26 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Jim,

Thanks for reply.  I tried what you said (Sam, have you got a species list selected, chosen the Field used to filter taxa, and entered a single species in the Taxon filter items?).
Same error still.  Attached to my email to you the species part of my form, with how I have filled it in.  I have tried changing the options around regarding multiple vs single occurrence entry, and still the same.

Any thoughts?  Thanks

I can give you access to our website to have a look at the whole form if that helps?

Thanks

Sam

27 Reply by Jim Bacon

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Sorry, Sam, I just read your original post properly.

You are using the "Sample with occurrences form" which firmly expects there to be an occurrence submitted with it. You have to add a [species] control to your form structure.

In my head I thought you didn't have a species input control because you were making a single species recording form. If you add a [species] control now, you will see nothing on your form but you'll be submitting hornet records with each environment record.

Probably the right solution is to create a "Sample without occurrence" form.

The reason I didn't have this problem was that I submitted habitat types for occurrences.

Jim Bacon.

28 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Aha yes, of course.  I didn't put 2 and 2 together. Hmm yes, I'm not sure I'm confident enough to create a "Sample without occurrence form".  I think I'm best trying to work in a habitats thing like you have or thinking of another way of adding occurrences in.

Cheers

Sam

29 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Jim,

Sorted, I have added an ad hoc/casual record box.  Which would probably useful in addition to an overall casual record form that we will have; but this can be just general records across the site, when you don't have a specific grid ref for where you saw it.  Plus to my surprise, if you don't input a species record it still submits and you have a sample in the warehouse, with images (if uploaded) and nothing in the occurrences.  Ideal

Thanks for your help in identifying the cause of this error.

Cheers

Sam

30 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

John,

I am getting this error when trying to set up and view an indicia form:

Fatal error: Out of memory (allocated 61603840) (tried to allocate 13611672 bytes) in /websites/123reg/LinuxPackage99/nb/is/_o/nbis.org.uk/public_html/sites/all/modules/iform/client_helpers/helper_base.php on line 693

Now I have had a similar error before (last week I believe) when trying to update my modules in drupal.  I changed my php memory in drupal by adding code to the settings.php file, this changed it to 128mb, but our host told me they limited shared hosting to 64mb.

Do you think this is a php memory limit issue that I need a new shared host for, or do you think there is some drupal or indicia issue that is causing this error and or the requirement for using so much memory at the moment?

Cheers

Sam

31 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

John,

I have sorted it I think.  It was just that I was asking the form to call all Fungi in the UK master list to populate the initial grid....which obviously made it fall over, as too big a list.

Thanks

Sam

32 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

John,

As discussed at the NFBR conference, I would like to be able to know how to remove the occurrences grid from a sample and occurrences form.  The form I mentioned to you  is our environmental data form: http://www.nbis.org.uk/SpeciesSurveillenceEnvDataForm.  You said you thought there maybe some simple css to change or add to remove the form's requirement for the [species] grid/input control.  Any thoughts?  It would be nice if the solution allowed me to either include or exclude the grid......as you know people change their mind on what they want in the forms!

Few other things:

Could you tell me how I make sure all the boxes on the my forms page list l-r and then down, rather than just down?  Plus if there is anyway of making this prettier in terms of the boxes etc? Our page is here: http://www.nbis.org.uk/forms_and_surveys_library

Also, we need to show some stats, graphs etc as providing feedback when volunteers have provided the records.  I can produce maps showing the distribution of records for a survey, is there an easy way of breaking this down by species (different colour dots or extra layers) for each survey?
Also are there any graphs etc that I can show the stats for feedback in indicia

Thanks

Sam

33 Reply by johnvanbreda

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Hi Sam
You could try adding the following CSS:
table.species-grid {
  display: none;
}

The documentation for how to add the CSS is at indicia-docs.readthedocs.org/en/latest/site-building/iform/customising-page-functionality.html

Specifically, see the line:
To include your own CSS files, you need to create a .css file and place it in the folder sites\all\modules\iform\client_helpers\prebuilt_forms\css. The file should be called node.nid.css where nid is the node id of the Drupal page your form is on.

The Instant Indicia CSS file contains the following CSS, which you might like to add to your theme's. Since you aren't using the Instant Indicia theme you aren't picking up some of the default stuff like this:

.gallery-item, .gallery li, .summary-report {
  text-align: center;
  padding: 0.5em;
  margin: 0.5em;
  display: -moz-inline-box;
  -moz-box-orient: vertical;
  display: inline-block;
  vertical-align: middle;
  *vertical-align: auto;
  list-style-type: none;
  background: none;
  -moz-box-shadow: silver 3px 3px 6px;
  -webkit-box-shadow: silver 3px 3px 6px;
  -o-box-shadow: silver 3px 3px 6px;
  box-shadow: silver 3px 3px 6px;
  border: solid silver 1px;
}

.gallery-item, .gallery li, .summary-report {
  *display: inline;
}

There is a report chart prebuilt form under reports, which supports pie charts, bar charts and line graphs. Or you can take a look at the summary reports feature.

Not sure how you are producing your maps. If it is using the "report map" method to load data from a report file, then the easiest way is to make a custom report file which outputs style information for each dot on the map, e.g. a fill colour. The explore_map reports (under library/occurrences) might help you to understand how this is done, or you can refer to the documentation for the feature_style attribute of a column definition, described at https://indicia-docs.readthedocs.org/en … umns-label

Cheers
John

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34 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

John,

Thanks for the response.  I will look into your suggestions and see what I can do.

sorry to bombard, but a couple of other things:

1.  We have set up several forms for our species surveillance project.  As with Pond net you add a location using the location form, you then add environmental data and then add in species records for which ever group you are recording.  Such as the vascular plant one (not yet finished) here: http://www.nbis.org.uk/SpeciesSurveillencePlantsForm.  This all works and the records go to the database, irecord etc and are visible in http://www.nbis.org.uk/browse-records.  However, despite been logged in etc, the records do not appear in http://www.nbis.org.uk/my-records.  However the records I have entered previously on our older forms without location are visible, irrespective of whether or not I was logged in when I recorded.  The same occurs for http://www.nbis.org.uk/my-sites and http://www.nbis.org.uk/all-sites.  So I suspect it is something to do with its link to the location attribute that means it does not list the records on these pages.

Any thoughts?

2.   With the project, all the forms were going to be similar by just choosing a location and then recording/listing the species recorded for each taxon group.  This is just like pond net and seemed to be the best solution as we were not worried about assigning species to a particular quadrat or transect....just the site.  This has now changed to fit in with the Butterfly Conservation transect methodologies.  So we need to have the location still chosen by and set as the site, but we need people to record species against each section of their transect.  I have tried the sectioned transect editor form before for our Green lanes survey with limited success.  How would the process work as I suspect people would need to set up a location in the location form (unless the site is already set as a location), then set up a transect with desired number of sections in maybe the transect editor form and then add the species to the sections using one of the other two transect forms in the iform module (e.g. UKBMS one).  Would this be roughly correct and if so what needs to be set up.  I have tried to set up the UKBMS one quickly but think I must need to set up the transect somewhere before, such as the transect editor....as I suspect location and transect are different attributes?

Thanks again!

Sam

35 Reply by johnvanbreda

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Hi Sam
So that I can investigate 1, I'd like to get an admin login to your website. I had a password a while back but I think it has changed- can you email it to me please, or better, give me an account with full access?

2. The UKBMS stuff is a bit fiddly to set up. When a new transect is created there are 3 steps - first, you provide a rough site centroid and some high level attributes (e.g. overall habitat info). Then you draw the sections. Finally, you provided details for each transect (e.g. detailed habitat and management info). So, the transect editor form creates the transect (the site) by itself and you don't need a separate location edit form. Once created, then you should use the input form and provide the site ID as an input parameter so it knows where you are recording, what the sections are etc.

Have you actually tried the ukbms.org/mydata site out yet? If you could confirm if this methodology is exactly what you are after (right down to the weekly calendars etc) then it will be much easier to work out if all you need is a bit of configuration, or there will be any custom code.

Cheers
John

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36 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Thanks John.

Sent email about 1.

2.  I think this looks not far off what we will need, except maybe to remove some of the site attributes and that we have a requirement to add in day-flying moths....but I suppose that does not matter as much as we would just create the species lists ourselves (as we have a butterfly list and a day-flying moth list, both Norfolk specific).  Also although you explained that it is not needed to link the location attribute in, can we still add this in when setting up the transect, as we need all our forms linked to the site location centroid....as this will be different to a transect location and is consistent over all taxa (as we are recording all taxa to the same location centroid).

37 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Will have a look with Martin at the UKBMS page and let you know what we think would fit our requirement and what would need changing.....

Thanks

38 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

John,

Just had a look at the UKBMS forms and I would be very happy with this to be replicated for us in almost its entirety.  The things we would want to change are:

As with all of our forms we would not want the initial grid on the my sites bit.

On My walks - preferably would not want the calender (unless it is more of a problem to remove) and just go straight to the my walks data entry form page and add the date in there using the usual pop up/appearing calender.   As said before,  if we can add in the location (attribute) drop-down here, so the user has to select their location then their transect, that would be great. In the data entry form we would not want an other, only butterflies and day flying moths (our species lists).

Based on the above, how simple do you think this would be to create and what would I need to do to achieve this?

Many thanks

39 Reply by johnvanbreda

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Hi Sam
I think this is less than a day's work - mostly a case of just copying over configuration. We can set up your own species lists no problems, as the species lists used are configuration. I also think that the form will let you pick a site and calendar date if they are not preset, though I reserve judgement on that so this area might need a tiny bit of coding to sort.
Cheers
John

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40 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

John,

could not view records red points on distribution maps such as nbis.org.uk/cuckoo_map and not add records to any form (click on map and add grid ref) on Friday due to bluecoat blocking site warehouse1.indicia.org.uk url.  This was at work and is hopefully being unblocked today.  At the time the records were displayed when I accessed our site on my mobile and the same with clicking on map to input grid reference of record.....so it seemed fine.  Today I have been trying to work on things and the whole website is slow, but especially the indicia forms and most importantly, although I can click on the map to get the grid ref when inputting a record, the red point records are not displayed on distribution maps such as the cuckoo one above...and the species layer name has gone all weird, depending on the browser.  Also, which was a problem on Friday, is that the plus icon on the map when inputting records is now on the left of the map and when clicked shows the map layer options behind the +/- and up/down icons in a weird text.  Any thoughts on these problems.  Can't really see with firebug, but inspecting element in chrome shows this error, I've pulled out the following from the inspected element's error:

<img class="olTileImage olImageLoadError" src="http://warehouse1.indicia.org.uk:8080/geoserver/wms?LAYERS=indicia%3Adetail_occurrences&amp;TRANSPARENT=TRUE&amp;CQL_FILTER=website_id%3D7%20AND%20taxon_meaning_id%3D127807%20AND(survey_id%3D107)&amp;STYLES=dist_point_red&amp;SERVICE=WMS&amp;VERSION=1.1.1&amp;REQUEST=GetMap&amp;FORMAT=image%2Fpng&amp;SRS=EPSG%3A3857&amp;BBOX=-31481.810327612,6831583.6830372,243691.49146071,7015032.550896&amp;WIDTH=900&amp;HEIGHT=600" style="visibility: inherit; opacity: 1; position: absolute; left: -150%; top: -100%; width: 900%; height: 600%;">

curl 'http://warehouse1.indicia.org.uk:8080/g … HEIGHT=600' -H 'Accept: image/webp,*/*;q=0.8' -H 'Referer: http://www.nbis.org.uk/Cuckoo_Map?' -H 'User-Agent: Mozilla/5.0 (Windows NT 6.2; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.72 Safari/537.36' --compressed

http://warehouse1.indicia.org.uk:8080/g … HEIGHT=600

Any thoughts?  Is it due to moving folders around in the module? Or is it something to do with geoserver/openlayers that are mentioned in the error?

Many thanks

Sam

41 Reply by johnvanbreda

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Hi Sam
The layers button issue normally means that you are not loading the openlayers theme css files properly on the web page. This could be to do with the folder move - I wonder if you need to clear your Drupal cache?

It does look like the GeoServer is down - probably since some problems with a hardware failure at the BRC site at the weekend. I've notified BRC so this should be sorted soon.

Cheers
John

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42 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

John,

thanks for this.  I have cleared drupal cache and has solved the issue with the openlayers issue and is now dislaying records correctly.  Thanks for informing BRC of the geoserver issue, in case that was part of the problem too. 

The + icon problem is still occurring on all maps (distribution or input of record), is this to do with the openlayers issue too or geoserver....I suspect not the latter?  All the map layers open, just the icon is in the top left not right and does not display correctly.....Im sure we have had a similar problem before, but can't for the life of me remember the solution.  Is it due to folder move too?

Also I have just noticed another seemingly connected issue (in terms of timing not necessarily technically connected) - all of our forms no longer display the "How many?" occurrence attribute in the single occurrence entry format, whereas it does display in the multiple occurrence or species grid format.  It currently does not display in either single of multile input for surveys where the attribute has not be selected in the warehouse.  In the warehouse this occurrence is ticked specifically for certain surveys as it is only required for some, whereas it used to be standard for all of our forms. The ticking for specific survey rather than non-specific survey happened a bit back, before this recent problem, due a previous problem of this attribute not displaying (maybe connected to the loading of some of the instant indicia modules etc) and coincidentally the need to specify as some of the Defra surveys do not need this attribute (although non of the Defra surveys use single occurrence entry).  I assumed that the [species attributes] predefined control would bring through all attributes set up in the survey in the warehouse?  Is this problem also connected to folder move do you think?

Many thanks

43 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

John,

Looked through the forms you set up for the butterfly/day-flying moths.  They all look fine as I can see at the moment, except the key one of adding the species records (i.e. http://www.nbis.org.uk/input-butterfly- … nsect-data or this page via the calender).  You go through the first page fine (selecting transect, date etc), as on UKBMS website, then the page where you add records does not have the proper tab set up as on the UKBMS, nor does it have the species lists (including titles showing). Any thoughts? Along with thoughts for my question yesterday when you have time.

I can add transects fine by the way.

Also please feel free to add transects, walks, records etc to test the pages and I can delete after, if you tell me what you have added.

Also, as asked before, is there anyway of associating (other than maybe centroid grid ref) the transects we create for butterflies with the sites we create in our locations form for the project......as all other species groups for this project involve picking an already set location/site and then adding records to it?  I notice that the form you have set up sets up a transect location and then a transect section location for each transect.  Would it therefore be possible to, at the top of the setting up transects form (http://www.nbis.org.uk/butterfly-moth-transect-details), to change the input of transect name and grid ref and replace with the location attribute control, we are using this control in our forms [Location map]. I will email the urls of all our NSSN forms so you can see.

Thanks

44 Reply by johnvanbreda

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Hi Sam
A response to the issue about the OpenLayers theme not loading. Your cuckoo map page has a configuration on the Edit tab under Advanced Base Map Layers - OpenLayers Options JSON which hard codes the path to the theme:
{"theme":"sites/all/modules/iform/media/js/theme/default/style.css"}
This needs to be removed to make it work as the theme path is calculated automatically. I'll try to get to the other points a bit later.
Best wishes
John

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45 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Thanks for this John.  Yes you were correct, I have removed this hard coding from all forms now.  I had orginally put it in on your suggestion because the layers were not displaying properly.....but I guess the change of location of folders has probably corrected the need for this....so thanks for that.
Thanks in advance for looking at the other issues.

Cheers

Sam

46 Reply by johnvanbreda

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

The problem with the transect input page was that I'd not filled in one of the configurations for a species list - now fixed. However there is an additional issue in that you have set up the butterfly species list with the common name in the preferred name field and the latin name in the synonyms field. The system is set up to display common names (which you have not provided) so the species name boxes are blank. To fix this you need to change the way that the species are stored in this species list so that the latin and common names are in the right boxes.

Also, as asked before, is there anyway of associating (other than maybe centroid grid ref) the transects we create for butterflies with the sites we create in our locations form for the project

Are you saying that you want the list of transects you create to also be available as sites in the other forms? Or that once you set up a site on your standard location form, you want to be able to convert it to use as a transect? If the former then it might be just a case of configuring the report used to load the available sites on your other forms to include the transects.

John van Breda
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47 Reply by samneal

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

John,

thanks for reply.  Im working at home today, so if there is other stuff in email could you forward to my home one...thanks.

Thanks for sorting transect input page issue.  Regarding the species list issue: Yes I see why this has happened, it is because I usually use this format to quickly display the preferred name, be it latin or english that we want displayed on the forms.....bad practice I'm sure, but probably to do with an historical reason when setting up first few forms (must have been good reason...I hope).  Is there any way of making the changes you suggest without going into each taxa and changing the names around?  This is as both the butterfly and moth lists are rather large (especially the latter).  I suppose the csv upload would work maybe?

Regarding the second question-
During the project there are a set number of sites.  Each site will have a number of different species groups recorded using different methods; these different species groups will each be recorded through a different form, these are the ones I emailed you plus the butterfly/moth one you set up. 
We want volunteers to be able to follow this process to input records for a particular species group: Set up the site as a location (if not already set up by NBIS) in the location form I sent you > Add environmental data for the site on each visit to it, using the environmental data form.  Assigning the data to that site location > Input the species records, using the relevant species group form, but assigning to the site location at the start of the process (by choosing the site from the drop-down menu).  Currently this works for all species groups, except the butterfly one.  I can select a transect set up in the form you have created, in either the environmental data form or any of the species forms I have set up; but I can't select a site I have already set up in our standard location form, in the transect set up form you have created......url as listed and mentioned below (http://www.nbis.org.uk/butterfly-moth-transect-details).  So the short answer to your question is that I'm asking the latter, as the former already works.
More explanation:  At the moment I could not set up a location in our standard form and it be used by all species group forms, as I can't use them with the butterfly one.  At the moment the process set out above, for butterflies, would be: set up location in standard location form > add environmental data for the site > set up transect and transect sections in butterfly form above > add butterfly species records, after choosing the transect just set up.  It would mean for each site I would have two locations (rather than one), one being the site for all species group records (other than butterfly/moth) and env data and other being the transect location set up just for butterflies/moths.  If we could be able to select a location already set up in our standard location form (even if we have to set the location to a transect rather than site as the location form default) in the above transect form and then add in the transect sections that would be ideal.  I.e. as said in previous message, could we could replace the "transect name", "grid ref" and map attributes in this form with the [location map] one, which brings in the location drop-down menu (to select from), the grid ref box and map to select location from or to just display the location you have picked from the drop-down (as in all the forms I sent you)?

Connected to the above: The locations available in the standard location drop-down I use ([location map] control) now include locations that we have not set, they previously only showed NBIS locations......how do we set this control to bring through only NBIS locations again? Do I need to go into these locations in the warehouse and change their availability to our website?

Finally do you have any thoughts yet on my problem regarding the "how many?" attribute no longer appearing in my forms, as per my message before last: http://forums.nbn.org.uk/viewtopic.php? … 81#p18081.
The +icon problem is now sorted by the way and appears correctly on the right hand side etc.

Many thanks again

Sam

48 Reply by johnvanbreda

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Hi Sam
Regarding the How Many attribute - would it not be best to tick it for the specific surveys you want it to appear for (and remember to clear the Indicia cache after)? Although the functionality to associate attributes at the website level has been around a long time, in my opinion it is rarely useful so I'd be keen to deprecate it at some point.

I'll keep my answers in separate posts - this is a bit unweildy otherwise! Actually I'd suggest starting new threads for each individual question so it is easier for me to reply piecemeal.

Cheers
John

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49 Reply by johnvanbreda

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Next point - I've managed to swap the butterfly list round for you ;)

John van Breda
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50 Reply by johnvanbreda

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Re: Defra Species Surveillence project - setting up Indicia for monitoring

Next point - about transects & normal sites. At the moment I don't think you are specifying the location type of your standard sites and your normal site surveillance forms don't care what type the site is. But your transect sites do need to be transects to make the various bits of information available correctly. So, can you not use the [location type] control on your normal site form to allow this form to create transects? They should then appear on your transects sites list where you can edit them to add in the sections.

Will that work?

John van Breda
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