Butterfly Transect Walks Example Setup¶

Indicia includes a prebuilt form designed for inputting flying insect counts along a transect walk which has been divided into sections. This form was designed for the UKBMS’s online recording facilities but can also be used to record other flying insects such as Odonata.

Some details on how you might set this form up follow, including the setup of a calendar grid to break walks down into weeks through the season. Before following these steps you will need an installation of Drupal plus the Indicia Forms and Easy Login modules as well as an account on a warehouse.

Here are some files you may like to have available to import into the system:

File	Description
Counties CSV	If not using the list of counties provided on the warehouse then provide a list of the counties that sites will be allocated to. This should be provided as a CSV file with a single column containing the county names, including a column title (which can be anything you like).
Habitats CSV	Provide a list of the habitats that will be available for describing sites in your recording scheme. This should be provided as a CSV file with a single column containing the habitat names, including a column title (which can be anything you like). If available, a sort order column containing an integer for each term can be used to enforce a non-alphabetical sort order.
Management CSV	Provide a list of the management terms that will be available for describing sites in your recording scheme. This should be provided as a CSV file with a single column containing the management terms, including a column title (which can be anything you like).
Branches CSV	This file is only required if your recording scheme is divided into regional branches. An ESRI SHP file format list of the boundaries of each branch, containing the branch names and the polygon defined in projection EPSG:27700 or EPSG:4326.
Transects CSV	If you want to prepopulate the list of sites available for transect walks, then provide a list of the transects as a spreadsheet in CSV format, including column titles. The spreadsheet should include the following columns: Site code. Provide a unique numeric code for each site. Site name. Provide a name for each site. Grid ref. Grid reference for each site’s centroid. County. Name of the county for each site. This must match one of the counties in the Counties CSV file. Number of sections. The number of sections the transect is divided into. If this column is ommitted then you will need to manually set the number of sections and input the section details before inputting count data. Overall transect length. The length of the transect in metres, can be omitted if not known. Transect width. The width of the transect in metres, can be omitted if not known. You will need to know the distinct list of widths in use so that you can later set up the appropriate entries for the list of available widths. Year established. Specify the 4 digit year each transect was established if known. All or single species. A column containing the word All or Single for each transect, depending on the transect type. Sensitive. A column containing t for sensitive sites and f for all others. Primary habitat. Set to one of the terms from the list of habitats where the primary habitat is known. Secondary habitat. Set to one of the terms from the list of habitats where the primary habitat is known. The exact column titles you use does not matter as long as you remember which is which.
Sections CSV	If you want to prepopulate the list of sites available for transect walks, then provide a list of the transects as a spreadsheet in CSV format, including column titles. The spreadsheet should include the following columns: Grid ref (if not importing a SHP file). This can be the same as the grid reference for the parent transect but the recorders will need to draw their routes on a map before inputting records.
Sections SHP	An ESRI SHP file of the section lines
Species CSV	A CSV file of each of the species you would like to be able to record. Should have a column for the latin name plus a column for the common name, plus one column for any species code systems you would like to be able to use, e.g. BRC codes. You can provide additional species lists if you want to be able to record additional species groups via additional tabs.
Wind Speed CSV	A CSV file of each of the wind speed terms you would like to be able to record.
Wind Dir CSV	A CSV file of each of the wind direction terms you would like to be able to record.

Website registration and survey¶

As with any Indicia based survey, you will need a website registration on the warehouse plus an entry in the list of surveys, belonging to the website. Give your survey a name that you will remember as being associated with the butterfly transect walk survey you are configuring.

Termlists¶

Before setting up the form, you will need to have certain terms and termlists configured on the warehouse as follows. All the termlists you create should be owned by your website registration on the warehouse.

Ensure that the existing Location Types termlist includes terms called Branch, Transect and Transect Section. Create them if they don’t already exist.
If not using the existing list of counties, then create a termlist called BMS Counties or similar. Use the warehouse import tool to import the CSV file of counties into the list, setting the language to English for all rows and mapping your column to the term field.
Create a termlist called Transect width (m) and setup terms called 5, 6, 10 and other, with the Sort Order set to 5, 6, 10 and 9999 respectively. You can modify this list if your scheme has a different set of possible transect widths.
Create a termlist called All or single species with terms for All and Single. Set both terms to English language, with their sort order set to 0 and 1 respectively.
Create a termlist called Climate of transect with terms for Lowland and Upland. Set both terms to English language, with their sort order set to 0 and 1 respectively.
Create a termlist called BMS Habitats or similar. Use the warehouse import tool to import the CSV file of habitats into the list, setting the language to English for all rows and mapping your column to the term field. Also import the sort order if provided to ensure the habitats are in the correct order.
Create a termlist called BMS Management. Use the warehouse import tool to import the CSV file of management terms into the list, setting the language to English for all rows and mapping your column to the term field.
Create a termlist called BMS Wind Speeds. Use the warehouse import tool to import the CSV file of wind speed terms into the list, setting the language to English for all rows and mapping your column to the term field.
Create a termlist called BMS Wind Directions. Use the warehouse import tool to import the CSV file of wind direction terms into the list, setting the language to English for all rows and mapping your column to the term field.
Create a termlist called BMS Temperatures. Use the warehouse import tool to import the CSV file of temperature terms into the list, setting the language to English for all rows and mapping your column to the term field.

Species Lists¶

Before importing the species lists you want to be able to record against, ensure that the Taxon Code types termlist contains a term for any species codes that you would like to import alongside the species names, e.g. for BRC codes or Species ID 2010. You must provide species names in a spreadsheet with the following columns, note that the exact column names used does not matter:

Latin name - the latin name of the species, imported into the Taxon > Taxon field.
Common names - the common name(s) of the species, imported into the Other Fields > CommonNames field. Provide as a comma separated list, with the preferred first. You can follow each name by a pipe (|) then the 3 letter ISO 639 language code for the language, e.g.:
```
Green Woodpecker|eng,Pic vert|fra
```
This field can be ommitted if common names are not used.
Codes - any coding systems for the species such as BRC codes, imported into the Other Fields > Codes field. The field can contain several codes separated by a comma. Each code must contain the code name (matching the term in the Taxon Code types termlist), followed by a pipe (|), then the actual code, e.g:
```
Species ID 2010|172500,BRC Code|123456
```

Custom Attributes¶

Setup the following location attributes for the UKBMS survey. Do not make any of them required at this stage or link them to the location types as this needs to be done after import. The attribute is described as block/sub-block/caption, followed by the description of the attribute. For example, you should create a location attribute called county which is a lookup, linked to the BMS Counties termlist. On the survey setup attributes you will need to make the attribute required and linked to the Transect location type, but only after the import of any existing transects.

Site details/Details/County Lookup, BMS Counties termlist, linked to Transect location type, required for the survey.
Site details/Details/Sensitive Boolean, available to other websites, linked to Transect location type
Site details/Details/No. of sections Integer, linked to Transect location type, minimum 0, required for survey
Site details/Details/Overall length (m) Integer, linked to Transect location type, minimum 0, required for survey
Site details/Details/Transect width (m) Lookup, Transect widths termlist, linked to Transect location type, required for survey
Site details/Details/Year established Integer, linked to Transect location type
Site details/Details/All or single species Lookup, All or single species termlist, linked to Transect location type
Site details/Details/Climate of transect Lookup, Climate of transect termlist, linked to Transect location type
Habitat and management/Habitat/Principal transect habitat Lookup, Habitats termlist, linked to Transect location type
Habitat and management/Habitat/2nd transect habitat Lookup, Habitats termlist, linked to Transect location type
Habitat and management/Habitat/Principal habitat present Lookup, Habitats termlist, linked to Section location type
Habitat and management/Habitat/2nd habitat present Lookup, Habitats termlist, linked to Section location type
Habitat and management/Habitat/3rd habitat present Lookup, Habitats termlist, linked to Section location type
Habitat and management/Habitat/4th habitat present Lookup, Habitats termlist, linked to Section location type
Habitat and management/Habitat/Habitat text description Text, linked to Section location type
Habitat and management/Habitat/Notes on land use and management Text, not linked to a specific location type
Habitat and management/Management/Primary management Lookup, Management termlist, linked to Section location type
Habitat and management/Management/Secondary management Lookup, Management termlist, linked to Section location type
Habitat and management/Management/Management text description Text, linked to Section location type
Section/Details/Section length (m) Integer, minimum 0, linked to Section location type
CMS User ID Integer, available to other websites, linked to Transect location type

Setup the following custom attributes for occurrences in your survey:

Abundance Count integer, required for the survey, minimum value 0, system function = Count or abundance of a sex or life stage.

Setup the following custom attributes for samples in your survey:

Recorder Name Text, system function=full name, sample method=Transect
Start Time (hh:mm) Text, regexp=/^([0-1][0-9]|2[0-3]):([0-5][0-9])$/, required for survey, default control type=text_input, sample Method=Transect, available to other websites
End Time (hh:mm) Text, regexp=/^([0-1][0-9]|2[0-3]):([0-5][0-9])$/, required for survey, default control type=text_input, sample Method=Transect, available to other websites
% sun Integer, min value=0, max value=100
Temp (Deg C) Lookup, BMS Temperatures list, required for survey, sample method=Transect
Wind Direction Lookup, BMS Wind Directions list, Default value=Not recorded/no data, required for survey, default control type=select, sample Method=Transect
Wind Speed Lookup, UKBMS Wind Speeds list, Default value=Not recorded/no data, required for survey, default control type=select, sample method=Transect
CMS User ID Use the existing attribute, Sample Method=Transect. This attribute is not needed if the Easy Login module is enabled.
CMS Username Use the existing attribute, Sample Method=Transect. This attribute is not needed if the Easy Login module is enabled.

Drupal site setup¶

Starting with a Drupal site setup with a configured Indicia forms module, perform the following setup tasks. Also ensure that your site is configured with the correct warehouse, website ID and password on the IForm settings page.

Install Drupal modules¶

Install the following modules for Drupal:

Chaos tools
Page manager
Panels
Views
Views UI
Views content panes

Create a home page¶

First we need to create a Drupal node to hold the chart which appears on the home page. Select Content management > Add content > Indicia pages from the Drupal admin menu. Set the Page title to “Records for this year so far”.
Under the Form Selection section, set Select Form Category to “Reporting” and the Select Form to “Report Calendar Summary”. Click the Load Settings Form button.
Specify the following settings for the form:
- Report Settings - Report Name =Reports for Prebuilt Forms/UKBMS/UKBMS Annual Summary Table Occurrence list
- Report Settings - Preset Parameter Values =
```
survey_id=n
user_id=
location_id=
occattrs=
date_from=
date_to=
taxon_list_id=n
```
  Make sure that you set n to the survey’s ID and the ID of your main species list respectively.
- Report Settings - Vertical Axis = taxon
- Report Settings - Count Column = Abundance Count
- Report Output - Output chart = ticked
- Report Output - Default output type = Chart.
- Controls - Date filter type = This year (no user control)
- Controls - Drupal permission for manager mode = manager
- Date Axis Options - Start of week definition = date=Apr-01
- Date Axis Options - Week One Contains = Apr-01
- Date Axis Options - Restrict displayed weeks = -3:30
- Chart Options - Chart Type = Line
- Chart Options - Chart X-axis labels = Week number only
- Chart Options - Include total series = ticked
- Chart Options - Chart Height = 200
- Advanced Chart Options - Axes Options - paste the following into the Edit source view then click Edit w/form to save it:
```
{
  "yaxis":
  {
    "min":0,
    "showMinorTicks":false,
    "tickOptions":
    {
      "showGridline":false,
      "formatString":"%.0f"
    },
    "max":500
  },
  "xaxis":
  {
    "labelOptions":
    {
      "label":"Week no."
    }
  }
}
```
  Click Save to save the node.
Visit the Site building > Views menu item on the Drupal admin menu. Click enable* beside the frontpage view.
Select Site building > Pages > Add custom page from the Drupal admin menu.
Set the Administrative title and Machine name of the page to “home”.
Set the path to “home” and tick Make this your site home page.
Set Variant type to Panel if it is not already.
Tick Visible menu item. Leave the other checkboxes unticked.
Click Continue.
On the next Menu settings page, select Normal menu entry, then enter “Home” as the title, and set the Menu to “Primary links”. This adds a menu item to the main site menu. Click Continue.
On the Choose layout page, select the radio button for Builders - Flexible. Click Continue.
On the Panel settings page, just click Continue.
On the Panel content page, click Show layout designer. On the Row drop down menu, select Add region to the left. Set the Region title to “News” and click Save.
Click Hide layout designer. On the gears icon in the top left of the News section, select Add content.
On the popup dialog that appears, select Views in the bar on the left, then select frontpage. Click Continue to select the defaults display. Click the Finish button to add the view to the page. On the gears icon in the top left of the Center pane, select Add content. In the popup that appears, select Existing node. Search for the “Records for this year so far” node, check the box to override the title but leave the title blank, and uncheck the tickbox for including node links. Set the Build mode to “Full node” and click Finish.
Click Update and Save.

Now might be a good time to create a new Story content item to check that this appears on the home page.

My Sites¶

Add a new Indicia Pages content item and use the following settings:

Page title = My sites
Menu settings - Menu link title = My Sites
Menu settings - Parent item = <Primary links>
Select Form Category = Reporting
Select Form = Report Grid
URL Path = site-list

Then, click the Load Settings Form button and enter the following settings in the configuration form which appears:

Report Settings - Report Name = Library/Locations/Species and occurrence counts by site

Report Settings - Preset parameter values =

date_from=
date_to=
survey_id=
location_type_id=Transect
locattrs=CMS User ID
attr_location_cms_user_id={user_id}

Report Settings - Columns Configuration = select the View Source mode then paste the following settings, finally click View w/form to save the settings.

[
  {
    "fieldname":"id",
    "visible":false
  },
  {
    "fieldname":"name",
    "display":"Site Name"
  },
  {
    "fieldname":"occurrences",
    "display":"No. of records"
  },
  {
    "fieldname":"taxa",
    "display":"No. of species"
  },
  {
    "fieldname":"groups",
    "visible":false
  },
  {
    "fieldname":"attr_location_cms_user_id",
    "visible":false
  },
  {
    "display":"Actions",
    "actions":
    [
      {
        "caption":"edit",
        "url":"{rootFolder}site-details",
        "urlParams":
        {
          "id":"{id}"
        }
      }
    ]
  }
]

Report Settings - Footer =

<a href="{rootFolder}site-details" class="pager-button">Add Site</a>

Todo

Remaining setup of forms in Drupal Enable easy login Site details form setup Enable AJAX Proxy - can be done after saving the site details form as “Enable AJAX Proxy” button appears.

Butterfly Transect Walks Example Setup¶

Website registration and survey¶

Termlists¶

Species Lists¶

Custom Attributes¶

Drupal site setup¶

Install Drupal modules¶

Create a home page¶

My Sites¶

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