blastochor 0.1.3
Harvest, transform, and export data from Te Papa's collections API.
License: MIT License
Requires Python: >=3.7
Keywords: python, museum, api

# Blastochor: Harvest data from Te Papa's collections API

["blastochory, where the stem of the plant crawls along the ground to deposit its seed far from the base of the plant"](https://en.wikipedia.org/wiki/Seed_dispersal#Autochory)

This tool lets you access Te Papa's collections API using some basic configuration options, transform the data based on a mapping file, and export the data as a single CSV or multiple CSVs that reference one another, such as can be combined in a Darwin Core Archive (DwC-A).

This repo includes a basic mapping file that will be used if another is not provided.

[API documentation](https://data.tepapa.govt.nz/docs/)

## Still to do
- A complete default mapping that dumps out as much data as possible
- JSON export
- Logging functionality
- Command line options to run a search or single record, returning json or flattened default csv
- New kind of output that relates records together based on given criteria

## Installation
Clone this repo using `git clone`. Install the following packages:
- askCO
- PyYAML
- click

Go to https://data.tepapa.govt.nz/docs/register.html and register for an API key. Add the API key to an environment variable called 'TE-PAPA-KEY'.

## Usage
The `config.yaml` file at the root level sets search and export parameters – this file has useful defaults, so if you want to change it much, create a new one in the `projects` directory. More on this below.

The main functional setting in the config file is `mode`: `search`, `scroll` or `list`. You can either send a search query, which will page through and return all relevant records (limit 50K), scroll through all records (no limit) or provide the app with a list of IRNs (internal reference numbers, Te Papa's record identifiers), which will be individually queried and returned.

The default mapping file (`resources/mapfiles/defaultmap.yaml`) will provide some basic object information. You can create a new one for your project.

When your config and mapping are ready, run the app with `python -m blasto`.

When run, the application runs validation on your config and mapping files. If any errors are found the application will exit and you'll find a report textfile at root containing the validation log. If the config's `quiet` is set to `false`, it will also be printed to the CLI.

## Command line parameters
Blastochor can be set up with projects using a pre-defined config and mapping file. Put the config file in `projects` with the name `[projectname]_config.yaml` and the mapfile (set the name in the config file) in `resources/mapfiles`.

To run a project, enter `python -m blasto --project=[projectname]`.

You can also set a limit on how many records to retrieve, outside what's in your config file - great for testing. Enter `python -m blasto --limit=[number]`. If search or scroll are set up to get more records (eg you ask for 100 but scroll is set up to get 1000 at a time), you'll get the larger number.

Run the application with a profiler using `python -m blasto --profiler=True`. A `.prof` file will be written to the `logging` directory.

Use multiple parameters by stringing them together: `python -m blasto --project=plants --limit=10000`.

## Config parameters

### Setup
`api_key_env`: Environment name for your unique API key. Default is `TE-PAPA-KEY`

`mapping_file`: Filename for file containing data mapping rules. Default is `default.yaml` (points to a default mapping inside the app)

`input_dir`: Directory holding any source files, like a skiplist or list or IRNs. Default is `input_files`

`output_dir`: Directory for exported CSVs. Default is `output_files`

`use_skiplist`: Set to `true` if using a skiplist. Default is `false`

`skipfile`: Filename for skiplist. Default is `null`

`min_image_size`: Only export object records that have images that are at least this many px on each side. Default is `0`

`max_list_size`: Only collate lists of values into a single value up to the specified size. Default is `100`

`clean_newlines`: Removes newlines (`\n`) from values, as CSVs treat them as literal linebreaks. Default is `true`.

`group_rows`: If exploding records into multiple rows, set to `true` to group them under a parent row. Default is `null`

`parent_label`: If grouping rows, sets a label for the parent. Only used if `group_rows` is `true`

`parent_fields`, `child_fields`, `ungrouped_fields`: Specify fields that need to be included or excluded for each kind of row. Set `include` to `true` to only include the specified fields, or `false` to include everything except those specified. Only used if `group_rows` is `true`

### Run
`mode`: Set to search, scroll, or list. Default is `search`

`quiet`: Set to `false` if you want detailed progress messages written to the CLI. Some broader messages and progress bars will be displayed either way. Default is `true`

`base_url`: URL used to query the API. Default is `https://data.tepapa.govt.nz/collection/`

`endpoint`: Set to the primary endpoint you want data from, or set to `null` if you want to search across all endpoints. Defaults to `object` when querying individual records if not set

`timeout`: How long in seconds to allow each query before timing out and retrying. Default is `5`

`attempts`: How many times to retry each query before returning `None`. Default is `3`

### List mode settings
`list_source`: Filename for list of IRNs to query

### Search/scroll mode settings
`record_limit`: Set a limit on the number of records you want to export. Default is `null` (no limit)

`size`: Set a limit on the number of records returned in one page of results. Set to a maximum of `1000` for scroll. Default is `100`

`query`: String to search for. Default is `*` (wildcard)

`sort`: Fieldname to sort results by, such as `id`, `_meta.modified`. Add a `-` before the field to sort in reverse order. Default is `null` (sorts by `id`)

Filters:

`collection`: Set collection to constrain search. Uses the APIs collection labels (`PacificCultures`, not Pacific Cultures). Default is `null`

`allows_download`: Set to `true` to only return object records that include downloadable images, `false` to only return records that don't. Default is `null`

`keyword_fields`: Fieldnames for extra filters on your search. Separate with `|`

`keyword_values`: Values for extra filters. Ensure you have the same number of terms as `keyword_fields` and they're in the right order. Separate with `|`

## Mapping
Mapping files are YAML (`.yaml`) files that name the CSVs that should be created, triggers for harvesting additional records, and lines of rules with the export-side fields in each file. Each rule then includes the API source field used and the transformation rules applied.

`label` is what the app uses to generate output files' names and ensure it's applying the right rules to the right records.

`reference_column` adds a column to the start of the CSV using the provided fieldname, providing a place for non-core files to reference the core file in each row.

`primary_endpoint` is the endpoint (eg `object`, `agent`, `taxon`) this file will mainly use. Other endpoints can be specified in certain processing functions.

`explode` sets a field containing list value where each child is written out separately, such as when you want a new row for every image attached to an object record.

`reduce` cuts down the record's data to just the specified section, for example the list of images under `hasRepresentation`. This makes it easier to then navigate to subfields. The script expects the reduced data to be a list.

`requires` checks each record, only letting the record be written if the specified field matches a specified value. If exploding the record, the check will run for each row. If reducing the record, make sure the specified field path takes account of that. For example:
```
reduce: hasRepresentation
requires:
  rights.allowsDownload: true
```

### Extend
`extend` contains a list of triggers, identifying certain fields that contain IRNs that should also be harvested. For example:
```
endpoint: fieldcollection
path: evidenceFor.atEvent.id
for_label: event
```

This checks harvested records for an IRN in the evidenceFor.atEvent.id field. If found, it will send a separate query to the fieldcollection endpoint, storing the record for later use in the `event` file.

If the record has already been harvested, the record object will just be updated with a flag that it needs to be included in that file.

`path` can contain multiple values for the same endpoint. Separate these with `, `.

To output another CSV with the same endpoint as the core file and using the same path, just add it to the same item's `for_label` with a `, `. For example:
```
endpoint: object
path: id
for_label: identification, multimedia
```

If `for_label` is `null`, the record will be saved but not written out anywhere - do this if you just need some of the record's data for another function.

Extension records are batched and retrieved in lots of 250 per endpoint.

### Fields
The `fields` section contains a list of data transformation rules, headed up with the output fieldnames. These need to be in the order you want them to show in your CSV. The rules are applied to every record included in the file.

Each field then contains a list of functions (one or multiple that run in sequence), which contain a dictionary of the API fields, strings, integers, or other parameters they'll be working on.

For example:
```
- occurrenceID:
  - literal:
      path: pid
```

This means the file will have a column called `occurrenceID`, which take a straight copy of the contents of the record's `pid` field.

When using a field name as a parameter, you need to provide the full path (unless you've `reduced` the record - see above). If one of the fields in the path contains a list, include an `i` to show it needs to be iterated through. For example:
`path: identification.i.identifiedBy.title`

Functions can be chained together by adding them as further list items under the fieldname.

### Available functions
`literal`

Copies the value at the given location. If the path includes a list, you can add an integer to copy a specified list member - if no integer is provided for a list, it will just get the first (`0`) value.
- parameters: `path`, `ordinal`
- example: `path: pid`
- example: `path: additionalType`, `ordinal: 0`
- example: `path: production.i.creator.title`, `ordinal: 1`

`hardcoded`

Sets the value to the string provided. Set the parameter to `value: explode_ordinal` if you want the value to be the row's order within the record.
- parameters: `value`
- example: `value: https://data.tepapa.govt.nz`

`collate_list`

Gets all values of a field within a list, or multiple lists. Automatically concatenated with " | " before writing out. Maximum length of list is controlled in `Config.yml`.
- parameters: `path`
- example: `path: hasRepresentation.i.rights.title`
- example: `path: depicts.i.title, influencedBy.i.title`

`clean_html`

Removes unwanted html markup from a value previously returned, such as a `description`.
- parameters: `null`

`concatenate`

Joins values in a list using " | ", after removing `None` values. Use after calling another function that produces a list.
- parameters: `null`

`conditional`

Returns a value for a given field if another field matches a specified value. Both paths need to be in the same section of the record. If the path given points to a list, each child of the list will be checked. If nothing is found with the initial match condition, an optional fallback condition can be tried.
- parameters: `path`, `condition_path`, `match`, `fallback_match`
- example: `path: related.i.contentUrl`, `condition_path: related.i.title`, `match: ORCID`, `fallback_match: Wikidata`

`country_code`

Finds a country name in a record and looks up its ISO 2-character country code. The file containing country codes is at `resources/countrycodes.json`.
- parameters: `path`
- example: `path: evidenceFor.atEvent.atLocation.country`

`create_filename`

Use after a function that returns a string. Replaces unsafe characters (` , ?, \, :, ;` and so on) with an underscore, or removes them.
- parameters: `suffix`
- example: `suffix: jpg`

`fallback`

Use to substitute another value if the original request returns None. Nest another set of functions and parameters underneath.
```
- format_string:
    string: {} ({})
    path: production.i.contributor.title, production.i.role
    required: true
- fallback:
  - literal:
      path: production.i.contributor.title
```

This returns a formatted string if both a contributor's title and their role are present. Because `format_string` uses the required parameter, if there's no `role` the function will return `None`, and then just the `title` will be returned as a literal value.

`first_match`

Try multiple paths in order and return the value of the first available one. Useful when trying to return the most precise available location.
- parameters: `path` (separated by `, `)
- example: `path: evidenceFor.atEvent.atLocation.locality, evidenceFor.atEvent.atLocation.stateProvince, evidenceFor.atEvent.atLocation.country`

`for_each`

Use after another function that returns a list. Goes through and performs further transformations on each member. You can add the `concatenate` function below `for_each`, or it will automatically happen when writing out. Format this in the mapping document by nesting the rest of the functions below, for example:
```
- recordedByID:
  - collate_list:
      path: evidenceFor.atEvent.recordedBy.i.id
  - for_each:
    - lookup:
        endpoint: agent
    - conditional:
        path: related.i.contentUrl
        condition_path: related.i.title
        match: ORCID
  - concatenate:
      null
```

This finds the agent id for every person at a specimen collection event, looks them up one at a time, and checks if they have an ORCID identifier. `None` values get stripped out once all child functions have run.

`format_string`

Finds a value and inserts it into a provided string at a specified place. Mark the location for each value using `{}`. Include an optional third parameter `required` to return None if any of the values are unavailable.
- parameters: `string`, `path` (if more than one, separated with `, `), `required`
- example: `string: https://collections.tepapa.govt.nz/object/{}`, `path: id`
- example: `string: {} of {}`, `path: typeStatus, qualifiedName`, `required: true`

`lookup`

Use after finding an IRN to return the associated record for the next function. Record needs to have been harvested either directly or using `extend` functionality.
- parameters: `endpoint`
- example: `endpoint: agent`

`map_value`

Use after another function that returns a value – this can be a single value or a list. Each parameter for this function contains a source value and what to map it to. Each value in a list will be checked. If the value doesn't match any parameter's key, it will return `None`. Note that this function's parameters are dictionary key/value pairs.
- parameters: key/value pairs
- example:

```
- literal:
  - path: restrictLocalityData
- map_value:
    true: precise location information not given for threatened species
```

`measure_geodistance`

Use after another function that returns a `fieldcollection` record. Finds the distance between the coordinate centroid and the first of a pair of coordinates, giving the uncertainty radius.

* parameters: `units` - optional, use "m" to return metres, otherwise will return kilometers


`must_match`

Use after another function that returns a value or list of values. Checks each term against an authority list and only keeps the ones you want. Not case-sensitive.
- parameters: `terms` (separated with `, `)
- example: `terms: canvas, paper, plaster, cardboard, ceramic, wood, clay`

`related`

Make a fresh query to the special `/related` endpoint for the current record, returning records that are connected in some way. Can only be used on a complete record as it requires the `href` value. Set a size to limit the number of results (default is `100`), and specify types of records to filter down.
- parameters: `size`, `types` (Capitalise and separate with `,` - note the lack of a space character)
- example: `size: 50` and `types: Object,Specimen`

`use_config`

Pull a specified term out of the config file. Can also use `hardcoded` but lets you avoid doubling up if you change the parameter.
- parameters: `key`
- example: `key: base_url`

`use_group_labels`

If grouping rows for each record, lets you set a label for the parent row, each child row, and standalone rows. Values can be `null`.
- parameters: `parent`, `child`, `other`
- example: `parent: sequence`, `child: image`, `other: image`