Elasticsearch Report Helper

This class provides functionality for generating reports and maps which use Elasticsearch as a datasource rather than the Indicia PostgreSQL database directly. For information on setting up Elasticsearch for Indicia see https://github.com/Indicia-Team/support_files/tree/master/Elasticsearch and Using the REST API to serve Elasticsearch data.

The functionality is based on the principle of a source (a connector to Elasticsearch data) plus one or more output controls which provide various views of the data via the source. Output controls include data grids, maps and downloads. When constructing a page it is possible to build dashboard style functionality by having several sources, e.g. one for raw data and one for aggregated data, plus several output controls per source.

This helper can be accessed:

Examples are given for how to use the controls from the prebuilt form’s Form Structure setting because that is the most common way of using them. They can be converted to PHP code as follows:

[source]
@id=sorted-data
@sort={"id":"desc"}

becomes:

<?php
echo ElasticsearchReportHelper::source([
  'id' => 'sorted-data',
  'sort' => '{"id":"desc"}',
]);

Note that when using PHP directly you should also call the ElasticsearchReportHelper::enableElasticsearchProxy() method as well to ensure that the required configuration for accessing Elasticsearch is added to he page.

Tip

A good way to use this documentation is to study the examples given for each control and cross-reference to the list of options. Once you’ve grasped the basics of each control’s usage, the list of advanced options provides further configuration possibilities.

Initialisation methods

ElasticsearchReportHelper::enableElasticsearchProxy

Prepares the page for interacting with the Elasticsearch proxy.

If coding in PHP directly, this method should be called before adding any other ElasticsearchReportHelper controls to the page. It is not necessary to call enableElasticsearchProxy if using the prebuilt form. The response is a boolean value which will be true if the Elasticsearch proxy was successfully enabled. The response should be checked and the false response handled appropriately, e.g. by displaying a “Service unavailable” message.

Data access control methods

Methods provided for accessing Elasticsearch data by this helper are listed below:

ElasticsearchReportHelper::source

The source control acts as a link from other controls on the page to a set of data from Elasticsearch. Think of the source as a way of defining the output of a query - by default a list of occurrence records but it can also generate data for aggregated reports, e.g. a count of records and species by country or record counts by species.

A source can declare it’s own query filtering (in addition to those specified on the page) and can also define an Elasticsearch aggregation if needed. On its own, a source control does nothing. It’s only when another output control is linked to it that data will be fetched and shown on the page.

Sources normally retrieve documents from Elasticsearch where each document represents a single occurrence record. It is also possible to configure an Elasticsearch index to hold documents which represent single samples.

When configuring a source control the list of available document field names can be found in the occurrences document structure documentation or the samples document structure documentation.

Typical configuration examples

A minimally configured source which lists Elasticsearch documents (each describing an occurrence):

[source]
@id=docs-list

A source which provides geohashed data ready for heat mapping (change the mode to ‘mapGridSquare’ for grid square based maps):

[source]
@id=map-geohash-output
@mode=mapGeoHash

A source which lists species using a composite aggregation:

[source]
@id=species-list
@mode=compositeAggregation
@uniqueField=taxon.accepted_taxon_id
@fields=[
  "taxon.kingdom",
  "taxon.order",
  "taxon.family",
  "taxon.accepted_name"
]

A source which provides data aggregated to show species counts by recorder using an Elasticsearch term aggregation. In this example, because of the potentially high number of recorders to aggregate on we use an alternative sort aggregation for this column which reduces the precision and associated memory requirements:

[source]
@id=recorder-summary
@sort={"event.recorded_by.keyword":"desc"}
@mode=termAggregation
@uniqueField=event.recorded_by
@size=30
@aggregation=<!--{
  "species_count": {
    "cardinality": {
      "field": "taxon.species_taxon_id"
    }
  }
}-->
@sortAggregation=<!--{
  "species_count": {
    "cardinality": {
      "field": "taxon.species_taxon_id",
      "precision_threshold": 100
    }
  }
}-->

Options

The following options are available:

aggregation

In termAggregation or compositeAggregation mode, provide a list of aggregations which provide the output for additional columns in the dataset in JSON format. See https://www.elastic.co/guide/en/elasticsearch/reference/current/search-aggregations.html. You can use Kibana to build an aggregation then inspect the request to extract the required JSON data. The value provided should be a JSON object where the property names are the keys given for each aggregation (i.e. the contents of the “aggregations” or “aggs” element in your query). The aggregation names given should not have a leading hyphen as these names are reserved.

The value for @aggregation can contain tokens which are replaced at runtime. Tokens are of the format {{ name }} where the name can be one of the following:

  • indicia_user_id - the user’s warehouse user ID.
  • a parameter from the URL query string.

When using termAggregation or compositeAggregation mode, the keys of this object represent additional calculated fields that will be added to the output dataset. Normally this means a single bucket aggregation per key but nested aggregations can be expanded into table columns using a dataGrid control.

disabled

Set to true to prevent the source from populating. You can then use JavaScript to change the setting:

var src = indiciaData.esSourceObjects['source_id'];
src.settings.disabled = false;
src.populate();

endpoint

If this source should use an Elasticsearch API endpoint (as configured in the warehouse’s REST API) that is different from the page’s default, then set the endpoint name in this option. Note that the endpoint must also be listed under the “Alternative endpoints” configuration option on the page’s Edit tab.

fields

An array of document field names to include in the output when using termAggregation or compositeAggregation mode. This list is for the non-aggregated fields, for calculated aggregated data fields use the @aggregation option.

In addition to standard document field names, it is possible to include a custom attribute value in the list of available fields using the same format as for table columns, i.e. #attr_value:<type>:<id># where <type> is event (sample), parent_event (sample identified by samples.parent_id) or occurrence and <id> is the attribute ID.

id

All source controls require a unique ID which allows other data bound controls to refer to it.

mode

Set the @mode option to define the overall behaviour of the source.

An Indicia occurrence document in Elasticsearch contains several pieces of spatial data. The ones which are relevant to aggregated data are the location.point field which contains a latidude and longitude, plus the location.grid_square fields which contain the center of the covering grid square in 1km, 2km and 10km sizes.

  • docs (default) - retrieve a set of Elasticsearch documents.

  • mapGeoHash - aggregates retrieved data using an Elasticsearch geohash_grid aggregation based on the location.point field value, suitable for providing data to a heat map layer, or for drawing rectangular grid cells which scale according to the map resolution. See https://en.wikipedia.org/wiki/Geohash. Set the type of the map layer’s @layerConfig to heat or geom if you want to draw the rectangle for the geohash grid cells.

  • mapGridSquare - aggregates retrieved data using an Elasticsearch terms aggregation on location.grid_square field values. These contain the centres of grid squares covering the record at 1km, 2km and 10km resolution. The default behaviour is to automatically select the grid square size depending on map zoom but this can be overriden by setting @mapGridSquareSize to the size of the required grid square in metres (10000, 2000 or 1000). The mapGridSquare option is similar to the mapGeoHash option with layer configured to type geom, except that the mapGridSquare option uses an exact square grid based on 1000, 2000 or 10,000m grid squares, whereas the mapGeoHash grid option grid is based on rectangles of varying aspect ratio, but works at more different resolutions.

  • compositeAggregation - generates a composite aggregation from the @uniqueField, @fields and @aggregation settings. Similar to the termAggregation mode but with different restrictions. Composite aggregations have the following features:

    • Fast and efficient.
    • Can be sorted on the unique field or any of the other fields.
    • Does not support sorting by one of the aggregated outputs. This is a limitation of Elasticsearch.
    • Supports the next/previous buttons for paging in a dataGrid.

    A separate count aggregation is automatically added to the request when required in in order to provide proper information for a dataGrid’s pager, since composite aggregations cannot themselves include a total buckets count.

  • termAggregation- generates a term aggregation from the @uniqueField, @fields and @aggregation settings. Similar to the compositeAggregation mode but with different restrictions. Term aggregations have the following features:

    • Can be sorted on any numeric or date field or any aggregated output.
    • Can not be sorted on a text field’s direct value.
    • Does not support the next/previous buttons for paging in a dataGrid.

size

Number of documents (each of which represents an occurrence) matching the current query to return. This might be the size of each page in a report grid for example. When @mode is set to compositeAggregation or termAggregation the size passed here is used to determine the number of aggregation buckets to retrieve and the number of documents to retrieve is set to zero.

sort

Sets the default sort order of the source. Object where the properties are the field names to sort by and the values are either “asc” or “desc” as appropriate. E.g.:

[source] @id=sorted-data @sort={"id":"desc"}

If using composite or term aggregation mode and sorting by an aggregate column, then the name given should be the name of the aggregate, not the name of the underlying field in the document. In these modes it is also possible to specify either the field specified in the unique_field option or any of the fields specified in the additional fields array option.

switchToGeomsAt

If the mode is mapGridSquare, then this can be set to a zoom level after which the layer will switch to show the geometries of the records as they were input, rather than the grid square or circle containing the record. Otherwise a record will only ever show at a maximum 1km precision. The 1km layer starts showing at zoom level 11, so a setting of around 13 is a good starting point.

uniqueField

Used when the mode is compositeAggregation or termAggregation. Name of a field in the Elasticsearch document which has one unique value per row in the output. This will typically be a field containing an ID or key, for example when each row represents a taxon you might set uniqueField to taxon.accepted_taxon_id, or when each row represents a sample it could be set to event.event_id.

Setting this value allows the source control to: * use the cardinality of this field as a quick way to count the output, since counting is

not directly possible using a composite aggregation.

Advanced options

filterPath

By default, requests for documents from Elasticsearch contain the entire document stored for each occurrence record. This can result in larger network packets than necessary especially where only a few fields are required. The filter path allows configuration of the fields returned for each document using the Elasticsearch response filter.

Use this option with care, since you need to understand the structure of the response and which parts are essential to the operation of the controls using the data. In the following example, data for a dataGrid are limited to information relating to the total row count and occurrence event:

[source]
@id=grid-data
@filterPath=hits.total,hits.hits._source.event

[dataGrid]
@source=grid-data

As the example uses the default columns which includes taxon and location based values, some data columns in the grid will be empty. Removing hits.total from the value will cause a JavaScript error since this would remove essential information required for grid operation.

See https://www.elastic.co/guide/en/elasticsearch/reference/7.0/common-options.html#common-options-response-filtering.

from

In docs mode, optional number of documents to offset by. Defaults to 0 and is normally controlled by a dataGrid’s paging behaviour.

initialMapBounds

When this source provides data to load onto a map, set to true to use this source’s dataset to define the bounds of the map on initial loading. This option is automatically set when using one of the map aggregation modes.

filterBoolClauses

A JSON definition of clauses to add to an Elasticsearch bool query (https://www.elastic.co/guide/en/elasticsearch/reference/current/query-dsl-bool-query.html). The property names should therefore be one of must, filter, should, must_not and they can be nested to support complex logic. Each top level property contains an array of objects defining a filter, with properties query_type, field, nested and value. Query types supported currently are:

  • match_all
  • match_none
  • term
  • match
  • match_phrase
  • match_phrase_prefix
  • exists

For example:

@filterBoolClauses=<!--{
  "must_not":[
    {"query_type": "term","field": "identification.verification_status","value":"R"}
  ]
}-->

filterSourceGrid

If set to the ID of a grid on the same page which is linked to a different source, then this [source] can apply an additional filter to the returned data depending on the selected row. In this case you should also set the following:

  • @filterSourceField to determine which field/column in the output dataset to use as a source for the filter value. This is normally the same as the field name in Elasticsearch but will be different if the value is being obtained from an aggregation bucket.
  • @filterField to determine the name of the field in Elasticsearch to match the filter value against.

For example you might have a 2 grids and a map where the map shows all the verified records of the species selected in the grid. This requires 2 [source] controls, a [dataGrid] and a [leafletMap]:

[source]
@id=grid-data
@size=30

[source]
@id=mapData
@filterSourceGrid=records-grid
@filterSourceField=taxon.accepted_taxon_id
@filterField=taxon.accepted_taxon_id
@mode=mapGeoHash

[dataGrid]
@id=records-grid
@source=grid-data
@columms=

[leafletMap]
@id=map
@source=<!--{
  "map-data": "Verified records of selected species"
}-->

Can also be set to a JSON array of table IDs, in which case the @filterSourceField and @filterField parameters should also be JSON arrays of matching fields names, allowing the datasource to obtain it’s filter data from more than one dataGrid. In this case, the last grid row clicked on is applied as a filter.

filterSourceField

See the description of filterSourceGrid above.

filterField

See the description of filterSourceGrid above.

filterBoundsUsingMap

This option is automatically set when using one of the map modes. If manually setting up the aggregation and the source is for a geohash aggregation used to populate a map layer then you probably don’t want the aggregation to calculate for the entire world view. For example, a heat map aggregation should increase its precision as you zoom the map in. In this case, set a filter for the geo_bounding_box to an empty object ({}). This will then automatically populate with the map’s bounding box.

For example:

[source]
@id=recordsGeoHash
@size=0
@aggregation=<!--
  {
    "filter_agg": {
      "filter": {
        "geo_bounding_box": {}
      },
      "aggs": {
        "2": {
          "geohash_grid": {
            "field": "location.point",
            "precision": 4
          },
          "aggs": {
            "3": {
              "geo_centroid": {
                "field": "location.point"
              }
            }
          }
        }
      }
    }
  }
-->
@filterBoundsUsingMap=map

[leafletMap]
@id=map
@layerConfig=<!--{
  "recordsHeatMap": {
    "title": "All records in current filter (heat map)",
    "source": "recordsGeoHash",
    "type":"heat",
    "style": {
      "gradient": {
        "0.4": "#fce7e2",
        "0.65": "#a6bddb",
        "1": "#2b8cbe"
      }
    }
  }
}-->

proxyCacheTimeout

To enable caching of the Elasticsearch content loaded on a page’s initial load, set @proxyCacheTimeout=n where n is the number of seconds after which the cached content will expire and therefore will refresh. Although performance of Elasticsearch is normally excellent, if a public facing reporting page is likely to receive a high volume of hits (e.g. the output of a citizen science project) then it can be pragmatic to set this value to prevent rapid identical Elasticsearch queries. A value of 300 would set the cache expiry to 5 minutes for example. Note that once a cached item expires, the chances of it refreshing on a page request are randomised, meaning that if there are multiple queries issued by a page, then they won’t all get refreshed on the same page hit.

Caching occurs in the Elasticsearch proxy layer and only applies to the initial load of each data source when the page loads. Subsequent hits are likely to be filtered AJAX requests so caching would not be relevant.

Data output methods

ElasticsearchReportHelper::cardGallery

Outputs a gallery of record cards.

Options

actions

Optional array defining additional action buttons to include for each card. For more information see the description of the actions option for the dataGrid control.

columns

List of report data fields that will be output in the card below the image. Syntax is the same as the columns option for the dataGrid control.

id

Optional. Specify an ID for the cardGallery control allowing you to refer to it from elsewhere, e.g. CSS. If not specified, then a unique ID is generated by the code which cannot be relied on.

includeFieldCaptions

Set to true to include the caption for each field shown below the photo, according to the columns option.

includeFullScreenTool

Set to false to disable the tool button for enabling full screen mode.

includePager

Set to false to disable the pager row at the bottom of the table.

keyboardNavigation

Set to true to allow use of the following keyboard shortcuts: * arrow keys to navigate the selected card in the gallery. * i to show the first image in the current row as a popup.

source

ID of the [source] control this cardGallery is populated from. Typically the source will limit the data in the response to records with media using @filterBoolClauses as in the following example:

[source]
@id=photos-data
@size=30
@sort={"id": "desc"}
@filterBoolClauses=<!--{
  "must":[
    {"query_type": "exists", "field": "occurrence.media.path", "nested":"occurrence.media"}
  ]
}-->

[cardGallery]
@id=card-gallery
@source=photos-data

ElasticsearchReportHelper::customScript

A flexible output of ES data which uses a custom JavaScript function to build the HTML.

Options

id

Optional. Specify an ID for the customScript control allowing you to refer to it from elsewhere, e.g. CSS. If not specified, then a unique ID is generated by the code which cannot be relied on.

source

ID of the [source] control this customScript is populated from.

functionName

Name of a function that should be added to the JavaScript global indiciaFns which formats the output. Takes 3 parameters:

  • el - the element the output should be added to.
  • sourceSettings - settings object for the source the control is linked to.
  • response - the response from Elasticsearch to be formatted by the function.

template

Template for the content to add to the output div. Defaults to empty.

ElasticsearchReportHelper::dataGrid

Generates an HTML table containing Elasticsearch data. The dataGrid control has built in support for sorting, filtering, column configuration and pagination.

Table rows holding data have the class data-row to identify them within the code. They also have a class added selected when the row is selected (e.g. showing the associated feature on the map). For rows linking to raw Elasticsearch documents, as opposed to aggregated data, there is a class zero-abundance added when the record is a record of absence. Finally, additional classes can be added to rows using the @rowClasses option.

Typical configuration examples

A minimal configuration for a dataGrid showing docs from a source with default columns:

[source]
@id=grid-data

[dataGrid]
@source=grid-data

Another minimal configuration of a dataGrid, this time auto-generating it’s columns from a source in aggregation mode:

[source]
@id=species-list
@mode=termAggregation
@uniqueField=taxon.accepted_taxon_id
@fields=<!--[
  "taxon.kingdom",
  "taxon.order",
  "taxon.family",
  "taxon.accepted_name"
]-->
@aggregation=<!--{
  "records": {
    "cardinality": {
      "field": "id"
    }
  }
}-->

[dataGrid]
@source=species-list

A dataGrid linked to a source with a composite aggregation, this time specifying the columns to show:

[source]
@id=recorder-summary
@sort={"event.recorded_by.keyword":"desc"}
@mode=compositeAggregation
@uniqueField=event.recorded_by
@size=30
@aggregation=<!--{
    "species_count": {
      "cardinality": {
        "field": "taxon.species_taxon_id"
      }
    }
}-->
@sortAggregation=<!--{
  "species_count": {
    "cardinality": {
      "field": "taxon.species_taxon_id",
      "precision_threshold": 100
    }
  }
}-->

[dataGrid]
@id=recorders-grid
@source=recorder-summary
@columns=<!--[
  {"caption": "Recorder", "field": "event.recorded_by"},
  {"caption": "Records", "field": "doc_count"},
  {"caption": "Species", "field": "species_count"}
]-->

Options

actions

An array defining additional action buttons to include for each row in the grid in the rightmost column. For example you might like an action button to navigate to a record edit page.

Each action entry can have the following properties:

  • title - text to add to the button’s title attribute, shown on hover as a tooltip. Required.

  • iconClass - class to attach which should define the icon. Normally a FontAwesome class is used.

  • path - base path to the page to navigate to. Tokens will be replaced as follows: * {rootFolder} will be replaced by the root folder of the site, allowing links to be

    specified as “{rootFolder}path” where the path is a Drupal alias (without leading slash).

    • {language} will be replaced by the current user’s 2 character selected language code.
    • Field values from the row’s Elasticsearch document can be specified by putting the field name in square brackets, e.g. [taxon.taxon_name] or [id].
  • tokenDefaults - allows a default value to be specified where the document doesn’t hold a value for the field used in a token replacement for an action’s path. E.g.:

    "tokenDefaults":{
      "[metadata.input_form]": "edit-generic-record"
    }
    
  • urlParams - additional parameters to add to the URL as key/value pairs. Can also contain field value replacements by putting the field name in square brackets.

  • hideIfFromOtherWebsite - set to true to hide the action button if the row is for a record input on another website that shares its records to this website.

  • hideIfFromOtherUser - set to true to hide the action button if the row is for a record input by another user.

  • onClickFn - set to the name of a JavaScript function that has been added to the indiciaFns object which will be run when the action is clicked. This is an alternative to setting a link path using the other options. The function will receive 2 parameters, the Elasticsearch document object and the table row element.

Note that the title, path and urlParams properties can all contain field name replacement tokens by putting the field name in square brackets. This can contain a list of field names separated by OR in which case the first field name with a value will be used. This is illustrated in the top_sample_id parameter in the example below.

The following action defines a button with a file icon that links to a species details page with a URL that might look like:

http://www.example.com/species-pages/Andrena%20cineraria?occurrence_id=123

@actions=<!--[
  {
    "iconClass":"far fa-file-alt",
    "path":"{rootFolder}/species-pages/[taxon.taxon_name]",
    "title":"View species details",
    "urlParams":{
      "occurrence_id":"[id]",
      "top_sample_id":"[event.parent_sample_id OR event.event_id]"
    }
  }
]
-->

columns

An array of column definition objects for the grid’s columns, with each object having the following properties:

  • caption - title for the column.

  • description - information displayed as a hint when hovering over the column title.

  • field - required - can be the name of a field in the Elasticsearch document, e.g. metadata.created_by_id, or one of the following special field names (case-sensitive):

    • #associations# - a list of the species names linked to this record as associated occurrences.

    • #attr_value:<entity>:<id># - a single custom attribute value. Specify the entity name (event (=sample), parent_event (sample identified by samples.parent_id or occurrence) plus the custom attribute ID as parameters. Note that if requesting an event attribute value, the parent events attribute values will also be included in the output, so when requesting an attribute value it is not necesssary to know if the value will be stored at the event or parent level.

    • #constant:<value># - outputs a static value. Pass an empty string if you need an empty column.

    • #data_cleaner_icons# - icons representing the results of data cleaner rule checks.

    • #datasource_code:<format># or #datasource_code# - This outputs a datasource identifier optionally composed from any of the following six elements (corresponding tokens are shown in parentheses): website title (<wt>), website id (<wi>), survey dataset title (<st>), survey dataset id (<si>), recording group title (<gt>), recording group id (<gi>). The format consists of a string containing one or more of the element tokens and any other characters requried, e.g. #datasource_code:<wt>-<gt>#. If no format is specified, the following default is used: <wi> (<wt>) | <si> (<st>). A group may not always be present. When it is not then <gt> and <gi> are replaced by empty strings. You can place any number of non-token characters before trailing group tokens within curly braces. Where a group is not present the characters between the braces are not output. For example <wt> | <st> {|} <gt> will ouput website-title | survey-dataset-title | group-title where a group is present but otherwise just website-title | survey-dataset-title - the training “|” is removed. Curly braces are always removed from the output.

    • #datetime:<field>:<format># - converts a specified field, which must be of the date/time type, to a given format. Specify formats using standard `PHP format strings. (https://www.php.net/manual/en/datetime.format.php)`_ If you want to use colons in the format string, e.g. Y-m-d H:i:s, they must be escaped to avoid confusion with colons in the rest of the field definition, e.g. #datetime:metadata.created_on:Y-m-d H:i:s#.

    • #event_date:<format># or #event_date# - where no format is specified, the event (sample) date or date range is output in a standard format. If the format is set to mapmate, the date or date range is formatted in a way that MapMate can handle for imports.

    • #higher_geography:<type>:<field>:<format># - provides the value of a field from one of the associated higher geography locations. The following parameter options are available:

      • With no additional parameters, provides all available higher geography data.
      • With the first <type> parameter set to the location type term you want to retrieve (e.g. “Country”) to provide all field values for that location type (i.e. the id, name, code and type).
      • Additionally provide a second <field> parameter to limit the response for the chosen type to a single field. This must be one of id, name, code or type.
      • The output will be formatted as readable text unless the optional third <format> parameter is set to json in which case JSON is returned.
      • If the third parameter can be set to mapmate where a vice county code is being retrieved in which case if there is more than one VC code, or no VC code, associated with the record, the output value is set to zero.
    • #lat:<format>:<precision># or #lat# - a formatted latitude value. If specified, <format> can be one of:

      • “decimal” - a decimal latitude is returned with negative values for locations south of the equator. Decimal places given by <precision>, default is all available.
      • “nssuffix” - a latitude rounded to n decimal places with a suffix of “N” or “S” location in relation to the equator. Decimal places given by <precision>, default is 3.
    • #lat_lon# or #lat_lon:<precision># - a formatted latitude and longitude value with number each rounded to n decimal places plus a suffix indicating location in relation to the equator and Greenwich meridian. Decimal places given by <precision>, default is 3.

    • #life_stage:<format># - the value of the occurrence.life_stage field formatted as specified. Currently there is only one format - mapmate - which translates values to values acceptable to MapMate, e.g. adult female to Adult.

    • #locality# - a summary of location information including the given location name and a list of higher geography locations.

    • #lon:<format>:<precision># or #lon# - a formatted longitude value. If specified, <format> can be one of:

      • decimal - a decimal longitude is returned with negative values for locations west of the Greenwich meridian. Decimal places given by <precision>, default is all available.
      • ewsuffix - a longitude rounded to n decimal places with a suffix of “E” or “W” location in relation to the Greenwich meridian. Decimal places given by <precision>, default is 3.
    • #null_if_zero:<field># - returns the field value, unless 0 when will be treated as null.

    • #occurrence_media# - returns thumbnails for the occurrence’s uploaded media with built in click to view at full size functionality.

    • #organism_quantity:<format># - returns the value of the occurrence.organism_quantity field formatted as specified. The value of <format> can be one of:

      • “integer” - the value is only returned if it is an integer.
      • “exclude-integer” - the value is only returned if it is not an integer.
      • “mapmate” - returns the value if it is an integer (other than zero). If the value is a zero, or if the value of occurrence.zero_abundance is not false, then a value of -7 is returned (used by MapMate to indicate negative records).
    • #query:<format># - the record query status formatted as specified. The unmodified field identification.query outputs a single letter code. Currently there is only one format - astext - which translates codes to meaningful text, Q to Queried, A to Answered.

    • #sex:<format># - the value of the occurrence.sex field formatted as specified. Currently there is only one format - mapmate - which translates codes to values acceptable to MapMate, e.g. female to f and mixed to g.

    • #sref_system:<field>:<format># - a formatted spatial reference system. The field must indicate a spatial reference system, e.g. location.input_sref_system. Currently there is only one format - alphanumeric - which replaces any values where the spatial reference system is stored as a numberic EPSG code with the recognised text equivalent (4326 becomes WGS84 and 27700 becomes OSGB36).

    • #status_icons# - icons representing the record status, confidential, sensitive and zero_abundance status of the record.

    • #taxon_label# - a label for the taxon. This combines the accepted name and vernacular where available. The rank is prefixed for higher taxa.

    • #verification_status:<format># - the record verification status formatted as specified. The unmodified field identification.verification_status outputs a single letter code. Currently there is only one modifer - astext - which translates codes to meaningful text, e.g. V to Accepted, C to Unconfirmed etc.

    • #verification_substatus:<format># - the record verification substatus formatted as specified. The unmodified field identification.verification_substatus outputs a single letter code. Currently there is only one modifer - astext - which translates codes to meaningful text, e.g. 1 to Correct, 2 to Considered correct etc.

    • Path to an aggregation’s output when using aggregated data.

When defining the path to a field in the Elasticsearch document, if the path contains aggregation buckets which holds an array, the index of the required bucket can be inserted in the path, for example by_group.buckets.0.species_count.value. Or, instead of an index a filter on the bucket contents can be used to select an item at any index by putting a key=value pair in square brackets, e.g. by_group.buckets.[key=flowering plant].species_count.value.

  • path - where fields are nested in the document response, it may be cleaner to set the field to the path to where to find the field in the document in this option. So, rather than set the field to fieldlist.hits.hits.0._source.my_count_agg.value for example, set the path to fieldlist.hits.hits.0._source and the field to my_count_agg.value, resulting in cleaner class names in the code among other benefits.
  • rangeField - name of a second field in the Elasticsearch document which defines a range when combined with the field’s value. If the value of the field pointed to by rangeField is different to the value pointed to by field then the output will be of the form value1 to value2.
  • ifEmpty - string to output when the field value is empty. May contain HTML.
  • handler - for date and datetime fields, set to date or datetime to ensure correct formatting if the date is displaying as a numeric value. This is not normally required as document fields should format correctly. For aggregations such as min or max date (which do generate a numeric value), specifying the format option in the aggregation to provide a correctly formatted value is preferable because this approach will also apply within downloaded datasets, whereas using the handler only affects the output of the data cell in the [dataGrid].
  • hideBreakpoints - Comma separated list of breakpoints. When a breakpoint is specified the column is hidden for pixel sizes between this breakpoint (or zero in the case of the smallest breakpoint) and the next highest breakpoint. So, setting a value of “sm” makes a column disappear between 760 and 992 pixels. Therefore it is more likely that you want to set it to “xs,sm” which means anything under 992 pixels. Following this logic, setting “lg” hides the column for any device over 1200 pixels. “xs,sm” to . The default breakpoints are: * xs: 480 (extra small) * sm: 760 (small) * md: 992 (medium) * lg: 1200 (large) These defaults can be set by specifying responsiveOptions.breakpoints.
  • dataType=”date|numeric”

If not provided, the list of columns will default depending on the source settings. When the source mode is an aggregation, all the fields and aggregation outputs are included in the list of columns. When the source mode is docs, a principle attributes of the occurrence record are included.

cookies

Set to false to disable use of cookies to remember the selected columns and their ordering. Cookies are only enabled when there is a specific id option set for this grid.

id

Optional. Specify an ID for the dataGrid control allowing you to refer to it from elsewhere, e.g. CSS. If not specified, then a unique ID is generated by the code which cannot be relied on.

includeColumnHeadings

Set to false to disable column headings.

includeColumnSettingsTool

Set to false to disable the tool button for showing the column settings popup.

includeFilterRow

Set to false to disable the filter row at the top of the table.

includeFullScreenTool

Set to false to disable the tool button for enabling full screen mode.

includePager

Set to false to disable the pager row at the bottom of the table.

includeMultiSelectTool

Set to true to include a multi-select tool button which enables tickboxes for each row. Normally used to support multiple record verification.

keyboardNavigation

Set to true to allow use of the following keyboard shortcuts: * up and down arrow keys to navigate the selected row in the grid. * i to show the first image in the current row as a popup.

rowClasses

An array of classes that will be included in the class attribute for each <tr> element in the grid’s body. Each may contain token replacements for the fields in the row’s document by wrapping the field name in square brackets. For example:

@rowClasses=<!--[
  "table-row",
  "status-[identification.verification_status]"
]-->

Since rows always have a class called data-row the above configuration might output the following:

<tr class="data-row table-row status-V">...</tr>

scrollY

Set to a CSS height in pixels (e.g. “800px”) to display a scrollbar on the table body with this as the maximum height. Allows the data to be scrolled whilst leaving the header fixed. Set to a negative height (e.g. “-50px”) to set the table body to occupy all available space to the bottom of the screen minus the height given.

source

ID of the source this dataGrid is populated from.

sortable

Set to false to disable sorting by clicking the sort indicator icons in the heading row.

Advanced options

applyFilterRowToSources

If a filter row is present in the grid, then changing the filter row contents will automatically apply the filter to the source the dataGrid is linked to. If any additional sources should also be filtered (e.g. sources driving maps or charts from the same data) then supply a JSON array of source IDs in this parameter.

containerElement

If you want to output the dataGrid in an existing element on the page with a known CSS selector then specify the selector here. If the selector matches multiple elements then only the first will be used.

autoResponsiveCols - set to true to automatically hide columns responsively when below each breakpoint. Priority is set by position in the grid with columns on the right being hidden first. Overrides hideBreakpoints setting for each column.

autoResponsiveExpand - set to true to automatically expand any additional information beneath the row when cells are dropped due to responsive hide behaviour. Otherwise the user has to click a + button to view the hidden information.

availableColumns

Defines which columns are available using the column configuration tool for the dataGrid. By default all known columns are made available but you may wish to simplify the list of columns in some circumstances. Specify an array of field names from the Elasticsearch index.

responsive

Defaults to true but can be disabled by setting to false.

responsiveOptions

Options for responsive behaviour which will be passed to the Footable component that makes the table responsive. Can include:

  • breakpoints - a JSON object where the properties are breakpoint names and the values are the number of pixels below which the breakpoint is triggered. The default is:

    {
      "xs": 480,
      "sm": 760,
      "md": 992,
      "lg": 1200
    }
    

ElasticsearchReportHelper::download

A button with associated progress display for generating downloadable zip files of CSV data from an associated [source] control. Files are added to a list of downloads and are kept available on the server for a period of time.

Typical configuration examples

A minimal configuration to download a set of documents (occurrences):

[source]
@id=data-to-download

[download]
@source=data-to-download

A download for a limited columns set:

[source]
@id=data-to-download

[download]
@source=data-to-download
@columnsTemplate=
@addColumns=<!--[
  {"caption": "Recorder", "field": "event.recorded_by"},
  {"caption": "Date", "field": "#event_date#"},
  {"caption": "Grid ref.", "field": "location.output_sref"},
  {"caption": "Taxon", "field": "taxon.accepted_name"}
]-->

A download using a source in term aggregation mode:

[source]
@id=recorder-summary
@sort={"event.recorded_by.keyword":"desc"}
@mode=termAggregation
@uniqueField=event.recorded_by
@size=30
@aggregation=<!--{
    "species_count": {
      "cardinality": {
        "field": "taxon.species_taxon_id"
      }
    }
}-->

[download]
@source=recorder-summary

A download using a dataGrid to define the columns in the resulting file:

[source]
@id=recorder-summary
@sort={"event.recorded_by.keyword":"desc"}
@mode=compositeAggregation
@uniqueField=event.recorded_by
@size=30
@aggregation=<!--{
    "species_count": {
      "cardinality": {
        "field": "taxon.species_taxon_id"
      }
    }
}-->
@orderbyAggregation=<!--{
  "species_count": {
    "cardinality": {
      "field": "taxon.species_taxon_id",
      "precision_threshold": 100
    }
  }
}-->

[dataGrid]
@id=recorders-grid
@source=recorder-summary
@columns=<!--[
  {
    "caption": "Recorder",
    "field": "event.recorded_by"
  },
  {"caption": "Records", "field": "doc_count"},
  {"caption": "Species", "field": "species_count"}
]-->

[download]
@linkToDataGrid=recorders-grid
@caption=Grid download

A download returning data in a format like that provided before Elasticsearch:

[source]
@id=data-to-download

[download]
@source=data-to-download
@columnsTemplate=easy-download
@caption="Download backward-compatible format"

A download with a format selector:

[source]
@id=data-to-download

[download]
@source=data-to-download
@columnsTemplate=["default","easy-download", "mapmate"]

Options

addColumns

Define additional columns to those defined in the template that you want to include in the download file. An array which uses the same format as the dataGrid @columns option.

caption

Button caption. Defaults to “Download” but will be translated. Can include HTML, e.g. a Font Awesome icon if supported by your theme:

@caption=Download <span class="fas fa-file-download"></span>

columnsTemplate

Named template that defines set of columns on the server which will be included in the download file. If an array of template names is provided in this parameter then a control is shown allowing the user to choose the template to use. The default value is “default” when the source is in docs mode, or blank for the aggregation modes. Options are currently “default”, “easy-download” and “mapmate”. It can be set to blank to disable loading a predefined set. Other sets may be provided on the warehouse in future.

The “default” format (corresponding to “Standard download format” in the download control’s format selection drop-down) provides a standard set of download fields.

The “easy-download” format (corresponding to “Backward-compatible format” in the download control’s format selection drop-down) produces a set of columns and formats which is very close to that provided by downloads before the use of Elasticsearch by Indicia.

The “mapmate” format (corresponding to “Mapmate-compatible format” in the download control’s format selection drop-down) produces a set of columns and formats that should allow for easy import into MapMate. Note that as well as the mandatory fields specified by MapMate a number of additional columns are added which could potentially help with evaluation or further manipulation of the records before importing into MapMate.

id

Optional. Specify an ID for the download control allowing you to refer to it from elsewhere, e.g. CSS. If not specified, then a unique ID is generated by the code which cannot be relied on.

linkToDataGrid

If specified, uses a dataGrid control to obtain the source and columns configuration. Columns specified in addColumns will be appended to the end.

removeColumns

Define columns from the selected column template to be removed from the CSV download. An array of the column titles to remove.

source

ID of the [source] control that provides the data for download. Required unless the linkToDataGrid option is specified.

title

Title attribute of the HTML button, displayed as a hint when the mouse hovers over it. Defaults to “Run the download” but will be translated.

Advanced options

buttonContainerElement

Set @buttonContainerElement to the CSS selector of a container if you want to output the download button in a separate location on the page to the output control listing the download files. For example to add the button to the footer of a [dataGrid] alongside the pagination information:

[download]
@linkToDataGrid=recorders-grid
@caption=Grid download
@buttonContainerElement=#recorders-grid tfoot td

containerElement

If you want to output the download control in an existing element on the page with a known CSS selector then specify the selector here. If the selector matches multiple elements then only the first will be used.

ElasticsearchReportHelper::groupIntegration

Links a reporting page to a recording group (activity). Applies a group_id filter to the data, either loading from the URL parameter or a preset ID. Optionally outputs a summary of the group and its pages.

Options

group_id

ID of the group to load data for, if fixed. If not set, then the group ID is obtained from a URL parameter called group_id.

missingGroupIdBehaviour

Defines what happens if a group ID is not provided either via a parameter or URL parameter. Default is “error” but can be set to “showAll” to allow the page to appear unfiltered.

showGroupSummary

If true, then a group summary panel is displayed including the group logo, title and description.

showGroupPages

If true, then a list of available group page links is shown.

ElasticsearchReportHelper::higherGeographySelect

A select box for choosing from a list of higher geography boundaries (indexed locations). May either act as a single control, or a linked set of select controls if multiple nested location types are specified where child locations are linked to their parent via the parent_id field in the databaes.

When a location is chosen, the map will show the boundary, pan and zoom to the boundary and the results are filtered to records intersecting the boundary.

Locations must be from an indexed location layer. See Spatial Index Builder Module for more info.

Options

blankText

Text shown for the option which corresponds to no location filter.

label

Attaches the given label to the control.

locationTypeId

Either a single ID of the location type of the locations to list, or an array of IDs of location types where the locations are hierarchical (parent first). Each type ID must be indexed by the spatial index builder module.

readAuth

Read authorisation tokens. Not required when used via the prebuilt form.

ElasticsearchReportHelper::leafletMap

A map panel which uses the leaflet library that can display occurrence data from Elasticsearch in a variety of ways.

Typical configuration examples

A heat map:

[source]
@id=map-data
@mode=mapGeoHash

[leafletMap]
@layerConfig=<!--{
  "recordsHeatMap": {
    "title": "All records heat map",
    "source": "map-data",
    "type": "heat"
  }
}-->

Options

baseLayerConfig

A JSON object defining the base layers to make available for addition to the map. Each property is the title of a base layer which contains a sub-object with configuration for that layer. The layer configuration options are:

  • type - OpenStreetMap, OpenTopoMap, Google or WMS.
  • config - a nested object containing configuration depending on the layer type.

For OpenStreetMap and OpenTopoMap, the config object is not used.

For Google layers, the config object can contain the following:

  • subType - roadmap, satellite, terrain or hybrid.

For WMS layers, the config object can contain the following:

  • sourceUrl - the URL of the WMS service if using type WMS.
  • wmsOptions - any additional options to pass to the WMS web service, which will normally at least include a layers property.

Defaults to OpenStreetMap and OpenTopoMap.

Example configuration:

@baseLayerConfig=<!--{
  "OpenStreetMap": {
    "type": "OpenStreetMap"
  },
  "Google Streets": {
    "type": "Google",
    "config": {
      "subType": "roadmap"
    }
  },
  "Google Satellite": {
    "type": "Google",
    "config": {
      "subType": "satellite"
    }
  },
  "Mundialis": {
    "type": "WMS",
    "config": {
      "sourceUrl": "http://ows.mundialis.de/services/service?",
      "wmsOptions": {
        "layers": "TOPO-OSM-WMS"
      }
    }
  }
}-->

cookies

Set to false to disable use of cookies to remember the selected layers plus the current map viewport. Cookies are only enabled when there is a specific id option set for this map.

id

Optional. Specify an ID for the leafletMap control allowing you to refer to it from elsewhere, e.g. CSS. If not specified, then a unique ID is generated by the code which cannot be relied on.

initialLat

Latitude the map will pan to on initial load, if not overridden by a saved cookie or the map being set up to display the bounding box of a report’s output. Defaults to the configuration setting for the IForm module.

initialLng

Longitude the map will pan to on initial load, if not overridden by a saved cookie or the map being set up to display the bounding box of a report’s output. Defaults to the configuration setting for the IForm module.

initialZoom

Level the map will zoom to on initial load, if not overridden by a saved cookie or the map being set up to display the bounding box of a report’s output. Defaults to the configuration setting for the IForm module.

layerConfig

A JSON object defining the foreground layers to add to the map. Each property is the ID of a layer which contains a sub-object containing the configuration for that layer. The layer objects can have the following properties:

  • title - Display title of the layer.

  • source - ID of a source that provides the data. This source can either provide un-aggregated raw data or one of the aggregation types defined for the aggregationMapMode setting for the source.

  • enabled - set to false if you want this layer to be initially hidden and only available via the layer switcher. Once enabled, the state of the layer will be remembered in a cookie unless cookies are explicitly disabled or the map has no specific id option set for this map.

  • forceEnabled - set to true if you want this layer to be enabled whenever the page is initiased. This will override the value stored in a cookie.

  • type - one of the following:

    • circle - see Leaflet circle
    • square - see Leaflet rectangle
    • marker (default) - see Leaflet marker.
    • heat - heat map generated using Leaflet.heat.
    • geom - a polygon representing the record’s original geometry. If the source used is set to mode mapGeoHash, then the geometry output will be the square covering the geohash grid cell.
    • WMS - A Web Mapping Service layer.
  • style - for circles, squares and markers, an object to pass to leaflet as options for the feature as described in the links for each feature type above, e.g. fillOpacity or radius.

    A special style option called size can be specified for circles and squares which defines the size of the feature in metres (similar to radius but the latter is calculated as a number of pixels). For non-aggregated data, the size defaults to the location.coordinate_uncertainty_in_meters field value so features reflect their known accuracy. Size can be set to the special value autoGridSquareSize so that it matches the current map grid square aggregation as you zoom the map in, showing 10km features when zoomed out, then 2km, then 1km when zoomed in. This setting is automatic when using a map source mode.

    A special value called metric can be specified for any style option. For non-aggregated data, this is the location.coordinate_uncertainty_in_meters value. For aggregated data, this value is set to an indication of the number of documents in the current bucket (i.e. the number of occurrences represented by the current feature). It is set to a scale from 0 - 20000, or for fillOpacity options it is set on a scale from 0 - 1.

  • labels - set to “hover” to enable hover-hints for records on the map, including the taxon name, date and recorder. Set to “permanent” to show them all the time.

  • sourceUrl - the URL of the WMS service if using type WMS.

  • wmsOptions - any additional options to pass to the WMS web service.

selectedFeatureStyle

Object containing style options to apply to the selected feature. For example:

@selectedFeatureStyle=<!--{
  "color": "#00FF00"
  "opacity": "0.6"
}-->

showSelectedRow

To make the map highlight the feature associated with a selected row in a dataGrid, set showSelectedRow to the id of that grid. The map will also zoom in to the feature when the grid row is double clicked.

ElasticsearchReportHelper::permissionFilters

Output a selector for various high level permissions filtering options.

Permission sets available in the selector will depend on the permissions set on the Permissions section of the Edit tab in combination with the settings passed in the options parameter. Options available are:

  • all_records_permission - set to the name of a Drupal permission which the user must have to enable the option to access all records.

  • includeFiltersForGroups - adds options for downloading records explicitly added to the user’s groups (activities). The user’s own records are always available; in addition group administrators can download the entire set of records for the group.

  • includeFiltersForSharingCodes - allows filters which define a user’s permissions, such as a set of verifiable records, to be included in the list of options. JSON array containing the sharing codes that are supported for filters which are available for the user and where defines_permissions=true. Defaults to an empty array so none are loaded. Possible options are ‘R’, ‘V’, ‘D’, ‘M’, ‘P’.

  • label - label given to the control. Default “Records to access”.

  • location_collation_records_permission - set to the name of a Drupal permission which the user must have to enable the option to filter for records in a location that the user has a Drupal permission to collate for (e.g. an LRC). To use this option, the user profile must have a field called location_collation which contains the ID of an indexed location from the Indicia locations table.

  • my_records_permission - set to the name of a Drupal permission which the user must have to enable the option to filter for a user’s own records.

  • useSharingPrefix - when @includeFiltersForSharingCodes is used to include filters which define sets of records a user can access, setting this to true will include a prefix for the entry in the selection list to clarify the sharing code (Verification, Download, Reporting etc).

  • notices - a JSON object with one or more keys that are matched against the start of the text of the selected item in the permissions filter control. If a match is found, then the value stored against the key - which can be an HTML string - is displayed below the selection control. In the folloinw example if a filter is selected in the control which starts with the text “LERC download - “, then the specified HTML is displayed below the control:

    @notices=<!--{
      "LERC download - ": "<p><b>For LERC downloads, you must abide by the
      <a href='https://www.brc.ac.uk/irecord/lrc-tc'>
      LERC Terms and Conditions</a>.</b></p>"
    }-->
    

ElasticsearchReportHelper::recordDetails

A tabbed panel showing key details of the record. Includes a tab for record field values, one for comments logged against the record and one to show the recorder’s level of experience for this and similar taxa.

Options available are:

explorePath

Path to an Explore all records page that can be used to show filtered records, e.g. the records underlying the data on the experience tab. Optional.

extraLocationTypes

As for locationTypes, but will be shown in the Derived Info block at the bottom of the pane rather than in the first block of attribute values. Therefore suitable for location types with a lower priority.

locationTypes

The record details pane will show all indexed location types unless you provide an array of the type names that you would like included, e.g. [“Country”,”Vice County”]. Optional.

readAuth

Read authorisation tokens. Not required when used via the prebuilt form.

showSelectedRow

ID of the grid whose selected row should be shown. Required.

ElasticsearchReportHelper::standardParams

A toolbar allowing the building of filters to be applied to the page’s report data.

Options

allowSave

Set to false to disable saving of filters.

indexedLocationTypeIds

An array of location_type_id values to define the list of indexed location types to make available for filtering. These are filtered by a higher geography query.

otherLocationTypeIds

An array of location_type_id values to define the list of non-indexed location types to make available for filtering. These are filtered by a polygon query.

sharing

Which sharing mode to save and load filters for. Set to reporting, verification, data_flow, editing, moderation or peer_review. Default reporting.

taxon_list_id

ID of the taxon list that species and other taxon names are selectable from.

Advanced options

Other options are described in the PHP documentation for the client_helpers/prebuilt_forms/includes/reports.php report_filter_panel() method.

ElasticsearchReportHelper::templatedOutput

A flexible output of ES data which uses templates to build the HTML.

Typical configuration examples

This example using templated output and the @containerElement option to build an HTML table:

[source]
@id=sample-agg
@size=0
@aggregation=<!--{
  "per_sample": {
    "terms": {
      "field": "event.event_id",
      "min_doc_count": 5,
      "size": 30,
      "order": {
        "_count": "desc"
      }
    }
  },
  "stats_per_sample": {
    "stats_bucket": {
      "buckets_path": "per_sample._count"
    }
  }
}-->

[templatedOutput]
@containerElement=#sample-table tbody
@source=sample-agg
@repeatField=aggregations.per_sample.buckets
@content=<tr><th>Count for {{ key }}</th><td>{{ doc_count }}</td></tr>

[templatedOutput]
@containerElement=#sample-total
@source=sample-agg
@content=Count returned: {{ aggregations.stats_per_sample.count }}, average: {{ aggregations.stats_per_sample.avg }}

<table id="sample-table">
  <tbody>
  </tbody>
</table>
<div id="sample-total"></div>

Options

content

HTML to output for each item. Replacements are field names {{ this.that }} within the path specified by repeatField.

footer

A piece of HTML that will be inserted into a div at the bottom of the control when a response is received.

header

A piece of HTML that will be inserted into a div at the top of the control when a response is received.

id

Optional. Specify an ID for the templatedOutput control allowing you to refer to it from elsewhere, e.g. CSS. If not specified, then a unique ID is generated by the code which cannot be relied on.

repeatField

Where the response from Elasticsearch contains an array of values that should be repeated in the output specify the path to the field containing the array here. A good example is the buckets list for an aggregation. E.g. aggregations.per_sample.buckets allows iteration over the response for an aggregation called per_sample.

source

ID of the [source] control this templatedOutput is populated from.

ElasticsearchReportHelper::urlParams

This control allows you to configure how the page uses parameters in the URL to filter the output shown on the page. By default, the following filter parameters are supported:

  • taxa_in_scratchpad_list_id - takes the ID of a scratcphad_list as a parameter and creates a hidden filter parameter which limits the returned records to those of species in the scratchpad list. For example, a report page which lists scratchpad lists could have an action in the grid that links to an Elasticsearch outputs page passing the list ID as a parameter.
  • sample_id - takes the ID of a sample as a parameter and creates a hidden filter parameter which limits the returned records to those in the sample.
  • taxa_in_sample_id - takes the ID of a sample as a parameter and creates a hidden filter parameter which limits the returned records to those of taxa in the sample. Note that records will be included from other samples as long as they are for the same taxa.

For example, a report page which lists samples or scratchpad lists could have an action in the grid that links to an Elasticsearch outputs page passing the ID as a parameter.

Additional filters can be configured via the fieldFilters option.

Typical configuration examples

An example where a page is configured to filter by &genus=… in the URL:

[urlParams]
@fieldFilters=<!--{
  "genus": {
    "name": "taxon.genus"
  }
}-->

Options

fieldFilters

Use this option to override the list of simple mappings from URL parameters to Elasticsearch index fields. Pass an array keyed by the URL parameter name to accept, where the value is an array of configuration items where each item defines how that parameter is to be interpreted. Therefore multiple filters may result from a single parameter. Each configuration item has the following data values:

  • name - Elasticsearch field name to filter

  • type - optional. If set to integer then validates that the field supplied is an integer. Other data types may be supported in future.

  • process - optional. possible values are:

    • taxonIdsInScratchpad - the value is used as a scratchpad_list_id which is used to look up a list of taxa. The value is replaced by a list of taxon.taxon_ids for filtering to the entire list.
    • taxonIdsInSample - the value is used as a sample_id which is used to look up a list of taxa. The value is replaced by a list of taxon.taxon_ids for filtering to the entire list.

    If the process is not specified then the value is used as is.

ElasticsearchReportHelper::userFilters

Provides a drop down populated with the user’s saved report filters. Selecting a filter applies that filter to the current page’s outputs.

Options

definesPermissions

Set to true if this control is to load permission filters such as those which define a verification context.

sharingCode

Code indicating the type of task the filters to load are for. Default R (=reporting).

label

Label for the control which will be translated before use. Set to empty string to exclude the label. Default is ‘Filter’, or ‘Context’ if @definesPermissions is true.

ElasticsearchReportHelper::statusFilters

Provides a drop down list of record status filters. Selecting a filter applies that filter to the current page’s outputs. The options mirror those available in the ‘records to include’ drop-down in the quality part of the [permissionFilters] control. applies that filter to the current page’s outputs. Changing the filter selected with this control changes the selected option in the [permissionFilters] control, if there is one on the page, and visa versa.

ElasticsearchReportHelper::surveyFilter

Provides a drop down list of surveys (datasets). Selecting a survey applies a filter to the current page’s outputs, limiting records to those belonging to the selected survey. It is anticipated that this control will be used on pages that provide dataset download facilities. When a survey is selected with this control, the returned records will include all custom sample and occurrence attributes associated with that survey.

ElasticsearchReportHelper::filterSummary

Provides a textual summary of all the filters applied on the page using any of the following controls: [standardParams], [permissionFilters], [userFilters], [statusFilters] and [surveyFilter]. This can be used to make it less likely that a user has a filter applied that they are not aware of, or two conflicting filters for example.

ElasticsearchReportHelper::verificationButtons

Outputs a panel containing action buttons for verification tasks, including changing the record status, querying the record and accessing the record edit page. Effectively allows an Elasticsearch report page to be converted into a verification tool.

Options

editPath

If a Drupal page path for a generic edit form is specified then a button is added to allow record editing.

id

ID of the HTML element. If not specified, a unique ID will be autogenerated which cannot be relied on.

includeUploadButton

If set to true, a button is added to enable upload of a spreadsheet of verification decisions. This allows a verification decisions spreadsheet with the following columns to be uploaded and automatically applied to the records:

  • ID - ID of the record
  • Decision status’ - for records where the status is to be changed, specify one of the following values: * Accepted * Accepted as correct * Accepted as considered correct * Plausible * Not accepted as unable to verify * Not accepted as incorrect * Queried
  • Decision comment’ - fill in with the comment to associate with the decision. A comment without a decision status will still be attached to the record but the status won’t be changed.

The decision spreadsheet upload tool checks each record to ensure that it is one of the set of records returned by the current verification context filter. Therefore it is impossible to update records you are not a verifier for.

Note that the warehouseName option must be provided when includeUploadButton is true.

In order to set the decisions spreadsheet functionality up, a [download] control can be modified to include the columns required for verification. It can also be configured to output the button and resulting download file link under the records grid by adding the following options:

[download]
@linkToDataGrid=records-grid
@buttonContainerElement=#records-grid tfoot td
@containerElement=#records-grid
@addColumns=<!--[
  {"caption":"Status","field":"#verification_status:astext#"},
  {"caption":"Sub-status","field":"#verification_substatus:astext#"},
  {"caption":"*Decision status*","field":"#constant:#"},
  {"caption":"*Decision comment*","field":"#constant:#"}
]-->

The verification buttons can be configured to output the upload decisions spreadsheet button into the report footer area as follows:

[verificationButtons]
@includeUploadButton=true
@warehouseName=myexamplewarehouse.com
@uploadButtonContainerElement=#records-grid tfoot td

keyboardNavigation

Enables the following shortcuts: * 1 = Verify current record (accepted as correct, or accepted when showing just tier 1 buttons). * 2 = Verify current record (accepted as considered correct). * 3 = Set current record as plausible. * 4 = Reject current record (unable to verify). * 5 = Verify current record (rejected as incorrect). * Q = Query current record. * R = Re-determine current record.

redeterminerNameAttributeHandling

To change the behaviour for updating the determiner name associated with a record after a redetermination, set to one of the following:

  • overwriteOnRedet - The determiner name attribute of a record is changed to the name of the user performing a redetermination. This is the default.
  • allowChoice - the user performing a redetermination is able to choose whether to overwrite the determiner name associated with a record or leave it as it is.

showSelectedRow

Specify the element ID of a [dataGrid] or [cardGallery] control which the buttons will source the selected occurrence from.

taxon_list_id

Allows the list that the redetermination functionality’s search box will use to be specified. If not set, then the master list set in the Indicia settings form will be used.

uploadButtonContainerElement

If you want to add the upload button somewhere else on the page (e.g. to a table footer alongside a download button, specify the element selector here.

viewPath

If a Drupal page path for a record details page is specified then a button is added to allow record viewing.

warehouseName

Name of the warehouse stored against records in Elasticsearch (in the metadata.warehouse field). Typically the domain name of the warehouse server. Must be set when the includeUploadButton option is set as it is required to ensure that uploaded decisions do not affect records imported into the Elasticsearch index from other warehouses.

Positioning of control elements

All output controls (data grids, maps etc) will output their content at the appropriate location on the page into a div element whose ID matches the id option you specify.

If you want to override the creation of a container div and, instead, inject the control content into an HTML element of your choice elsewhere on the page, then you can specify the CSS selector of that element in the @containerElement option.

The following example shows how a single aggregation request can be injected as rows into a table elsewhere on the page:

[source]
@id=sample-agg
@size=0
@aggregation=<!--{
  "per_sample": {
    "terms": {
      "field": "event.event_id",
      "min_doc_count": 5,
      "size": 30,
      "order": {
        "_count": "desc"
      }
    }
  },
  "stats_per_sample": {
    "stats_bucket": {
      "buckets_path": "per_sample._count"
    }
  }
}-->

[templatedOutput]
@containerElement=#sample-table tbody
@source=sample-agg
@repeatField=aggregations.per_sample.buckets
@content=<tr><th>Count for {{ key }}</th><td>{{ doc_count }}</td></tr>

[templatedOutput]
@containerElement=#sample-total
@source=sample-agg
@content=<div>Count of samples {{ aggregations.stats_per_sample.count }}</div>

<table id="sample-table">
  <tbody>
  </tbody>
</table>
<div id="sample-total"></div>

You could also set @containerElement to the selector of a div element output elsewhere on the page, e.g. part of the theme’s header.

Using controls directly from JS

As all the functionality in the ElasticsearchReportHelper’s output controls is driven by JavaScript in the client, it is possible to write JS directly with minimal PHP. source controls are defined by appending an object containing the options to the indiciaData.esSources array. Other controls are provided as jQuery plugins where the plugin name is ‘idc’ plus the method name, e.g. ElasticsearchReportHelper::leafletMap is represented by the jQuery plugin idcLeafletMap. The option are passed as a parameter.

Example code:

HTML

<div id="dataGrid1" class="idc-output idc-output-dataGrid"></div>

JavaScript

jQuery(document).ready(function docReady($) {
  indiciaData.esSources.push({
    id: 'source-league',
    size: 0,
    aggregation: {
      recorder_agg: {
        terms: {
          field: "event.recorded_by.keyword",
          size: 100,
          order: {
            _count: "desc"
          }
        },
        aggs: {
          species_count: {
            cardinality: {
              field: "taxon.species_taxon_id"
            }
          }
        }
      }
    }
  });
  $('#dataGrid1').idcDataGrid({
    id: 'dataGrid1',
    source: {'source-league': 'League table'},
    aggregation: simple,
    columns: [
      {"caption":"Recorder name", "field":"key"},
      {"caption":"Number of records", "field":"doc_count"},
      {"caption":"Number of species", "field":"species_count.value"}
    ]
  });
  indiciaFns.populateDataSources();
});

PHP

<?php

iform_load_helpers(['ElasticsearchProxyHelper']);
ElasticsearchReportHelper::enableElasticsearchProxy();
handle_resources();

?>