",
+                "sha256:9b0f98481ad5dc4cb430a60bbb8869f05505283b9ae1c62bdb65eb5e020ee8e3",
+                "sha256:9bea9138b0fc6e2218147e9c6ce1ff76ff8e29dc00bb1b64842bd1ca107aee9f",
+                "sha256:a09bfb51953930e7e838972ddf646c5d5f984992a66d79da6ba7f6a8d8a890cd",
+                "sha256:a0be99b599da95b7a90a918dd927b20c434bea5e1c9b3efc6a3c6cd67c23f813",
+                "sha256:a49aca4d961823b2846b739380c847e8964ff7ae0f0a683992b9d926054f0d6d",
+                "sha256:a4dc1319d0c162919ee7f4ee6face076becae2abbd351cc14f1fe70af5fb20d9",
+                "sha256:a8273e1abbcff1d7d29cbbb1ea7e57d38be72f1af3c597c854168508b91516c2",
+                "sha256:a8f7f9feecae53fa18d6a3ea7c75f9e9a1d4d20e5c3f9ce3fba83f07bcc4eee2",
+                "sha256:ad4f66fbb893b55f96f03020e67dcab49ffde0177c6565ccf9dec4fdf974eb61",
+                "sha256:af425f323fce1b07755edd783581e7283557296946212f5b1a934441718e7528",
+                "sha256:b14dd73f595199f4275bed4fb509277470d9b9059310537e3b3daba12b30c157",
+                "sha256:b4ad70d7cac4ca0c7b31444a0148bd3af01a2662fa12b1ad6f57cd4a04e21766",
+                "sha256:b80a4ee19b3442c57c38afa978adca546521a8822d663310b63ae2a7d7b13f3a",
+                "sha256:ba51129fcc510824b6ca6e2ce1c27e3e4d048b6e35d3ae6f7e517bed1b8b25ce",
+                "sha256:c011bd5ad03cc096f99ffcfdd18a1817354132c1331bed7a837a25226659845f",
+                "sha256:cc94f9fea17a5af8cf1a343597711a26b0117c0b812550d99934acb89d526ed2",
+                "sha256:ccd785fafa1c931deff6a7116e9a0d402d59fabe51644b0d0c268295ff847b25",
+                "sha256:d16a534da0e39785687b7295e2fcf9a339f4a20689024983d11afaa4657f8507",
+                "sha256:d3077a31633beef77d057c6523f5de7271ddef7bde5e019285b00c0cc9cac1e3",
+                "sha256:d603edea1ff7408638b2504905c032193b7dcee7af269802dbb35bc8c3310ed5",
+                "sha256:db082f728160369d9a6ed2e722438291558fc15ce06d0a7d696a8dad735c236b",
+                "sha256:ddef295aaf80cefb0c1606f1995899efcb17edc6b327eb6589e234e614b87756",
+                "sha256:e16ade71c93f6814d095d25cd6d28a90d63511ea396bd96e9ffcb886b278baaa",
+                "sha256:e3db7d833a7c38c317dc95b54e27f1d27012e031b45a7c24e360b53197d5f6e7",
+                "sha256:e5e193f89f4f8c1fe273f9a6e6df915092c9f2af6db2d1afb8bd53855025c11f",
+                "sha256:eb438a8bf6b695bf50d57e6a059ff09652a07968b2041178b3744ea785fcef9b",
+                "sha256:ebf02c32afa6b67e5861a27183dd98ed88419a94a2ab843cc145fb0bafcc5b28",
+                "sha256:ecd9e1fa97aa11bf67472220285775fa15e896da108f425e55d23d7540a712ce",
+                "sha256:ef67fedd863ffffd4adfd46d9d992b0f929c7f61a8307366d664d93517f2c78e",
+                "sha256:f28ae33dc5a0b9cee06e95fd420e42155d83271ab75964baf747ce959cac5f52",
+                "sha256:fb1c56d891f9e34303c451998ef62ba52659648bb0d75b03c5e4ac223a3342c2",
+                "sha256:fe03bf25fae4b95d8afe40004a321df644400fdcba4c8e5e1a19c1085b740888"
             ],
             "index": "pypi",
-            "version": "==4.5.0"
+            "version": "==4.6.0"
         },
         "pyparsing": {
             "hashes": [
@@ -2488,18 +2548,18 @@
         },
         "traitlets": {
             "hashes": [
-                "sha256:7564b5bf8d38c40fa45498072bf4dc5e8346eb087bbf1e2ae2d8774f6a0f078e",
-                "sha256:98277f247f18b2c5cabaf4af369187754f4fb0e85911d473f72329db8a7f4fae"
+                "sha256:9b232b9430c8f57288c1024b34a8f0251ddcc47268927367a0dd3eeaca40deb5",
+                "sha256:baf991e61542da48fe8aef8b779a9ea0aa38d8a54166ee250d5af5ecf4486619"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==5.11.2"
+            "version": "==5.13.0"
         },
         "wcwidth": {
             "hashes": [
-                "sha256:77f719e01648ed600dfa5402c347481c0992263b81a027344f3e1ba25493a704",
-                "sha256:8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4"
+                "sha256:9a929bd8380f6cd9571a968a9c8f4353ca58d7cd812a4822bba831f8d685b223",
+                "sha256:a675d1a4a2d24ef67096a04b85b02deeecd8e226f57b5e3a72dbb9ed99d27da8"
             ],
-            "version": "==0.2.8"
+            "version": "==0.2.9"
         }
     }
 }
diff --git a/src/service/data_products/common_models.py b/src/service/data_products/common_models.py
index 75d4e7097..c9dca4642 100644
--- a/src/service/data_products/common_models.py
+++ b/src/service/data_products/common_models.py
@@ -148,6 +148,15 @@ class DataProductMissingIDs(SubsetProcessStates):
 )]
 
 
+QUERY_VALIDATOR_MATCH_ID_NO_MARK = Annotated[str, Query(
+    description="A match ID to set the view to the match rather than "
+        + "the entire collection. Authentication is required. If a match ID is "
+        # matches are against a specific load version, so...
+        + "set, any load version override is ignored. "
+        + "If a selection filter and a match filter are provided, they are ANDed together."
+)]
+
+
 QUERY_VALIDATOR_MATCH_MARK = Annotated[bool, Query(
     description="Whether to mark matched rows rather than filter based on the match ID."
 )]
@@ -168,6 +177,13 @@ class DataProductMissingIDs(SubsetProcessStates):
 )]
 
 
+QUERY_VALIDATOR_SELECTION_ID_NO_MARK = Annotated[str, Query(
+    description="A selection ID to set the view to the selection rather than the entire "
+        + "collection. If a selection ID is set, any load version override is ignored. "
+        + "If a selection filter and a match filter are provided, they are ANDed together."
+)]
+
+
 QUERY_VALIDATOR_SELECTION_MARK = Annotated[bool, Query(
     description="Whether to mark selected rows rather than filter based on the selection ID."
 )]
@@ -199,3 +215,9 @@ class DataProductMissingIDs(SubsetProcessStates):
 QUERY_VALIDATOR_OUTPUT_TABLE = Annotated[bool, Query(
     description="Whether to return the data in table form or dictionary list form"
 )]
+
+
+QUERY_VALIDATOR_CONJUNCTION = Annotated[bool, Query(
+    description="Whether to AND (true) or OR (false) filters together."
+)]
+
diff --git a/src/service/data_products/genome_attributes.py b/src/service/data_products/genome_attributes.py
index 08c4f648f..0b3da456c 100644
--- a/src/service/data_products/genome_attributes.py
+++ b/src/service/data_products/genome_attributes.py
@@ -7,6 +7,10 @@
 from typing import Any, Callable, Annotated
 
 from fastapi import APIRouter, Request, Depends, Query
+from pydantic import BaseModel
+from pydantic import Field
+
+import numpy as np
 
 import src.common.storage.collection_and_field_names as names
 from src.common.product_models import columnar_attribs_common_models as col_models
@@ -25,6 +29,7 @@
     remove_marked_subset,
     override_load_version,
     query_table,
+    query_simple_collection_list,
     get_collection_singleton_from_db,
 )
 from src.service.data_products import common_models
@@ -48,6 +53,52 @@
 
 _ROUTER = APIRouter(tags=["Genome Attributes"], prefix=f"/{ID}")
 
+_FILTERING_TEXT = """
+**FILTERING:**
+
+The returned data can be filtered by column content by adding query parameters of the format
+```
+filter_<column name>=<filter criteria>
+```
+For example:
+```
+GET <host>/collections/GTBD/data_products/genome_attribs/?filter_Completeness=[80,90]
+```
+
+The filter criteria depends on the type of the column and its filter strategy.
+
+```
+Type    Strategy  Filter criteria
+------  --------  ---------------
+string  fulltext  arbitrary string
+string  prefix    arbitrary string
+date              range (see below)
+int               range (see below)
+float             range (see below)
+```
+
+Full text searches tokenize, stem, and normalize the input and removes stop words.  
+Prefix searches tokenize and lower case the input and match the beginning of words in the
+data being searched.  
+
+Range criteria takes the form of a low and high limit to apply to the data. At least one of the
+two limits must be provided. A comma separated the limits. Square brackets on either side
+of the limits denote the limit is inclusive; parentheses or no character denote that the limit
+is exclusive. For example:
+
+```
+1,          numbers greater than 1
+[1,         numbers greater or equal to 1
+,6)         numbers less than 6
+,6]         numbers less than or equal to six
+1,6         numbers greater than 1 and less than six
+[1,6]       numbers between 1 and 6, inclusive
+```
+
+Note that the OpenAPI UI does not allow entering arbitrary query parameters and therefore is
+not usable for column filtering operations.
+"""
+
 
 class GenomeAttribsSpec(common_models.DataProductSpec):
 
@@ -235,21 +286,7 @@ def _remove_keys(doc):
 _FILTER_PREFIX = "filter_"
 
 
-async def _get_filters(
-    r: Request,
-    arango_coll,
-    coll: models.ActiveCollection,
-    load_ver: str,
-    load_ver_override: bool,
-    count: bool,
-    sort_on: str,
-    sort_desc: bool,
-    filter_conjunction: bool,
-    match_spec: SubsetSpecification,
-    selection_spec: SubsetSpecification,
-    skip: int,
-    limit: int,
-) -> FilterSet:
+def _get_filter_map(r: Request) -> dict[str, str]:
     filter_query = {}
     for q in r.query_params.keys():
         if q.startswith(_FILTER_PREFIX):
@@ -258,19 +295,52 @@ async def _get_filters(
                 raise errors.IllegalParameterError(
                     f"More than one filter specification provided for field {field}")
             filter_query[field] = r.query_params[q]
+    return filter_query
+
+
+async def _get_filters(
+    r: Request,
+    arango_coll: str,
+    coll_id: str,
+    load_ver: str,
+    load_ver_override: bool,
+    view_name: str = None,
+    count: bool = False,
+    sort_on: str = None,
+    sort_desc: bool = False,
+    filter_conjunction: bool = True,
+    match_spec: SubsetSpecification = None,
+    selection_spec: SubsetSpecification = None,
+    keep: dict[str, set[col_models.ColumnType]] = None,
+    skip: int = 0,
+    limit: int = 1000,
+) -> FilterSet:
+    filter_query = _get_filter_map(r)
     appstate = app_state.get_app_state(r)
     column_meta = await _get_genome_attributes_meta_internal(
-        appstate.arangostorage, coll.id, load_ver, load_ver_override)
-    view_name = coll.get_data_product(ID).search_view
+        appstate.arangostorage, coll_id, load_ver, load_ver_override)
     if filter_query and not view_name:
-        raise ValueError(f"No search view name configured for collection {coll.id}, "
+        if load_ver_override:
+            # If we need this feature than the admin needs to supply the view name to use
+            # via the API
+            raise ValueError("Filtering is not supported with a load version override.")
+        raise ValueError(f"No search view name configured for collection {coll_id}, "
             + "data product {ID}. Cannot perform filtering operation")
     columns = {c.key: c for c in column_meta.columns}
     if sort_on and sort_on not in columns:
         raise errors.IllegalParameterError(
-            f"No such field for collection {coll.id} load version {load_ver}: {sort_on}")
+            f"No such field for collection {coll_id} load version {load_ver}: {sort_on}")
+    if keep:
+        for col in keep:
+            if col not in columns:
+                raise errors.IllegalParameterError(
+                    f"No such field for collection {coll_id} load version {load_ver}: {col}")
+            if keep[col] and columns[col].type not in keep[col]:
+                raise errors.IllegalParameterError(
+                    f"Column {col} is type '{columns[col].type}', which is not one of the "
+                    + f"acceptable types for this operation: {[t.value for t in keep[col]]}")
     fs = FilterSet(
-        coll.id,
+        coll_id,
         load_ver,
         collection=arango_coll,
         view=view_name,
@@ -280,9 +350,18 @@ async def _get_filters(
         conjunction=filter_conjunction,
         match_spec=match_spec,
         selection_spec=selection_spec,
+        keep=list(keep.keys()) if keep else None,
         skip=skip,
         limit=limit
     )
+    return _append_filters(fs, filter_query, columns)
+
+
+def _append_filters(
+    fs: FilterSet,
+    filter_query: dict[str, str],
+    columns: dict[str, col_models.AttributesColumn]
+) -> FilterSet:
     for field, querystring in filter_query.items():
         if field not in columns:
             raise errors.IllegalParameterError(f"No such filter field: {field}")
@@ -364,50 +443,8 @@ async def _get_genome_attributes_meta_internal(
 When creating selections from genome attributes, use the
 `{names.FLD_KBASE_ID}` field values as input.
 
-**FILTERING:**
-
-The returned data can be filtered by column content by adding query parameters of the format
-```
-filter_<column name>=<filter criteria>
-```
-For example:
-```
-GET <host>/collections/GTBD/data_products/genome_attribs/?filter_Completeness=[80,90]
-```
-
-The filter criteria depends on the type of the column and its filter strategy.
-
-```
-Type    Strategy  Filter criteria
-------  --------  ---------------
-string  fulltext  arbitrary string
-string  prefix    arbitrary string
-date              range (see below)
-int               range (see below)
-float             range (see below)
-```
-
-Full text searches tokenize, stem, and normalize the input and removes stop words.  
-Prefix searches tokenize and lower case the input and match the beginning of words in the
-data being searched.  
-
-Range criteria takes the form of a low and high limit to apply to the data. At least one of the
-two limits must be provided. A comma separated the limits. Square brackets on either side
-of the limits denote the limit is inclusive; parentheses or no character denote that the limit
-is exclusive. For example:
-
-```
-1,          numbers greater than 1
-[1,         numbers greater or equal to 1
-,6)         numbers less than 6
-,6]         numbers less than or equal to six
-1,6         numbers greater than 1 and less than six
-[1,6]       numbers between 1 and 6, inclusive
-```
-
-Note that the OpenAPI UI does not allow entering arbitrary query parameters and therefore is
-not usable for column filtering operations.
-""")
+""" + _FILTERING_TEXT
+)
 async def get_genome_attributes(
     r: Request,
     collection_id: str = PATH_VALIDATOR_COLLECTION_ID,
@@ -417,9 +454,7 @@ async def get_genome_attributes(
     limit: common_models.QUERY_VALIDATOR_LIMIT = 1000,
     output_table: common_models.QUERY_VALIDATOR_OUTPUT_TABLE = True,
     count: common_models.QUERY_VALIDATOR_COUNT = False,
-    conjunction: Annotated[bool, Query(
-        description="Whether to AND (true) or OR (false) filters together."
-    )] = True,
+    conjunction: common_models.QUERY_VALIDATOR_CONJUNCTION = True,
     match_id: common_models.QUERY_VALIDATOR_MATCH_ID = None,
     # TODO FEATURE support a choice of AND or OR for matches & selections
     match_mark: common_models.QUERY_VALIDATOR_MATCH_MARK_SAFE = False,
@@ -437,8 +472,21 @@ async def get_genome_attributes(
     match_spec = await _get_match_spec(appstate, user, coll, match_id, match_mark)
     sel_spec = await _get_selection_spec(appstate, coll, selection_id, selection_mark)
     filters = await _get_filters(
-        r, names.COLL_GENOME_ATTRIBS, coll, load_ver, load_ver_override, count,
-        sort_on, sort_desc, conjunction, match_spec, sel_spec, skip, limit)
+        r,
+        names.COLL_GENOME_ATTRIBS,
+        collection_id,
+        load_ver,
+        load_ver_override,
+        view_name=coll.get_data_product(ID).search_view if coll else None,
+        count=count,
+        sort_on=sort_on,
+        sort_desc=sort_desc,
+        filter_conjunction=conjunction,
+        match_spec=match_spec,
+        selection_spec=sel_spec,
+        skip=skip,
+        limit=limit,
+    )
     res = await query_table(
         appstate.arangostorage, filters, output_table=output_table, document_mutator=_remove_keys)
     return {
@@ -451,12 +499,84 @@ async def get_genome_attributes(
     }
 
 
+class Histogram(BaseModel):
+    
+    bins: Annotated[list[float], Field(
+        example=[2.5, 3.5, 4.5],
+        description="The location of the histogram bins. Each bin starts at index i, "
+            + "inclusive, and ends at index i + 1, exclusive, except for the last bin which is "
+            + "inclusive at both sides."
+    )]
+    values: Annotated[list[int], Field(
+        example=[78.5, 96, 1],
+        description="The values of the bins."
+    )]
+
+
+@_ROUTER.get(
+    "/hist",
+    response_model=Histogram,
+    description=
+"""
+Get a histogram for the data in one column in the table.
+
+Authentication is not required unless submitting a match ID or overriding the load
+version; in the latter case service administration permissions are required.
+
+""" + _FILTERING_TEXT
+)
+async def get_histogram(
+    r: Request,
+    column: Annotated[str, Query(
+        example="Completeness",
+        description="The column containing the data to include in the histogram."
+    )],
+    collection_id: str = PATH_VALIDATOR_COLLECTION_ID,
+    conjunction: common_models.QUERY_VALIDATOR_CONJUNCTION = True,
+    match_id: common_models.QUERY_VALIDATOR_MATCH_ID_NO_MARK = None,
+    # TODO FEATURE support a choice of AND or OR for matches & selections
+    selection_id: common_models.QUERY_VALIDATOR_SELECTION_ID_NO_MARK = None,
+    load_ver_override: common_models.QUERY_VALIDATOR_LOAD_VERSION_OVERRIDE = None,
+    user: kb_auth.KBaseUser = Depends(_OPT_AUTH)
+):
+    appstate = app_state.get_app_state(r)
+    lvo = override_load_version(load_ver_override, match_id, selection_id)
+    coll, load_ver = await get_load_version(appstate.arangostorage, collection_id, ID, lvo, user)
+    match_spec = await _get_match_spec(appstate, user, coll, match_id)
+    sel_spec = await _get_selection_spec(appstate, coll, selection_id)
+    filters = await _get_filters(
+        r,
+        names.COLL_GENOME_ATTRIBS,
+        collection_id,
+        load_ver,
+        load_ver_override,
+        view_name=coll.get_data_product(ID).search_view if coll else None,
+        filter_conjunction=conjunction,
+        match_spec=match_spec,
+        selection_spec=sel_spec,
+        # May want to support strings & dates in the future, but will need to figure out how to
+        # get the histogram code to work with dates (truncated ISO8601 in the DB).
+        # For strings just need to make a sorted dict and skip the histogram code altogether
+        keep={column: {col_models.ColumnType.FLOAT, col_models.ColumnType.INT}},
+        limit=0,
+    )
+    data = []
+    await query_simple_collection_list(
+        appstate.arangostorage,
+        filters,
+        lambda d: data.append(d[column]),
+    )
+    # may want to add some controls for histogram, like bin count / range?
+    hist, bin_edges = np.histogram(data)
+    return Histogram(bins=bin_edges, values=hist)
+
+
 async def _get_match_spec(
     appstate: CollectionsState,
     user: kb_auth.KBaseUser,
     coll: models.SavedCollection,
     match_id: str,
-    match_mark: bool,
+    match_mark: bool = False,
 ) -> SubsetSpecification:
     if not match_id:
         return SubsetSpecification()
@@ -477,7 +597,7 @@ async def _get_selection_spec(
     appstate: CollectionsState,
     coll: models.SavedCollection,
     selection_id: str,
-    selection_mark: bool,
+    selection_mark: bool = False,
 ) -> SubsetSpecification:
     if not selection_id:
         return SubsetSpecification()

From 14ced609dd8dc058b0857f1aa33a7381c999ccb3 Mon Sep 17 00:00:00 2001
From: Gavin <gaprice@lbl.gov>
Date: Tue, 7 Nov 2023 09:23:35 -0800
Subject: [PATCH 2/2] Fix histogram example docs

---
 src/service/data_products/genome_attributes.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/service/data_products/genome_attributes.py b/src/service/data_products/genome_attributes.py
index 0b3da456c..cc356eea1 100644
--- a/src/service/data_products/genome_attributes.py
+++ b/src/service/data_products/genome_attributes.py
@@ -502,13 +502,14 @@ async def get_genome_attributes(
 class Histogram(BaseModel):
     
     bins: Annotated[list[float], Field(
-        example=[2.5, 3.5, 4.5],
+        example=[2.5, 3.5, 4.5, 5.5],
         description="The location of the histogram bins. Each bin starts at index i, "
             + "inclusive, and ends at index i + 1, exclusive, except for the last bin which is "
-            + "inclusive at both sides."
+            + "inclusive at both sides. As such, if there are n bins, there will be n + 1 bin "
+            + "locations in the array."
     )]
     values: Annotated[list[int], Field(
-        example=[78.5, 96, 1],
+        example=[78, 96, 1],
         description="The values of the bins."
     )]