quietlight/skraak_mcp - Change 5LMYPB2QHNVDLYCRWLOMCPY35ZKHHPYVW5XHASE66L6PJZSOCXYQC

finished migration, and fixed README.md

Created by quietlight on February 13, 2026

5LMYPB2QHNVDLYCRWLOMCPY35ZKHHPYVW5XHASE66L6PJZSOCXYQC

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main

Change contents

File addition: schema_old.sql (---x------)

[4.161589]

-- NOTE: DBML does not like functions and materialised views
-- from this: $npm install -g @dbml/cli
-- sql2dbml schema.sql --postgres -o schema.dbml
-- from this: $npm install -g @softwaretechnik/dbml-renderer
-- dbml-renderer -i schema.dbml -o schema.svg
-- junction table for files-dataset relationship
-- (file can be a member of many datasets)
-- (selections apply only to 1 dataset)
-- use suncalc.js
-- could use a function for night, on client not db, but want to filter on night
-- in file table use mid point of file as time
-- all times must be zoned to utc
-- dataset type enum
CREATE TYPE dataset_type AS ENUM ('organise', 'test', 'train');
-- ALTER TYPE dataset_type ADD VALUE 'miscellaneous';
-- Dataset Table
-- Add type column to the dataset table, so that I do not ever mix testing data with training data.
CREATE TABLE dataset (
    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    name VARCHAR(255) NOT NULL,
    description VARCHAR(255),
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    type dataset_type NOT NULL DEFAULT 'organise'
);
-- Not implemented but desirable, used uniqe index instead
-- ALTER TABLE dataset ADD CONSTRAINT uq_dataset_name UNIQUE (name);
-- Not implemented Error:
-- No support for that ALTER TABLE option yet!
CREATE UNIQUE INDEX idx_dataset_name ON dataset(name);
CREATE INDEX idx_dataset_active ON dataset(active);
CREATE INDEX idx_dataset_public ON dataset(public);
-- Locations Table
CREATE TABLE location (
    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    dataset_id VARCHAR(12) NOT NULL, -- nanoid, link to dataset
    name VARCHAR(140) NOT NULL,
    latitude DECIMAL(10, 7) NOT NULL CHECK (latitude BETWEEN -90.0 AND 90.0), -- -45.5027
    longitude DECIMAL(10, 7) NOT NULL CHECK (longitude BETWEEN -180.0 AND 180.0), -- 167.48406
    description VARCHAR(255), -- Limited to 255 characters for efficiency
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    timezone_id VARCHAR(40) NOT NULL, -- XXnot required as may need to auto generate cluster, can't always ask or check
    FOREIGN KEY (dataset_id) REFERENCES dataset(id)
);
-- N
--ALTER TABLE location ADD CONSTRAINT uq_location_dataset_name UNIQUE (dataset_id, name);
CREATE UNIQUE INDEX idx_location_dataset_name ON location(dataset_id, name);
CREATE INDEX idx_location_name ON location(name);
CREATE INDEX idx_location_dataset ON location(dataset_id); -- ??
CREATE INDEX idx_location_active ON location(active); -- ??
CREATE INDEX idx_location_dataset_active ON location(dataset_id, active);
-- Add recording pattern, mainly so it can be searchable,
-- this is an optional field, audio moth needs this, to help
-- with searching and filtering
-- i have 24/7: 1 in 30 and 1 in 40
CREATE TABLE cyclic_recording_pattern (
    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    record_s INTEGER NOT NULL,
    sleep_s INTEGER NOT NULL,
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    -- UNIQUE (record_s, sleep_s) -- not implemented as duckdb won't allow an alter table, should be though.
);
-- Could not do this as duckdb refuses, the unique index is meant to do it.
-- Add unique constraint
-- ALTER TABLE cyclic_recording_pattern
-- ADD CONSTRAINT unique_record_sleep UNIQUE (record_s, sleep_s);
CREATE INDEX idx_cyclic_recording_pattern_active ON cyclic_recording_pattern(active);
-- Ensure no duplicate record/sleep combinations
CREATE UNIQUE INDEX idx_cyclic_recording_pattern_unique_combo ON cyclic_recording_pattern(record_s, sleep_s);
-- Cluster Table (think of a cluster of files as all the files on 1 SD Card)
-- a statistical unit with no major time gaps, to enable call rate stats
-- See changes below, added foreign key on location, added recording pattern
-- added timezone_id for iana timezone id
CREATE TABLE cluster (
    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    dataset_id VARCHAR(12) NOT NULL, -- nanoid, link to dataset
    location_id VARCHAR(12) NOT NULL, -- A cluster must have a location, as well as a dataset
    name VARCHAR(140) NOT NULL,
    description VARCHAR(255), -- Limited to 255 characters for efficiency
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    cyclic_recording_pattern_id VARCHAR(12),
    sample_rate INTEGER NOT NULL,
    path VARCHAR(255) NULL, -- optional hint for local access
    FOREIGN KEY (dataset_id) REFERENCES dataset(id),
    FOREIGN KEY (location_id) REFERENCES location(id),
    FOREIGN KEY (cyclic_recording_pattern_id) REFERENCES cyclic_recording_pattern(id)
);
-- Not implemented but desirable, using unique index instead
-- ALTER TABLE cluster ADD CONSTRAINT uq_cluster_location_name UNIQUE (location_id, name);
CREATE UNIQUE INDEX idx_cluster_location_name ON cluster(location_id, name);
CREATE INDEX idx_cluster_dataset ON cluster(dataset_id);
CREATE INDEX idx_cluster_active ON cluster(active);
CREATE INDEX idx_cluster_dataset_active ON cluster(dataset_id, active);
CREATE INDEX idx_cluster_recording_pattern ON cluster(cyclic_recording_pattern_id);
CREATE INDEX idx_cluster_location_id ON cluster(location_id);
-- values in my data is medium and medium-high
CREATE TYPE gain_level AS ENUM ('low', 'low-medium', 'medium', 'medium-high', 'high');
-- Files Table (removed dataset_id as now use junction table)
-- Note: timestamp_local should reflect local time, not timestamp in filename, this is important
-- duration must not have more than 3 decimal places, check in ui
CREATE TABLE file (
    id VARCHAR(21) PRIMARY KEY, -- nanoid
    file_name VARCHAR(255) NOT NULL,
    xxh64_hash VARCHAR(16) NOT NULL, -- hash of original file cbe675a69a5fef1c
    location_id VARCHAR(12) NOT NULL, -- nanoid, from locations table
    timestamp_local TIMESTAMP WITH TIME ZONE NOT NULL, -- parsed from filename, adjust for daylight saving
    cluster_id VARCHAR(12), -- nanoid(12), optional if imported one by one
    duration DECIMAL(7, 3) NOT NULL CHECK (duration > 0), -- in seconds, allowing for millisecond precision (9999.999s)
    sample_rate INTEGER NOT NULL,
    description VARCHAR(255), -- Limited to 255 characters for efficiency
    maybe_solar_night BOOLEAN, --calculate with function on client. this is a more accurate value to file table
    maybe_civil_night BOOLEAN, --calculate with function on client. this is a more accurate value to file table
    moon_phase DECIMAL(3,2) CHECK (moon_phase BETWEEN 0.00 AND 1.00), -- 0.00 to 1.00 (new moon to full moon)
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    FOREIGN KEY (location_id) REFERENCES location(id),
    FOREIGN KEY (cluster_id) REFERENCES cluster(id)
);
CREATE INDEX idx_file_location ON file(location_id);
CREATE INDEX idx_file_active ON file(active);
CREATE INDEX idx_file_timestamp_local ON file(timestamp_local);
CREATE INDEX idx_file_cluster ON file(cluster_id);
CREATE INDEX idx_file_maybe_solar_night ON file(maybe_solar_night);
CREATE INDEX idx_file_maybe_civil_night ON file(maybe_civil_night);
-- ALTER TABLE file
--     ALTER COLUMN location_id DROP NOT NULL;
-- UNIMPLEMENTED
-- Unique constraint on xxh64_hash to prevent duplicate file hashes
-- ALTER TABLE file ADD CONSTRAINT unique_xxh64_hash UNIQUE (xxh64_hash);
CREATE TABLE moth_metadata (
    file_id VARCHAR(21) PRIMARY KEY,
    timestamp TIMESTAMP WITH TIME ZONE NOT NULL,
    recorder_id VARCHAR(16), -- 24F31901603710CD (16)
    gain gain_level NULL, -- low, medium, high or null
    battery_v DECIMAL(2, 1) CHECK (battery_v >= 0), -- for values from 0 to 9.9
    temp_c DECIMAL(3, 1), -- e.g., 24.2
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    FOREIGN KEY (file_id) REFERENCES file(id)
);
CREATE INDEX idx_moth_metadata_active ON moth_metadata(active);
CREATE TABLE file_metadata (
    file_id VARCHAR(21) PRIMARY KEY,
    json JSON, -- For noise levels and other file-level metadata
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    FOREIGN KEY (file_id) REFERENCES file(id)
);
-- CREATE INDEX idx_file_metadata_json ON file_metadata USING gin(json); -- unimplemented
CREATE INDEX idx_file_metadata_active ON file_metadata(active);
-- Junction Table for Files to Dataset (many-to-many)
CREATE TABLE file_dataset (
    file_id VARCHAR(21) NOT NULL,
    dataset_id VARCHAR(12) NOT NULL,
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    PRIMARY KEY (file_id, dataset_id),
    FOREIGN KEY (file_id) REFERENCES file(id),
    FOREIGN KEY (dataset_id) REFERENCES dataset(id)
);
-- indexes for the junction table
CREATE INDEX idx_file_dataset_file ON file_dataset(file_id);
CREATE INDEX idx_file_dataset_dataset ON file_dataset(dataset_id);
-- Selection Table
CREATE TABLE selection(
    id VARCHAR(21) PRIMARY KEY, -- nanoid
    file_id VARCHAR(21) NOT NULL, -- nanoid
    dataset_id VARCHAR(12) NOT NULL, -- nanoid, link to dataset
    start_time DECIMAL(7,3) NOT NULL, --up to 9999.999 seconds
    end_time DECIMAL(7,3) NOT NULL, -- up to 9999.999 seconds
    freq_low DECIMAL(9,3) CHECK (freq_low < 300000), -- LOOK AT CHECK
    freq_high DECIMAL(9,3) CHECK (freq_high < 300000), -- LOOK AT CHECK
    description VARCHAR(255), -- Limited to 255 characters for efficiency
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    FOREIGN KEY (file_id) REFERENCES file(id),
    FOREIGN KEY (dataset_id) REFERENCES dataset(id)
);
CREATE INDEX idx_selection_file ON selection(file_id);
CREATE INDEX idx_selection_dataset ON selection(dataset_id);
CREATE INDEX idx_selection_active ON selection(active);
CREATE TABLE selection_metadata (
    selection_id VARCHAR(21) PRIMARY KEY,
    json JSON, -- for loudness, noise, and other selection-level metadaata
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    FOREIGN KEY (selection_id) REFERENCES selection(id)
);
-- CREATE INDEX idx_selection_metadata_json ON selection_metadata USING gin(json); -- unimplemensed
CREATE INDEX idx_selection_metadata_active ON selection_metadata(active);
-- eBird Taxonomy Table
-- will need to update INDEX too when introducing a new version
-- see working with ebird taxonomies, aichat, deepseek, macbook
-- see materialised view and index on it
-- see alter table stuff below, modifications
CREATE TABLE ebird_taxonomy (
    id VARCHAR(12) PRIMARY KEY,
    taxonomy_version VARCHAR(4) NOT NULL,
    taxon_order INTEGER NOT NULL,
    category VARCHAR(15) NOT NULL,
    species_code VARCHAR(15) NOT NULL,
    taxon_concept_id VARCHAR(15),
    primary_com_name VARCHAR(100) NOT NULL,
    sci_name VARCHAR(100) NOT NULL,
    bird_order VARCHAR(30),
    family VARCHAR(100),
    species_group VARCHAR(100),
    report_as VARCHAR(15),
    valid_from DATE NOT NULL,
    valid_to DATE,
    UNIQUE (species_code, taxonomy_version)
);
-- Species Table (mutable)
CREATE TABLE species (
    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    label VARCHAR(100) NOT NULL, -- display label for the species
    ebird_code VARCHAR(12), -- link to ebird taxonomy
    taxonomy_version VARCHAR(4),
    description VARCHAR(255),
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    FOREIGN KEY (ebird_code, taxonomy_version) REFERENCES ebird_taxonomy(species_code, taxonomy_version)
);
CREATE INDEX idx_species_label ON species(label);
CREATE INDEX idx_species_ebird ON species(ebird_code);
-- Call Types Table (mutable)
CREATE TABLE call_type (
    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    species_id VARCHAR(12) NOT NULL, -- link to parent species
    label VARCHAR(100) NOT NULL, -- display name like "male", "female", "duet"
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN DEFAULT TRUE,
    FOREIGN KEY (species_id) REFERENCES species(id)
);
CREATE INDEX idx_call_type_species ON call_type(species_id);
CREATE INDEX idx_call_type_label ON call_type(label);
CREATE TABLE filter (
    id VARCHAR(12) PRIMARY KEY, -- nanoid
    name VARCHAR(140) NOT NULL,
    description VARCHAR(255),
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN NOT NULL DEFAULT true
);
-- Label Table, many to 1 relationship with
CREATE TABLE label (
    id VARCHAR(21) PRIMARY KEY, -- nanoid
    selection_id VARCHAR(21) NOT NULL, -- link to selection table
    species_id VARCHAR(12) NOT NULL, -- link to species table
    filter_id VARCHAR(12),
    certainty DECIMAL(5,2) CHECK (certainty <= 100 AND certainty >= 0),
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN NOT NULL DEFAULT true,
    FOREIGN KEY (selection_id) REFERENCES selection(id),
    FOREIGN KEY (species_id) REFERENCES species(id),
    FOREIGN KEY (filter_id) REFERENCES filter(id)
);
CREATE INDEX idx_label_selection_id ON label(selection_id);
CREATE INDEX idx_label_species_id ON label(species_id);
-- Label Sub-type Table (optional 1:1 relationship with label)
CREATE TABLE label_subtype (
    id VARCHAR(21) PRIMARY KEY, -- nanoid
    label_id VARCHAR(21) NOT NULL, -- link to parent label
    calltype_id VARCHAR(12) NOT NULL, -- link to call_type table
    filter_id VARCHAR(12),
    certainty DECIMAL(5,2) CHECK (certainty <= 100 AND certainty >= 0),
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    active BOOLEAN NOT NULL DEFAULT true,
    FOREIGN KEY (label_id) REFERENCES label(id),
    FOREIGN KEY (calltype_id) REFERENCES call_type(id),
    FOREIGN KEY (filter_id) REFERENCES filter(id)
    -- UNIQUE (label_id) -- ensures 1:1 relationship with label. how do i handle multiple call type filters? needs 1:many relation
);
-- UNIMPLEMENTED
-- file_dataset must exist first
-- Referential Integrity for Selections
-- To ensure `selections.dataset_id` is valid for the associated file:
-- Add composite foreign key (requires file_dataset to exist first)
-- ALTER TABLE selection ADD CONSTRAINT fk_selection_file_dataset
-- FOREIGN KEY (file_id, dataset_id) REFERENCES file_dataset(file_id, dataset_id);
-- 2024 Taxonomy View, after populating underlying table
-- see working with ebird taxonomies, aichat, deepseek, macbook
-- I think I still need this to display the options when someone creates a species
CREATE TABLE ebird_taxonomy_v2024 AS
SELECT
    id,
    species_code,
    primary_com_name,
    sci_name,
    bird_order, -- AS "order",  order is reserved word in pgsql
    family
FROM ebird_taxonomy
WHERE taxonomy_version = '2024';
-- to help with plain text search on common name and scientific name
CREATE INDEX idx_ebird_name_search ON ebird_taxonomy_v2024 USING gin(to_tsvector('english', primary_com_name || ' ' || sci_name));
CREATE INDEX ebird_taxonomy_species_code ON ebird_taxonomy_v2024(species_code);
-- Junction Table for Species to Dataset (many-to-many)
CREATE TABLE species_dataset (
    species_id VARCHAR(12) NOT NULL,
    dataset_id VARCHAR(12) NOT NULL,
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    PRIMARY KEY (species_id, dataset_id),
    FOREIGN KEY (species_id) REFERENCES species(id),
    FOREIGN KEY (dataset_id) REFERENCES dataset(id)
);
-- indexes for the junction table
CREATE INDEX idx_species_dataset_species ON species_dataset(species_id);
CREATE INDEX idx_species_dataset_dataset ON species_dataset(dataset_id);

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Replacement in db/schema.svg at line 355 [4.172440]

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Replacement in db/schema.svg at line 363 [4.172440]

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Replacement in db/schema.svg at line 393 [4.172440]
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Replacement in db/schema.svg at line 395 [4.172440]

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B:BD[4.283190] → [4.283190:283219]
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[4.283190]
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Replacement in db/schema.svg at line 912 [4.172440]

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Replacement in db/schema.svg at line 959 [4.172440]

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Replacement in db/schema.svg at line 968 [4.172440]

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Replacement in db/schema.svg at line 975 [4.172440]
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Replacement in db/schema.svg at line 977 [4.172440]

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<text text-anchor="start" x="4600.21" y="-443.85" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c"> </text>
<text text-anchor="start" x="4609.1" y="-443.85" font-family="Helvetica,sans-Serif" font-weight="bold" font-size="32.00" fill="#29235c">(!)</text>
<polygon fill="none" stroke="#29235c" stroke-width="2" points="4205.8,-421.65 4205.8,-843.65 4650.8,-843.65 4650.8,-421.65 4205.8,-421.65"/>

Replacement in db/schema.svg at line 1079 [4.172440]
B:BD[4.303183] → [4.303183:303212]
```
<g id="edge36" class="edge">
```
[4.303183]
[4.303212]
```
<g id="edge38" class="edge">
```

Replacement in db/schema.svg at line 1081 [4.172440]

B:BD[4.303252] → [5.92887:93409]

<path fill="none" stroke="#29235c" stroke-width="3" d="M3884.15,-2333.95C4032.29,-2333.95 4022.99,-2162.28 4163.76,-2154.24"/>
<polygon fill="#29235c" stroke="#29235c" stroke-width="3" points="4164.26,-2157.72 4174.16,-2153.95 4164.06,-2150.73 4164.26,-2157.72"/>
<text text-anchor="middle" x="4167.93" y="-2163.55" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">*</text>
<text text-anchor="middle" x="3875.25" y="-2343.55" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">1</text>

[4.303252]

[4.303774]

<path fill="none" stroke="#29235c" stroke-width="3" d="M4651.3,-752.65C4759.42,-752.65 4764.78,-841.08 4804.48,-941.65 4877.56,-1126.81 4743.51,-1818.45 4931.22,-1842.03"/>
<polygon fill="#29235c" stroke="#29235c" stroke-width="3" points="4931.11,-1845.53 4941.3,-1842.65 4931.54,-1838.55 4931.11,-1845.53"/>
<text text-anchor="middle" x="4935.08" y="-1813.85" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">*</text>
<text text-anchor="middle" x="4642.4" y="-723.85" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">1</text>

Replacement in db/schema.svg at line 1088 [4.172440]
B:BD[4.303855] → [4.303855:303884]
```
<g id="edge42" class="edge">
```
[4.303855]
[4.303884]
```
<g id="edge44" class="edge">
```

Replacement in db/schema.svg at line 1090 [4.172440]

B:BD[4.303932] → [5.93410:94079]

<path fill="none" stroke="#29235c" stroke-width="3" d="M3884.15,-2333.95C4086.61,-2333.95 3978.83,-2098.76 4037.33,-1904.95 4056.52,-1841.38 4021.03,-1800.85 4073.33,-1759.95 4311.97,-1573.31 4517.54,-1571.79 4754.98,-1759.95 4955.08,-1918.51 4638.12,-2315.88 4877.79,-2326.72"/>
<polygon fill="#29235c" stroke="#29235c" stroke-width="3" points="4878,-2330.22 4888.08,-2326.95 4878.16,-2323.23 4878,-2330.22"/>
<text text-anchor="middle" x="4881.86" y="-2336.55" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">*</text>
<text text-anchor="middle" x="3875.25" y="-2305.15" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">1</text>

[4.303932]

[4.304601]

<path fill="none" stroke="#29235c" stroke-width="3" d="M4651.3,-752.65C5038.81,-752.65 5200.48,-579.54 5522.13,-795.65 5635.22,-871.64 5521.51,-1070.22 5645.08,-1080.26"/>
<polygon fill="#29235c" stroke="#29235c" stroke-width="3" points="5645.1,-1083.76 5655.23,-1080.65 5645.37,-1076.76 5645.1,-1083.76"/>
<text text-anchor="middle" x="5649" y="-1051.85" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">*</text>
<text text-anchor="middle" x="4642.4" y="-762.25" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">1</text>

Replacement in db/schema.svg at line 1097 [4.172440]
B:BD[4.304680] → [4.304680:304709]
```
<g id="edge38" class="edge">
```
[4.304680]
[4.304709]
```
<g id="edge40" class="edge">
```

Replacement in db/schema.svg at line 1099 [4.172440]

B:BD[4.304756] → [5.94080:94601]

<path fill="none" stroke="#29235c" stroke-width="3" d="M4654.16,-2333.95C4766.12,-2333.95 4772.33,-2440.21 4877.9,-2446.64"/>
<polygon fill="#29235c" stroke="#29235c" stroke-width="3" points="4877.98,-2450.14 4888.08,-2446.95 4878.19,-2443.15 4877.98,-2450.14"/>
<text text-anchor="middle" x="4881.86" y="-2456.55" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">*</text>
<text text-anchor="middle" x="4645.26" y="-2343.55" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">1</text>

[4.304756]

[4.305277]

<path fill="none" stroke="#29235c" stroke-width="3" d="M5421.3,-2022.65C5607.79,-2022.65 5470.47,-1230.08 5645.26,-1201.45"/>
<polygon fill="#29235c" stroke="#29235c" stroke-width="3" points="5645.54,-1204.94 5655.23,-1200.65 5644.98,-1197.96 5645.54,-1204.94"/>
<text text-anchor="middle" x="5649" y="-1171.85" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">*</text>
<text text-anchor="middle" x="5412.41" y="-1993.85" font-family="Helvetica,sans-Serif" font-size="32.00" fill="#29235c">1</text>

Deletion in db/schema.sql at line 6 [4.305331]

∅:D[2.99] → [4.305489:305769]

B:BD[4.305489] → [4.305489:305769]


-- junction table for files-dataset relationship
-- (file can be a member of many datasets)
-- (selections apply only to 1 dataset)
-- use suncalc.js
-- could use a function for night, on client not db, but want to filter on night
-- in file table use mid point of file as time

Replacement in db/schema.sql at line 7 [4.305331]

B:BD[4.305770] → [2.100:134]

-- all times must be zoned to utc

[4.305770]

[4.305805]

CREATE TYPE dataset_type AS ENUM ('structured', 'unstructured', 'test', 'train');

Deletion in db/schema.sql at line 9 [4.305331]

B:BD[4.305806] → [4.305806:305891]

B:BD[4.305891] → [3.107:162]

∅:D[3.162] → [4.305891:306009]

B:BD[4.305891] → [4.305891:306009]

-- dataset type enum
CREATE TYPE dataset_type AS ENUM ('organise', 'test', 'train');
-- ALTER TYPE dataset_type ADD VALUE 'miscellaneous';
-- Dataset Table
-- Add type column to the dataset table, so that I do not ever mix testing data with training data.

Replacement in db/schema.sql at line 10 [4.305331]

B:BD[4.306032] → [4.306032:306110]

    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    name VARCHAR(255) NOT NULL,

[4.306032]

[4.306110]

    id VARCHAR(12) PRIMARY KEY, 
    name VARCHAR(255) UNIQUE NOT NULL,

Replacement in db/schema.sql at line 16 [4.305331]

B:BD[4.306310] → [4.306310:306360]

    type dataset_type NOT NULL DEFAULT 'organise'

[4.306310]

[4.306360]

    type dataset_type NOT NULL DEFAULT 'structured'

Deletion in db/schema.sql at line 18 [4.305331]

B:BD[4.306363] → [4.306363:306364]

B:BD[4.306364] → [2.135:336]


-- Not implemented but desirable, used uniqe index instead
-- ALTER TABLE dataset ADD CONSTRAINT uq_dataset_name UNIQUE (name);
-- Not implemented Error:
-- No support for that ALTER TABLE option yet!

Deletion in db/schema.sql at line 19 [4.305331]

B:BD[2.337] → [2.337:392]

∅:D[2.392] → [4.306412:306536]

B:BD[4.306412] → [4.306412:306536]

CREATE UNIQUE INDEX idx_dataset_name ON dataset(name);
CREATE INDEX idx_dataset_active ON dataset(active);
CREATE INDEX idx_dataset_public ON dataset(public);
-- Locations Table

Replacement in db/schema.sql at line 20 [4.305331]

B:BD[4.306560] → [4.306560:306670]

    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    dataset_id VARCHAR(12) NOT NULL, -- nanoid, link to dataset

[4.306560]

[4.306670]

    id VARCHAR(12) PRIMARY KEY, 
    dataset_id VARCHAR(12) NOT NULL,

Replacement in db/schema.sql at line 23 [4.305331]

B:BD[4.306702] → [4.306702:306961]

    latitude DECIMAL(10, 7) NOT NULL CHECK (latitude BETWEEN -90.0 AND 90.0), -- -45.5027
    longitude DECIMAL(10, 7) NOT NULL CHECK (longitude BETWEEN -180.0 AND 180.0), -- 167.48406
    description VARCHAR(255), -- Limited to 255 characters for efficiency

[4.306702]

[4.306961]

    latitude DECIMAL(10, 7) NOT NULL CHECK (latitude BETWEEN -90.0 AND 90.0), 
    longitude DECIMAL(10, 7) NOT NULL CHECK (longitude BETWEEN -180.0 AND 180.0), 
    description VARCHAR(255),

Replacement in db/schema.sql at line 29 [4.305331]

B:BD[4.307131] → [4.307131:307303]

    timezone_id VARCHAR(40) NOT NULL, -- XXnot required as may need to auto generate cluster, can't always ask or check
    FOREIGN KEY (dataset_id) REFERENCES dataset(id)

[4.307131]

[4.307303]

    timezone_id VARCHAR(40) NOT NULL, 
    FOREIGN KEY (dataset_id) REFERENCES dataset(id),
    UNIQUE (dataset_id, name)

Deletion in db/schema.sql at line 33 [4.305331]

B:BD[4.307306] → [2.393:488]

∅:D[2.488] → [4.307306:307307]

B:BD[4.307306] → [4.307306:307307]

B:BD[4.307307] → [2.489:566]

∅:D[2.566] → [4.307307:307556]

B:BD[4.307307] → [4.307307:307556]

-- N
--ALTER TABLE location ADD CONSTRAINT uq_location_dataset_name UNIQUE (dataset_id, name);
CREATE UNIQUE INDEX idx_location_dataset_name ON location(dataset_id, name);
CREATE INDEX idx_location_name ON location(name);
CREATE INDEX idx_location_dataset ON location(dataset_id); -- ??
CREATE INDEX idx_location_active ON location(active); -- ??
CREATE INDEX idx_location_dataset_active ON location(dataset_id, active);

Deletion in db/schema.sql at line 34 [4.305331]

B:BD[4.307557] → [4.307557:307744]

-- Add recording pattern, mainly so it can be searchable,
-- this is an optional field, audio moth needs this, to help
-- with searching and filtering
-- i have 24/7: 1 in 30 and 1 in 40

Replacement in db/schema.sql at line 35 [4.305331]
B:BD[4.307784] → [4.307784:307830]
```
    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
```
[4.307784]
[4.307830]
```
    id VARCHAR(12) PRIMARY KEY, 
```

Replacement in db/schema.sql at line 41 [4.305331]

B:BD[6.67722] → [6.67722:67831]

    -- UNIQUE (record_s, sleep_s) -- not implemented as duckdb won't allow an alter table, should be though.

[6.67722]

[4.308060]

    UNIQUE (record_s, sleep_s)

Deletion in db/schema.sql at line 43 [4.305331]

B:BD[4.308063] → [4.308063:308064]

B:BD[4.308064] → [6.67832:68040]

∅:D[6.68040] → [4.308064:308151]

B:BD[4.308064] → [4.308064:308151]

B:BD[4.308151] → [6.68041:68200]


-- Could not do this as duckdb refuses, the unique index is meant to do it.
-- Add unique constraint
-- ALTER TABLE cyclic_recording_pattern
-- ADD CONSTRAINT unique_record_sleep UNIQUE (record_s, sleep_s);
CREATE INDEX idx_cyclic_recording_pattern_active ON cyclic_recording_pattern(active);
-- Ensure no duplicate record/sleep combinations
CREATE UNIQUE INDEX idx_cyclic_recording_pattern_unique_combo ON cyclic_recording_pattern(record_s, sleep_s);

Deletion in db/schema.sql at line 44 [4.305331]

∅:D[6.68201] → [4.308151:308420]

B:BD[4.308151] → [4.308151:308420]

-- Cluster Table (think of a cluster of files as all the files on 1 SD Card)
-- a statistical unit with no major time gaps, to enable call rate stats
-- See changes below, added foreign key on location, added recording pattern
-- added timezone_id for iana timezone id

Replacement in db/schema.sql at line 45 [4.305331]

B:BD[4.308443] → [4.308443:308647]

    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    dataset_id VARCHAR(12) NOT NULL, -- nanoid, link to dataset
    location_id VARCHAR(12) NOT NULL, -- A cluster must have a location, as well as a dataset

[4.308443]

[4.308647]

    id VARCHAR(12) PRIMARY KEY, 
    dataset_id VARCHAR(12) NOT NULL, 
    location_id VARCHAR(12) NOT NULL,

Replacement in db/schema.sql at line 49 [4.305331]

B:BD[4.308679] → [4.308679:308753]

    description VARCHAR(255), -- Limited to 255 characters for efficiency

[4.308679]

[4.308753]

    description VARCHAR(255),

Replacement in db/schema.sql at line 55 [4.305331]
B:BD[4.309002] → [7.9689:9751]
```
    path VARCHAR(255) NULL, -- optional hint for local access
```
[4.309002]
[4.309002]
```
    path VARCHAR(255) NULL, 
```

Replacement in db/schema.sql at line 58 [4.305331]

B:BD[4.309110] → [4.309110:309196]

    FOREIGN KEY (cyclic_recording_pattern_id) REFERENCES cyclic_recording_pattern(id)

[4.309110]

[4.309196]

    FOREIGN KEY (cyclic_recording_pattern_id) REFERENCES cyclic_recording_pattern(id),
    UNIQUE (location_id, name)

Deletion in db/schema.sql at line 62 [4.305331]

B:BD[2.568] → [2.568:720]

∅:D[2.720] → [4.309199:309200]

B:BD[4.309199] → [4.309199:309200]

B:BD[4.309200] → [2.721:798]

∅:D[2.798] → [4.309200:309575]

B:BD[4.309200] → [4.309200:309575]

-- Not implemented but desirable, using unique index instead
-- ALTER TABLE cluster ADD CONSTRAINT uq_cluster_location_name UNIQUE (location_id, name);
CREATE UNIQUE INDEX idx_cluster_location_name ON cluster(location_id, name);
CREATE INDEX idx_cluster_dataset ON cluster(dataset_id);
CREATE INDEX idx_cluster_active ON cluster(active);
CREATE INDEX idx_cluster_dataset_active ON cluster(dataset_id, active);
CREATE INDEX idx_cluster_recording_pattern ON cluster(cyclic_recording_pattern_id);
CREATE INDEX idx_cluster_location_id ON cluster(location_id);
-- values in my data is medium and medium-high

Deletion in db/schema.sql at line 64 [4.305331]

B:BD[4.309663] → [4.309663:309888]

-- Files Table (removed dataset_id as now use junction table)
-- Note: timestamp_local should reflect local time, not timestamp in filename, this is important
-- duration must not have more than 3 decimal places, check in ui

Replacement in db/schema.sql at line 65 [4.305331]
B:BD[4.309908] → [4.309908:309950]
```
    id VARCHAR(21) PRIMARY KEY, -- nanoid
```
[4.309908]
[4.309950]
```
    id VARCHAR(21) PRIMARY KEY, 
```

Replacement in db/schema.sql at line 67 [4.305331]

B:BD[4.310049] → [4.310049:310500]

    xxh64_hash VARCHAR(16) NOT NULL, -- hash of original file cbe675a69a5fef1c
    location_id VARCHAR(12) NOT NULL, -- nanoid, from locations table
    timestamp_local TIMESTAMP WITH TIME ZONE NOT NULL, -- parsed from filename, adjust for daylight saving
    cluster_id VARCHAR(12), -- nanoid(12), optional if imported one by one
    duration DECIMAL(7, 3) NOT NULL CHECK (duration > 0), -- in seconds, allowing for millisecond precision (9999.999s)

[4.309987]

[4.310500]

    xxh64_hash VARCHAR(16) UNIQUE NOT NULL, 
    location_id VARCHAR(12), 
    timestamp_local TIMESTAMP WITH TIME ZONE NOT NULL, 
    cluster_id VARCHAR(12), 
    duration DECIMAL(7, 3) NOT NULL CHECK (duration > 0),

Replacement in db/schema.sql at line 73 [4.305331]

B:BD[4.310534] → [4.310534:310942]

    description VARCHAR(255), -- Limited to 255 characters for efficiency
    maybe_solar_night BOOLEAN, --calculate with function on client. this is a more accurate value to file table
    maybe_civil_night BOOLEAN, --calculate with function on client. this is a more accurate value to file table
    moon_phase DECIMAL(3,2) CHECK (moon_phase BETWEEN 0.00 AND 1.00), -- 0.00 to 1.00 (new moon to full moon)

[4.310534]

[4.310942]

    description VARCHAR(255), 
    maybe_solar_night BOOLEAN, 
    maybe_civil_night BOOLEAN, 
    moon_phase DECIMAL(3,2) CHECK (moon_phase BETWEEN 0.00 AND 1.00),

Deletion in db/schema.sql at line 83 [4.305331]

B:BD[4.311222] → [4.311222:311573]

B:BD[4.311573] → [3.163:232]

∅:D[3.232] → [4.311573:311733]

B:BD[4.311573] → [4.311573:311733]


CREATE INDEX idx_file_location ON file(location_id);
CREATE INDEX idx_file_active ON file(active);
CREATE INDEX idx_file_timestamp_local ON file(timestamp_local);
CREATE INDEX idx_file_cluster ON file(cluster_id);
CREATE INDEX idx_file_maybe_solar_night ON file(maybe_solar_night);
CREATE INDEX idx_file_maybe_civil_night ON file(maybe_civil_night);
-- ALTER TABLE file
--     ALTER COLUMN location_id DROP NOT NULL;
-- UNIMPLEMENTED
-- Unique constraint on xxh64_hash to prevent duplicate file hashes
-- ALTER TABLE file ADD CONSTRAINT unique_xxh64_hash UNIQUE (xxh64_hash);

Replacement in db/schema.sql at line 87 [4.305331]

B:BD[4.311849] → [4.311849:312078]

    recorder_id VARCHAR(16), -- 24F31901603710CD (16)
    gain gain_level NULL, -- low, medium, high or null
    battery_v DECIMAL(2, 1) CHECK (battery_v >= 0), -- for values from 0 to 9.9
    temp_c DECIMAL(3, 1), -- e.g., 24.2

[4.311849]

[4.312078]

    recorder_id VARCHAR(16), 
    gain gain_level NULL, 
    battery_v DECIMAL(2, 1) CHECK (battery_v >= 0), 
    temp_c DECIMAL(3, 1),

Deletion in db/schema.sql at line 97 [4.305331]
B:BD[4.312298] → [4.312298:312363]
```
CREATE INDEX idx_moth_metadata_active ON moth_metadata(active);
```
Replacement in db/schema.sql at line 99 [4.305331]
B:BD[4.312429] → [4.312429:312494]
```
    json JSON, -- For noise levels and other file-level metadata
```
[4.312429]
[4.312494]
```
    json JSON, 
```

Deletion in db/schema.sql at line 106 [4.305331]

B:BD[4.312714] → [4.312714:312868]

-- CREATE INDEX idx_file_metadata_json ON file_metadata USING gin(json); -- unimplemented
CREATE INDEX idx_file_metadata_active ON file_metadata(active);

Deletion in db/schema.sql at line 107 [4.305331]
B:BD[4.312869] → [4.312869:312923]
```
-- Junction Table for Files to Dataset (many-to-many)
```

Deletion in db/schema.sql at line 117 [4.305331]

B:BD[4.313301] → [4.313301:313463]

-- indexes for the junction table
CREATE INDEX idx_file_dataset_file ON file_dataset(file_id);
CREATE INDEX idx_file_dataset_dataset ON file_dataset(dataset_id);

Deletion in db/schema.sql at line 118 [4.305331]
B:BD[4.313464] → [4.313464:313483]
```
-- Selection Table
```

Replacement in db/schema.sql at line 119 [4.305331]

B:BD[4.313507] → [4.313507:313998]

    id VARCHAR(21) PRIMARY KEY, -- nanoid
    file_id VARCHAR(21) NOT NULL, -- nanoid
    dataset_id VARCHAR(12) NOT NULL, -- nanoid, link to dataset
    start_time DECIMAL(7,3) NOT NULL, --up to 9999.999 seconds
    end_time DECIMAL(7,3) NOT NULL, -- up to 9999.999 seconds
    freq_low DECIMAL(9,3) CHECK (freq_low < 300000), -- LOOK AT CHECK
    freq_high DECIMAL(9,3) CHECK (freq_high < 300000), -- LOOK AT CHECK
    description VARCHAR(255), -- Limited to 255 characters for efficiency

[4.313507]

[4.313998]

    id VARCHAR(21) PRIMARY KEY, 
    file_id VARCHAR(21) NOT NULL, 
    dataset_id VARCHAR(12) NOT NULL, 
    start_time DECIMAL(7,3) NOT NULL, 
    end_time DECIMAL(7,3) NOT NULL, 
    freq_low DECIMAL(9,3) CHECK (freq_low < 300000), 
    freq_high DECIMAL(9,3) CHECK (freq_high < 300000), 
    description VARCHAR(255),

Replacement in db/schema.sql at line 131 [4.305331]

B:BD[4.314215] → [4.314215:314267]

    FOREIGN KEY (dataset_id) REFERENCES dataset(id)

[4.314215]

[4.314267]

    FOREIGN KEY (dataset_id) REFERENCES dataset(id),
    FOREIGN KEY (file_id, dataset_id) REFERENCES file_dataset(file_id, dataset_id)

Deletion in db/schema.sql at line 135 [4.305331]

B:BD[4.314271] → [4.314271:314444]

CREATE INDEX idx_selection_file ON selection(file_id);
CREATE INDEX idx_selection_dataset ON selection(dataset_id);
CREATE INDEX idx_selection_active ON selection(active);

Replacement in db/schema.sql at line 137 [4.305331]
B:BD[4.314520] → [4.314520:314595]
```
    json JSON, -- for loudness, noise, and other selection-level metadaata
```
[4.314520]
[4.314595]
```
    json JSON, 
```

Deletion in db/schema.sql at line 144 [4.305331]

B:BD[4.314825] → [4.314825:315239]

-- CREATE INDEX idx_selection_metadata_json ON selection_metadata USING gin(json); -- unimplemensed
CREATE INDEX idx_selection_metadata_active ON selection_metadata(active);
-- eBird Taxonomy Table
-- will need to update INDEX too when introducing a new version
-- see working with ebird taxonomies, aichat, deepseek, macbook
-- see materialised view and index on it
-- see alter table stuff below, modifications

Deletion in db/schema.sql at line 162 [4.305331]
B:BD[4.315780] → [4.315780:315807]
```
-- Species Table (mutable)
```

Replacement in db/schema.sql at line 163 [4.305331]

B:BD[4.315830] → [4.315830:315996]

    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    label VARCHAR(100) NOT NULL, -- display label for the species
    ebird_code VARCHAR(12), -- link to ebird taxonomy

[4.315830]

[2.903]

    id VARCHAR(12) PRIMARY KEY, 
    label VARCHAR(100) NOT NULL, 
    ebird_code VARCHAR(12),

Deletion in db/schema.sql at line 173 [4.305331]

B:BD[4.316341] → [4.316341:316447]


CREATE INDEX idx_species_label ON species(label);
CREATE INDEX idx_species_ebird ON species(ebird_code);

Deletion in db/schema.sql at line 174 [4.305331]
B:BD[4.316448] → [4.316448:316478]
```
-- Call Types Table (mutable)
```

Replacement in db/schema.sql at line 175 [4.305331]

B:BD[4.316503] → [4.316503:316691]

    id VARCHAR(12) PRIMARY KEY, -- nanoid(12)
    species_id VARCHAR(12) NOT NULL, -- link to parent species
    label VARCHAR(100) NOT NULL, -- display name like "male", "female", "duet"

[4.316503]

[4.316691]

    id VARCHAR(12) PRIMARY KEY, 
    species_id VARCHAR(12) NOT NULL, 
    label VARCHAR(100) NOT NULL,

Deletion in db/schema.sql at line 183 [4.305331]

B:BD[4.316916] → [4.316916:317032]


CREATE INDEX idx_call_type_species ON call_type(species_id);
CREATE INDEX idx_call_type_label ON call_type(label);

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B:BD[4.317055] → [4.317055:317097]
```
    id VARCHAR(12) PRIMARY KEY, -- nanoid
```
[4.317055]
[4.317097]
```
    id VARCHAR(12) PRIMARY KEY, 
```
Deletion in db/schema.sql at line 193 [4.305331]
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```
-- Label Table, many to 1 relationship with
```

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B:BD[4.317407] → [4.317407:317577]

    id VARCHAR(21) PRIMARY KEY, -- nanoid
    selection_id VARCHAR(21) NOT NULL, -- link to selection table
    species_id VARCHAR(12) NOT NULL, -- link to species table

[4.317407]

[4.317577]

    id VARCHAR(21) PRIMARY KEY, 
    selection_id VARCHAR(21) NOT NULL, 
    species_id VARCHAR(12) NOT NULL,

Deletion in db/schema.sql at line 206 [4.305331]

B:BD[4.318018] → [4.318018:318135]


CREATE INDEX idx_label_selection_id ON label(selection_id);
CREATE INDEX idx_label_species_id ON label(species_id);

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B:BD[4.318136] → [4.318136:318199]
```
-- Label Sub-type Table (optional 1:1 relationship with label)
```

Replacement in db/schema.sql at line 208 [4.305331]

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    id VARCHAR(21) PRIMARY KEY, -- nanoid
    label_id VARCHAR(21) NOT NULL, -- link to parent label
    calltype_id VARCHAR(12) NOT NULL, -- link to call_type table

[4.318228]

[4.318394]

    id VARCHAR(21) PRIMARY KEY, 
    label_id VARCHAR(21) NOT NULL, 
    calltype_id VARCHAR(12) NOT NULL,

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    -- UNIQUE (label_id) -- ensures 1:1 relationship with label. how do i handle multiple call type filters? needs 1:many relation

[4.318827]

[4.318958]

    );
CREATE TABLE species_dataset (
    species_id VARCHAR(12) NOT NULL,
    dataset_id VARCHAR(12) NOT NULL,
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    PRIMARY KEY (species_id, dataset_id),
    FOREIGN KEY (species_id) REFERENCES species(id),
    FOREIGN KEY (dataset_id) REFERENCES dataset(id)

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B:BD[4.318961] → [4.318961:319341]


-- UNIMPLEMENTED
-- file_dataset must exist first
-- Referential Integrity for Selections
-- To ensure `selections.dataset_id` is valid for the associated file:
-- Add composite foreign key (requires file_dataset to exist first)
-- ALTER TABLE selection ADD CONSTRAINT fk_selection_file_dataset
-- FOREIGN KEY (file_id, dataset_id) REFERENCES file_dataset(file_id, dataset_id);

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-- 2024 Taxonomy View, after populating underlying table
-- see working with ebird taxonomies, aichat, deepseek, macbook
-- I think I still need this to display the options when someone creates a species

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-- to help with plain text search on common name and scientific name
CREATE INDEX idx_ebird_name_search ON ebird_taxonomy_v2024 USING gin(to_tsvector('english', primary_com_name || ' ' || sci_name));
CREATE INDEX ebird_taxonomy_species_code ON ebird_taxonomy_v2024(species_code);
-- Junction Table for Species to Dataset (many-to-many)
CREATE TABLE species_dataset (
    species_id VARCHAR(12) NOT NULL,
    dataset_id VARCHAR(12) NOT NULL,
    created_at TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    last_modified TIMESTAMP WITH TIME ZONE DEFAULT CURRENT_TIMESTAMP,
    PRIMARY KEY (species_id, dataset_id),
    FOREIGN KEY (species_id) REFERENCES species(id),
    FOREIGN KEY (dataset_id) REFERENCES dataset(id)
);
-- indexes for the junction table
CREATE INDEX idx_species_dataset_species ON species_dataset(species_id);

[4.319781]

[4.320621]

-- FK indexes on file table (1.26M rows)
CREATE INDEX idx_file_location ON file(location_id);
CREATE INDEX idx_file_cluster ON file(cluster_id);
-- Performance index on file for time-based queries
CREATE INDEX idx_file_timestamp_local ON file(timestamp_local);
-- FK indexes on selection table (201K rows)
CREATE INDEX idx_selection_file ON selection(file_id);
CREATE INDEX idx_selection_dataset ON selection(dataset_id);
-- FK indexes on label table (200K rows)
CREATE INDEX idx_label_selection_id ON label(selection_id);
CREATE INDEX idx_label_species_id ON label(species_id);
-- FK indexes on label_subtype table (114K rows)
CREATE INDEX idx_label_subtype_label_id ON label_subtype(label_id);
CREATE INDEX idx_label_subtype_calltype_id ON label_subtype(calltype_id);
CREATE INDEX idx_label_subtype_filter_id ON label_subtype(filter_id);
-- FK lookup for ebird taxonomy (used by species table FK)
CREATE INDEX idx_ebird_taxonomy_species_code ON ebird_taxonomy(species_code, taxonomy_version);
-- Junction table reverse lookups
CREATE INDEX idx_file_dataset_dataset ON file_dataset(dataset_id);

Insertion in db/schema.sql at line 262 [4.305331]

[4.320694]

CREATE INDEX idx_species_dataset_species ON species_dataset(species_id);

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```
  "organise"
```
[4.320756]
[4.320769]
```
  "structured"
  "unstructured"
```
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```
  "name" VARCHAR(255) [not null]
```
[4.320915]
[4.320948]
```
  "name" VARCHAR(255) [unique, not null]
```

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  "type" dataset_type [not null, default: 'organise']
  Indexes {
    name [name: "idx_dataset_name"]
    active [name: "idx_dataset_active"]
    public [name: "idx_dataset_public"]
  }

[4.321127]

[4.321314]

  "type" dataset_type [not null, default: 'structured']

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B:BD[4.321739] → [4.321739:321926]

    name [name: "idx_location_name"]
    dataset_id [name: "idx_location_dataset"]
    active [name: "idx_location_active"]
    (dataset_id, active) [name: "idx_location_dataset_active"]

[4.321739]

[4.321926]

    (dataset_id, name) [unique]

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```
    active [name: "idx_cyclic_recording_pattern_active"]
```
[4.322218]
[4.322275]
```
    (record_s, sleep_s) [unique]
```

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B:BD[4.322705] → [4.322705:322974]

    dataset_id [name: "idx_cluster_dataset"]
    active [name: "idx_cluster_active"]
    (dataset_id, active) [name: "idx_cluster_dataset_active"]
    cyclic_recording_pattern_id [name: "idx_cluster_recording_pattern"]
    location_id [name: "idx_cluster_location_id"]

[4.322705]

[4.322974]

    (location_id, name) [unique]

Replacement in db/schema.dbml at line 77 [4.320733]

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  "xxh64_hash" VARCHAR(16) [not null]
  "location_id" VARCHAR(12) [not null]

[4.323058]

[4.323157]

  "xxh64_hash" VARCHAR(16) [unique, not null]
  "location_id" VARCHAR(12)

Deletion in db/schema.dbml at line 93 [4.320733]

B:BD[4.323621] → [4.323621:323713]

    active [name: "idx_file_active"]
    timestamp_local [name: "idx_file_timestamp_local"]

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    maybe_solar_night [name: "idx_file_maybe_solar_night"]
    maybe_civil_night [name: "idx_file_maybe_civil_night"]

[4.323755]

[4.323873]

    timestamp_local [name: "idx_file_timestamp_local"]

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```
  Indexes {
    active [name: "idx_moth_metadata_active"]
  }
```
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B:BD[4.324500] → [4.324500:324563]
```
  Indexes {
    active [name: "idx_file_metadata_active"]
  }
```
Deletion in db/schema.dbml at line 126 [4.320733]
B:BD[4.324821] → [4.324821:324865]
```
    file_id [name: "idx_file_dataset_file"]
```
Deletion in db/schema.dbml at line 146 [4.320733]
B:BD[4.325448] → [4.325448:325490]
```
    active [name: "idx_selection_active"]
```
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B:BD[4.325724] → [4.325724:325792]
```
  Indexes {
    active [name: "idx_selection_metadata_active"]
  }
```

Insertion in db/schema.dbml at line 175 [4.320733]

[4.326329]

    (species_code, taxonomy_version) [name: "idx_ebird_taxonomy_species_code"]

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  Indexes {
    label [name: "idx_species_label"]
    ebird_code [name: "idx_species_ebird"]
  }

Deletion in db/schema.dbml at line 197 [4.320733]

B:BD[4.327017] → [4.327017:327121]


  Indexes {
    species_id [name: "idx_call_type_species"]
    label [name: "idx_call_type_label"]
  }

Insertion in db/schema.dbml at line 233 [4.320733]

[4.328173]


  Indexes {
    label_id [name: "idx_label_subtype_label_id"]
    calltype_id [name: "idx_label_subtype_calltype_id"]
    filter_id [name: "idx_label_subtype_filter_id"]
  }

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B:BD[4.328440] → [4.328440:328493]
```
    species_id [name: "idx_species_dataset_species"]
```
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[4.328546]
[4.328546]
```
    species_id [name: "idx_species_dataset_species"]
```

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[4.329127]


Ref:"file_dataset".("file_id", "dataset_id") < "selection".("file_id", "dataset_id")

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# Skraak MCP Server
A production-ready Model Context Protocol (MCP) server implemented in Go that provides a generic SQL interface for an acoustic monitoring database, plus time utilities for AI assistants.
## Overview
This MCP server provides AI assistants with direct SQL query access to an acoustic monitoring database containing recordings, locations, species data, and classifications. Built using the official MCP Go SDK, it follows MCP's three-primitive architecture with an LLM-friendly design focused on providing schema context rather than rigid tool APIs.
## Features
### Tools (Model-Controlled)
- **execute_sql**: Execute arbitrary SQL SELECT queries against the database
  - Supports: SELECT, WITH (CTEs), parameterized queries (? placeholders)
  - Security: Read-only database access, forbidden keyword validation
  - Limits: Default 1000 rows (max 10000)
- **get_current_time**: Returns current system time in RFC3339 format with timezone and Unix timestamp
### Resources (Application-Driven)
- **schema://full**: Complete database schema (348 lines)
- **schema://table/{name}**: Individual table definitions
- Provides full context for LLM to construct any query

[4.334405]

[8.64178]

# Skraak

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### Prompts (User-Controlled)
- 6 SQL workflow templates teaching query patterns
- Examples for JOINs, aggregates, filtering, hierarchical queries
- Help LLMs construct appropriate queries for common tasks

[8.64179]

[8.64385]

Acoustic monitoring database toolkit in Go. Use as an MCP server for AI assistants or as a CLI for direct access.

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### Architecture Benefits
- **Generic SQL > Specialized Tools**: Infinite query flexibility vs rigid APIs
- **Schema-Driven**: LLMs construct queries from full database context
- **Read-Only Safety**: Database enforced read-only mode + validation layers
- **Full SQL Expressiveness**: JOINs, aggregates, CTEs, subqueries all available
### Utility Libraries
- **Filename parsing**: Smart date format detection (YYYYMMDD, YYMMDD, DDMMYY) with variance-based disambiguation
- **Timezone handling**: Fixed-offset strategy for DST transitions
- **AudioMoth parsing**: Extract metadata from AudioMoth WAV comments
- **WAV metadata**: Efficient header parsing for duration, sample rate, INFO chunks
- **Astronomical calculations**: Solar/civil night detection, moon phase
- **XXH64 hashing**: Fast file hashing for deduplication
### Testing
- **136 unit tests** with **91.5% code coverage**
- Comprehensive test suite ported from TypeScript original
- End-to-end shell script tests for MCP protocol
- Full MCP protocol compliance via stdio transport
- Type-safe tool handlers with automatic JSON schema generation
- Extensible architecture for adding new tools
### Tool Count
- **14 total tools**: Read (2) + Write (8) + Import (4)
## Requirements
- Go 1.25.6 or later
- MCP-compatible client (Claude Desktop, etc.)

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# Clone or navigate to the project directory
cd /home/david/go/src/skraak_mcp
# Download dependencies
go mod download
# Build the server
go build -o skraak_mcp

[4.335198]

[4.335360]

go build -o skraak

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```
### Running the Server
```
[4.335375]
[4.335398]
```
### MCP Server
```

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The server communicates over stdio (standard input/output) as per MCP specification and requires a DuckDB database path as an argument:

[4.335399]

[4.335535]

Start the server for use with Claude Desktop or other MCP clients:

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```
./skraak_mcp /path/to/database.duckdb
```
[4.335544]
[4.335582]
```
./skraak mcp ./db/skraak.duckdb
```

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**Database Options:**
- **Production**: `./db/skraak.duckdb` - Real data, use for Claude Desktop
- **Testing**: `./db/test.duckdb` - Test data, use for development/testing
**⚠️ IMPORTANT**: Always use `test.duckdb` for testing and development to avoid corrupting production data!

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Examples:
```bash
# Production use (Claude Desktop)
./skraak_mcp ./db/skraak.duckdb
# Testing (development, shell scripts)
./skraak_mcp ./db/test.duckdb
```
### Configuring with Claude Desktop
Add to your Claude Desktop MCP configuration file:
**macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`
**Windows**: `%APPDATA%\Claude\claude_desktop_config.json`
**Linux**: `~/.config/Claude/claude_desktop_config.json`

[8.65667]

[4.335919]

**Claude Desktop config** (`~/.config/Claude/claude_desktop_config.json`):

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    "skraak_mcp": {
      "command": "/home/david/go/src/skraak_mcp/skraak_mcp",
      "args": ["/path/to/database.duckdb"]

[4.335947]

[4.336071]

    "skraak": {
      "command": "/home/david/go/src/skraak/skraak",
      "args": ["mcp", "/home/david/go/src/skraak/db/skraak.duckdb"]

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}
```
## Available Tools
### Query Tools
### execute_sql
Execute arbitrary SQL SELECT queries against the acoustic monitoring database.
**Input**:
```json
{
  "query": "SELECT id, name FROM dataset WHERE active = true",
  "parameters": [],
  "limit": 1000
}
```
**Parameters**:
- `query` (required): SQL query (must start with SELECT or WITH)
- `parameters` (optional): Array of values for ? placeholders
- `limit` (optional): Row limit (default 1000, max 10000)
**Output**:
```json
{
  "rows": [...],
  "row_count": 42,
  "columns": ["id", "name", "active"]
}
```
**Security**:
- Database is read-only (enforced by DuckDB)
- Forbidden keywords blocked: INSERT, UPDATE, DELETE, DROP, CREATE, ALTER
- Row limits prevent overwhelming responses
**Example Queries**:
```sql
-- Basic query
SELECT * FROM dataset WHERE active = true
-- Parameterized query
SELECT * FROM location WHERE dataset_id = ? AND active = true
-- JOIN with aggregates
SELECT d.name, COUNT(l.id) as locations
FROM dataset d
LEFT JOIN location l ON d.id = l.dataset_id
WHERE d.active = true
GROUP BY d.name
```
### get_current_time
Returns the current system time with comprehensive timezone information.
**Input**: None
**Output**:
```json
{
  "time": "2024-01-25T10:30:45Z",
  "timezone": "UTC",
  "unix": 1706181045
}
```
**Fields**:
- `time`: Current system time in RFC3339 format (ISO 8601 compatible)
- `timezone`: System timezone identifier
- `unix`: Unix timestamp in seconds since epoch
### Import Tools
### import_audio_files
Batch import WAV files from a folder into the database.
**Input**:
```json
{
  "folder_path": "/absolute/path/to/recordings",
  "dataset_id": "abc123xyz789",
  "location_id": "def456uvw012",
  "cluster_id": "ghi789rst345",
  "recursive": true
}
```
**Parameters**:
- `folder_path` (required): Absolute path to folder containing WAV files
- `dataset_id` (required): Dataset ID (12 characters)
- `location_id` (required): Location ID (12 characters)
- `cluster_id` (required): Cluster ID (12 characters)
- `recursive` (optional): Scan subfolders recursively (default: true)
**Features**:
- Automatically parses AudioMoth and filename timestamps
- Calculates XXH64 hashes for deduplication
- Extracts WAV metadata (duration, sample rate, channels)
- Computes astronomical data (solar/civil night, moon phase)
- Skips duplicates (by hash)
- Imports in single transaction (all-or-nothing)
### import_file
Import a single WAV file into the database.
**Input**:
```json
{
  "file_path": "/absolute/path/to/recording.wav",
  "dataset_id": "abc123xyz789",
  "location_id": "def456uvw012",
  "cluster_id": "ghi789rst345"
}
```
**Output**:
```json
{
  "file_id": "nB3xK8pLm9qR5sT7uV2wX",
  "file_name": "recording.wav",
  "hash": "a1b2c3d4e5f6g7h8",
  "duration_seconds": 60.0,
  "sample_rate": 250000,
  "timestamp_local": "2024-01-15T20:30:00+13:00",
  "is_audiomoth": true,
  "is_duplicate": false,
  "processing_time": "250ms"
}
```
**Use Cases**:
- Import individual files with detailed feedback
- Programmatic import with known file paths
- Get immediate duplicate detection feedback
### import_ml_selections
Import ML-detected kiwi call selections from folder structure.
**Input**:
```json
{
  "folder_path": "/path/to/Clips_filter_date",
  "dataset_id": "abc123xyz789",
  "cluster_id": "def456uvw012"
}
```
**Features**:
- **Folder structure**: `Clips_{filter_name}_{date}/Species/CallType/*.wav+.png`
- **Filename parsing**: `{base}-{start}-{end}.wav` format
- **Two-pass file matching**: Exact match, then fuzzy date_time pattern match
- **Comprehensive validation**: Filter, species, call types, files, selection bounds
- **Transactional import**: All-or-nothing with error collection
- **Database relations**: selection → label (species) → label_subtype (call type)
### bulk_file_import
Batch import WAV files across multiple locations/clusters using a CSV file.
**Input**:
```json
{
  "dataset_id": "abc123xyz789",
  "csv_path": "/absolute/path/to/import.csv",
  "log_file_path": "/absolute/path/to/progress.log"
}
```
**CSV Format**:
```csv
location_name,location_id,directory_path,date_range,sample_rate,file_count
Site A,loc123456789,/path/to/siteA,2024-01,48000,150
Site B,loc987654321,/path/to/siteB,2024-02,48000,200
```
**Required CSV Columns**:
- `location_name`: Human-readable location name
- `location_id`: 12-character location ID from database
- `directory_path`: Absolute path to folder containing WAV files
- `date_range`: Cluster name (typically date range like "2024-01" or "Jan-2024")
- `sample_rate`: Sample rate in Hz (e.g., 48000, 250000)
- `file_count`: Expected number of files (for validation)
**Features**:
- **Auto-creates clusters**: Creates clusters if they don't exist for location/date_range
- **Progress logging**: Writes detailed logs to file for real-time monitoring (use `tail -f`)
- **Synchronous execution**: Processes locations sequentially, fail-fast on errors
- **Summary statistics**: Returns counts for clusters, files, duplicates, errors
- **Duplicate handling**: Skips files with duplicate hashes across all clusters
**Output**:
```json
{
  "total_locations": 10,
  "clusters_created": 5,
  "clusters_existing": 5,
  "total_files_scanned": 1500,
  "files_imported": 1200,
  "files_duplicate": 250,
  "files_error": 50,
  "processing_time": "5m30s",
  "errors": []
}
```
**Use Cases**:
- Bulk import across many locations at once
- Automated import pipelines with CSV generation
- Large-scale data migration
- Batch processing with progress monitoring
### Write Tools
### create_dataset
Create a new dataset.
**Input**:
```json
{
  "name": "My Dataset",
  "description": "Description of dataset",
  "type": "organise"

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**Parameters**:
- `name` (required): Dataset name (max 255 characters)
- `description` (optional): Dataset description (max 255 characters)
- `type` (optional): Dataset type - "organise", "test", or "train" (default: "organise")

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### CLI Commands

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### create_location

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```bash
# Execute SQL query
./skraak sql --db ./db/skraak.duckdb "SELECT COUNT(*) FROM file WHERE active = true"

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Create a new location within a dataset.
**Input**:
```json
{
  "dataset_id": "abc123xyz789",
  "name": "Recording Site A",
  "latitude": -41.2865,
  "longitude": 174.7762,
  "timezone_id": "Pacific/Auckland",
  "description": "Forest recording site"
}

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# Bulk import from CSV
./skraak import bulk --db ./db/skraak.duckdb --dataset abc123 --csv import.csv --log progress.log

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**Parameters**:
- `dataset_id` (required): Parent dataset ID (12 characters)
- `name` (required): Location name (max 140 characters)
- `latitude` (required): Latitude in decimal degrees (-90 to 90)
- `longitude` (required): Longitude in decimal degrees (-180 to 180)
- `timezone_id` (required): IANA timezone ID (e.g., "Pacific/Auckland")
- `description` (optional): Location description (max 255 characters)

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## Available Tools

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```
### create_cluster
```
[9.5315]
[9.5334]
```
### MCP Tools (10 total)
```

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Create a new cluster within a location.

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**Query:**
- `execute_sql` - Run SQL SELECT queries (JOINs, aggregates, CTEs supported)
- `get_current_time` - Current time with timezone

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**Input**:
```json
{
  "dataset_id": "abc123xyz789",
  "location_id": "def456uvw012",
  "name": "2024-01",
  "sample_rate": 48000,
  "description": "January 2024 recordings",
  "cyclic_recording_pattern_id": "pat123456789"
}
```

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**Write:**
- `create_or_update_dataset` - Create or update a dataset
- `create_or_update_location` - Create or update a location with GPS/timezone
- `create_or_update_cluster` - Create or update a cluster within a location
- `create_or_update_pattern` - Create or update a cyclic recording pattern

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**Parameters**:
- `dataset_id` (required): Parent dataset ID (12 characters)
- `location_id` (required): Parent location ID (12 characters)
- `name` (required): Cluster name (max 140 characters)
- `sample_rate` (required): Sample rate in Hz (must be positive)
- `description` (optional): Cluster description (max 255 characters)
- `cyclic_recording_pattern_id` (optional): Recording pattern ID (12 characters)

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**Import:**
- `import_audio_files` - Batch import WAV files from a folder
- `import_file` - Import a single WAV file
- `import_ml_selections` - Import ML-detected selections from folder structure
- `bulk_file_import` - Bulk import from CSV across multiple locations

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```
### create_cyclic_recording_pattern
```
[9.6017]
[9.6053]
```
### CLI Commands
```

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Create a reusable recording pattern with record/sleep cycle.

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- `sql` - Execute SQL queries directly
- `import bulk` - Bulk import from CSV file

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**Input**:
```json
{
  "record_seconds": 60,
  "sleep_seconds": 540
}
```

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[9.6190]

## Resources & Prompts

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**Parameters**:
- `record_seconds` (required): Number of seconds to record (must be positive)
- `sleep_seconds` (required): Number of seconds to sleep between recordings (must be positive)

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MCP server provides:
- `schema://full` - Complete database schema
- `schema://table/{name}` - Individual table definitions
- 6 SQL workflow prompts teaching query patterns

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**Best Practice**: Query existing patterns first with execute_sql to reuse matching patterns:
```sql
SELECT id FROM cyclic_recording_pattern
WHERE record_s = ? AND sleep_s = ? AND active = true
```

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## Database

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### update_dataset, update_location, update_cluster, update_pattern
Update metadata for existing entities. See tool descriptions for parameters.

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- Production: `./db/skraak.duckdb`
- Testing: `./db/test.duckdb` (use for development)

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### Project Structure
```
skraak_mcp/
├── go.mod                        # Go module definition
├── go.sum                        # Dependency checksums
├── main.go                       # Server entry point, tool registration
├── README.md                     # This file
├── CLAUDE.md                     # Development notes and best practices
├── db/                           # Database files
│   ├── db.go                     # Database connection (read-only)
│   ├── types.go                  # Type definitions
│   ├── schema.sql                # Database schema (348 lines)
│   ├── skraak.duckdb             # Production database ⚠️
│   └── test.duckdb               # Test database ✅
├── tools/                        # MCP tool implementations
│   ├── time.go                   # get_current_time
│   ├── sql.go                    # execute_sql
│   ├── import_files.go           # import_audio_files (batch WAV import)
│   ├── import_file.go            # import_file (single WAV file)
│   ├── import_ml_selections.go   # import_ml_selections (ML detections)
│   ├── bulk_file_import.go       # bulk_file_import (CSV-based bulk import)
│   ├── write_dataset.go          # create_dataset
│   ├── write_location.go         # create_location
│   ├── write_cluster.go          # create_cluster
│   ├── write_pattern.go          # create_cyclic_recording_pattern
│   ├── update_dataset.go         # update_dataset
│   ├── update_location.go        # update_location
│   ├── update_cluster.go         # update_cluster
│   └── update_pattern.go         # update_pattern
├── resources/                    # MCP resources
│   └── schema.go                 # Database schema resources
├── prompts/                      # MCP prompts
│   └── examples.go               # SQL workflow templates
├── utils/                        # Utility functions
│   ├── astronomical.go           # Solar/civil night, moon phase
│   ├── astronomical_test.go      # Tests (11 cases)
│   ├── audiomoth_parser.go       # AudioMoth WAV parsing
│   ├── audiomoth_parser_test.go  # Tests (36 cases)
│   ├── filename_parser.go        # Filename timestamp parsing
│   ├── filename_parser_test.go   # Tests (60 cases)
│   ├── wav_metadata.go           # WAV header parsing
│   ├── wav_metadata_test.go      # Tests (22 cases)
│   ├── xxh64.go                  # File hashing
│   └── xxh64_test.go             # Tests (6 cases)
└── shell_scripts/                # End-to-end test scripts
    ├── test_sql.sh               # SQL tool tests
    ├── test_resources_prompts.sh # Resources/prompts tests
    ├── test_all_prompts.sh       # All prompts tests
    └── get_time.sh               # Time tool test
```
### Database Schema
The acoustic monitoring database contains:
**Core Tables:**
- **dataset** - Recording projects (organise/test/train types)
- **location** - Recording sites with GPS coordinates (139 active locations)
- **cluster** - Grouped recordings at each location
- **file** - Individual audio files with metadata

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**Annotation Tables:**
- **selection** - Time-frequency selections within files
- **label** - Classifications and annotations
- **kiwi_call**, **call**, **syllable** - Hierarchical call structure
**Taxonomy Tables:**
- **species**, **genus**, **family**, **order**, **class**, **phylum**, **kingdom**
- **species_group**, **family_group**, **order_group** - Grouping tables
**Key Fields:**
- Most tables have `active` boolean for soft deletes
- Timestamps use `timestamp_local` (with timezone) and may include `timestamp_utc`
- Files include astronomical data: `maybe_solar_night`, `maybe_civil_night`, `moon_phase`
- AudioMoth metadata: `recorder_id`, `gain`, `battery_v`, `temp_c`
Full schema available via `schema://full` resource.
### Adding New Tools
The server follows MCP best practices with type-safe tool handlers:
1. **Create tool file** in `tools/` package (e.g., `tools/analysis.go`)
2. **Define input/output structures** with jsonschema tags:
```go
type AnalysisInput struct {
    ClusterID string `json:"cluster_id" jsonschema:"Cluster to analyze"`
    Metric    string `json:"metric" jsonschema:"Metric to calculate"`
}
type AnalysisOutput struct {
    Value  float64 `json:"value" jsonschema:"Calculated metric value"`
    Unit   string  `json:"unit" jsonschema:"Unit of measurement"`
}
```
3. **Implement handler function**:
```go
func Analyze(ctx context.Context, req *mcp.CallToolRequest, input AnalysisInput) (
    *mcp.CallToolResult,
    AnalysisOutput,
    error,
) {
    // Implementation
    return &mcp.CallToolResult{}, output, nil
}
```
4. **Register in main.go**:
```go
err := mcp.AddTool(
    server,
    "analyze_cluster",
    "Calculate metrics for a recording cluster",
    tools.Analyze,
)
```
5. **Add tests** in `tools/analysis_test.go`
### Testing
#### Unit Tests
Comprehensive test suite with **91.5% code coverage**:

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```
# Run all tests
```
[4.337718]
[8.70911]
```
# Run tests
```

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# Run specific package tests
go test ./utils/
# Verbose output with test names
go test -v ./utils/
# Run specific test
go test -v ./utils/ -run TestParseFilenameTimestamps
# Coverage report
go test -cover ./utils/
# Generate HTML coverage report
go test -coverprofile=coverage.out ./utils/
go tool cover -html=coverage.out
```
**Test Coverage:**
- **136 unit tests** across 5 test files
- Filename parsing: Format detection, variance disambiguation, timezone handling
- AudioMoth: Comment parsing, all gain levels, temperature/battery
- WAV metadata: Duration, sample rate, INFO chunks
- Astronomical: Solar/civil night, moon phase calculations
- Edge cases: Invalid dates, leap years, DST transitions

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#### End-to-End Tests
Shell scripts test the MCP protocol integration:
```bash
# Navigate to test scripts
cd shell_scripts
# ⚠️ ALWAYS use test.duckdb for testing!
# Test SQL tool (pipe to file to avoid token overflow)
./test_sql.sh ../db/test.duckdb > test.txt 2>&1
rg '"result":' test.txt | wc -l  # Count successful queries
# Test resources and prompts
./test_resources_prompts.sh ../db/test.duckdb > test_resources.txt 2>&1
cat test_resources.txt | jq '.'
# Test all prompts
./test_all_prompts.sh ../db/test.duckdb > test_prompts.txt 2>&1
# Test time tool (no database needed)
./get_time.sh

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# Run with coverage
go test -cover ./...

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**Important**: Always use `test.duckdb` for testing to avoid corrupting production data!
## Dependencies
### Core
- Go 1.25.6 or later
- [MCP Go SDK](https://github.com/modelcontextprotocol/go-sdk) v1.2.0+
- [DuckDB Go SDK](https://github.com/duckdb/duckdb-go) v2
### Utilities
- [SunCalc Go](https://github.com/sixdouglas/suncalc) - Astronomical calculations
- [XXHash](https://github.com/cespare/xxhash/v2) - Fast hashing algorithm

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## Protocol Compliance
This server implements:
- MCP Protocol version: Latest
- Transport: stdio (JSON-RPC 2.0)
- Capabilities: Tools
- Future support: Resources, Prompts
## License
MIT
## Contributing
Contributions welcome! Please ensure:
- Code follows Go best practices
- Tools include comprehensive descriptions
- JSON schema tags document all fields
- Error handling is robust
## Troubleshooting
**Server won't start**:
- Check Go version: `go version`
- Rebuild: `go build -o skraak_mcp`
- Check logs in stderr
**Tool not appearing in client**:
- Verify MCP configuration path
- Restart Claude Desktop
- Check server binary path is correct
**Time format issues**:
- Output uses RFC3339 (ISO 8601) format
- Timezone reflects system configuration
- Unix timestamp is in seconds (not milliseconds)

[4.338111]

See `CLAUDE.md` for detailed development notes.