See results as catalog record summary produces csv that my (and perhaps other's) excel cannot parse properly

[DerekSikes]

Issue Documentation is http://handbook.arctosdb.org/how_to/How-to-Use-Issues-in-Arctos.html

Describe the bug A clear and concise description of what the bug is.

Search & choose 'see results as catalog record summary' with results that include species that have lots of catalog records. I don't know what constitutes "lots" but thousands is a good guess.

see screenshot of what happens

Expected behavior A clear and concise description of what you expected to happen.

No parse failure.

Data If this involves external data, attach the actual data that caused the problem. Do not attach a transformation or subset. You may ZIP most formats to attach, or request a Box email address for very large files. ArctosSpecimenSummary872094.csv

This csv file resulted from a search that includes Bombus (some of the Bombus species have lots of specimens) when opened in my copy of excel (2018, Mac) fails to parse some of the rows properly leading to major cleanup headaches and potential losses of data.

I feel like I've made this bug report before, years ago, perhaps multiple times.

Priority Please assign a priority-label. Unprioritized issues get sent into a black hole of despair. High.

Note - summary searches are excellent for saving as simple ways for the public to access Arctos data. Thus, they are of particularly high 'public-profile' value and when they fail, as has been happening in this case for years, they could easily discourage new members or interest in Arctos as a platform. I have many such saved searches on my collection's homepage and would like to see this fixed asap. Hopefully, no one reading my grant proposals explore those links too deeply!

[dustymc]

Need more info, I can't reproduce. KNWR ento (the whole collection) loads into Excel fine for me, UAM:Ento gets me a 4.2MB download and Excel politely refusing to play.

[DerekSikes]

Why not just try the csv I provided?

Or just search UAM:Ento for Bombus

-D

On Tue, Oct 11, 2022 at 9:56 AM dustymc @.***> wrote:

Need more info, I can't reproduce. KNWR ento (the whole collection) loads into Excel fine for me, UAM:Ento gets me a 4.2MB download and Excel politely refusing to play.

[image: Screen Shot 2022-10-11 at 10 54 46 AM] https://user-images.githubusercontent.com/5720791/195164836-1fc2adda-adcb-4f23-8c65-c5dfa3c8d762.png

— Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/5152#issuecomment-1275069730, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACFNUM64LAWWPHILILX3UT3WCWS6NANCNFSM6AAAAAARCQXMR4 . You are receiving this because you authored the thread.Message ID: @.***>

--

+++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 @.*** phone: 907-474-6278 he/him/his University of Alaska Museum https://www.uaf.edu/museum/collections/ento/

• search 357,704 digitized arthropod records http://arctos.database.museum/uam_ento +++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological Society and / or sign up for the email listserv "Alaska Entomological Network" at http://www.akentsoc.org/contact_us

[dustymc]

Why not just try the csv I provided?

Derp... - and THANKS!

If I let Excel do magic stuff it does what I expect from Microsoft and mangles everything.

If I import and tell it the first column is text it seems to work.

[Jegelewicz]

@dustymc I have the same experience as @DerekSikes This

LINKTOSPECIMENS	COUNTOFCATALOGEDITEM	PHYLORDER	FAMILY	SCIENTIFIC_NAME	ISPUBLISHED

Then there is a row that includes all of the catnums, each in it's own column with the final columns including

LINKTOSPECIMENS	COUNTOFCATALOGEDITEM	PHYLORDER	FAMILY	SCIENTIFIC_NAME	ISPUBLISHED
4225	Hymenoptera	Apidae	Bombus flavifrons	1

Something weird about the huge number of comma separated numbers causing a problem?

In notepad it looks like this

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flavifrons","1"

seems like something weird with the ""?

[DerekSikes]

Expecting the naive public user to have advanced digital text skills doesn't seem like a good solution.

-Derek

On Tue, Oct 11, 2022 at 10:15 AM dustymc @.***> wrote:

Why not just try the csv I provided?

Derp... - and THANKS!

If I let Excel do magic stuff it does what I expect from Microsoft and mangles everything.

If I import and tell it the first column is text it seems to work.

[image: Screen Shot 2022-10-11 at 11 12 47 AM] https://user-images.githubusercontent.com/5720791/195168259-6d8d3182-b088-4b41-aec2-6a8888e0abe9.png

— Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/5152#issuecomment-1275092332, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACFNUM4NUN5ZZDAZX7VRYEDWCWVDHANCNFSM6AAAAAARCQXMR4 . You are receiving this because you were mentioned.Message ID: @.***>

--

+++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 @.*** phone: 907-474-6278 he/him/his University of Alaska Museum https://www.uaf.edu/museum/collections/ento/

• search 357,704 digitized arthropod records http://arctos.database.museum/uam_ento +++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological Society and / or sign up for the email listserv "Alaska Entomological Network" at http://www.akentsoc.org/contact_us

[dustymc]

I see no evidence that the CSV provided by Arctos is in any way lacking compliancy.

It should be no surprise that I have no influence over how Microsoft - nor anything else that's not Arctos - works.

I'm not sure what else I could do.

[DerekSikes]

Anticipating that most people will try to open such csv in microcrappysoft excel perhaps the csv we provide should be something that excel can handle.

-D

On Tue, Oct 11, 2022 at 10:54 AM dustymc @.***> wrote:

I see no evidence that the CSV provided by Arctos is in any way lacking compliancy.

It should be no surprise that I have no influence over how Microsoft - nor anything else that's not Arctos - works.

I'm not sure what else I could do.

— Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/5152#issuecomment-1275134548, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACFNUM7XS34DY5KIRABO32TWCWZUPANCNFSM6AAAAAARCQXMR4 . You are receiving this because you were mentioned.Message ID: @.***>

--

+++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 @.*** phone: 907-474-6278 he/him/his University of Alaska Museum https://www.uaf.edu/museum/collections/ento/

• search 357,704 digitized arthropod records http://arctos.database.museum/uam_ento +++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological Society and / or sign up for the email listserv "Alaska Entomological Network" at http://www.akentsoc.org/contact_us

[Mesibov]

@DerekSikes. Hi, Derek. The "?" in the URL doesn't break "automatic" (default) parsing in LibreOffice Calc or ModernCSV. Both are available for Mac. In your Excel, is there a "List separator" option where you can specify "comma"?

[DerekSikes]

Thanks. However, I'm not seeking a behavioral change solution on the user side. I'm seeking a data fix that allows naive users that download these results and open them in excel to not have parsing failures. We all agree that excel is a problem but I bet plenty of potential Arctos users (who might be considering joining & paying) and granting agency reviewers are using it. When they find these Arctos data are corrupted they are not going to blame themselves for using excel, they are going to blame Arctos for producing corrupt data and they are likely not going to be impressed. It seems to me like a high priority to fix at the source.

-Derek

On Thu, Oct 13, 2022 at 12:44 AM Mesibov @.***> wrote:

@DerekSikes https://github.com/DerekSikes. Hi, Derek. The "?" in the URL doesn't break "automatic" (default) parsing in LibreOffice Calc or ModernCSV. Both are available for Mac. In your Excel, is there a "List separator" option where you can specify "comma"?

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+++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 @.*** phone: 907-474-6278 he/him/his University of Alaska Museum https://www.uaf.edu/museum/collections/ento/

• search 357,704 digitized arthropod records http://arctos.database.museum/uam_ento +++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological Society and / or sign up for the email listserv "Alaska Entomological Network" at http://www.akentsoc.org/contact_us

[dustymc]

Arctos data are corrupted

If you can help me understand how that might be true I'd be glad to fix it.

high priority to fix

Same as above, I think. As far as I can tell I'm following the standard (to the extent it exists), and doing anything else is going to make things worse for everyone.

[DerekSikes]

How about this fix:

The download csv should not include the "link to specimens" data at all. Those links are obviously useful in a web browser (although this reminds me that those links fail even in browsers in an unpredictable and irreproducible way that needs addressing in a separate issue) but when one downloads csv of summary data these are for off-line manipulation so the links that produce parsing failures are best not included in the download.

Alternatively, a compromise solution could be to add some sort of checkbox to allow users to opt-in for which columns of the summary data they download (and I would argue strongly that the link to specimen data column NOT be checked by default).

-Derek

On Thu, Oct 13, 2022 at 9:01 AM dustymc @.***> wrote:

Arctos data are corrupted

If you can help me understand how that might be true I'd be glad to fix it.

high priority to fix

Same as above, I think. As far as I can tell I'm following the standard (to the extent it exists), and doing anything else is going to make things worse for everyone.

— Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/5152#issuecomment-1277917235, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACFNUM5JRVQS5MSGGSY5LGLWDA54ZANCNFSM6AAAAAARCQXMR4 . You are receiving this because you were mentioned.Message ID: @.***>

--

+++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 @.*** phone: 907-474-6278 he/him/his University of Alaska Museum https://www.uaf.edu/museum/collections/ento/

• search 357,704 digitized arthropod records http://arctos.database.museum/uam_ento +++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological Society and / or sign up for the email listserv "Alaska Entomological Network" at http://www.akentsoc.org/contact_us

[dustymc]

merge-->https://github.com/ArctosDB/arctos/issues/4439