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NCEAS / metacatui

MetacatUI: A client-side web interface for DataONE data repositories
https://nceas.github.io/metacatui
Apache License 2.0
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Issues rendering the response form the view service #2403

Closed rushirajnenuji closed 3 months ago

rushirajnenuji commented 7 months ago

MetacatUI runs into erros while rendering response from the view service.

Screenshot:

Screenshot 2024-05-03 at 12 12 52
robyngit commented 4 months ago

We're getting this again on the KNB on Jul 22, 2024 at 2pm eastern time.

For dataset https://knb.ecoinformatics.org/view/nceas.988.17, here is the error and response:

Error message ``` Error rendering metadata from the view service TypeError: entityId.replace is not a function storeEntityPIDs MetadataView.js:3614 forEach Underscore storeEntityPIDs MetadataView.js:3612 success MetadataView.js:502 jQuery 6 renderMetadata MetadataView.js:540 getModel MetadataView.js:300 p/t[e]< Backbone before Underscore Backbone 4 success SolrResult.js:436 jQuery 6 getInfo SolrResult.js:520 getModel MetadataView.js:416 render MetadataView.js:203 showView AppView.js:282 renderMetadata router.js:467 execCb require.js:1635 check require.js:871 enable require.js:1112 bind require.js:129 emit require.js:1155 each require.js:57 emit require.js:1154 check require.js:925 enable require.js:1112 bind require.js:129 emit require.js:1155 each require.js:57 emit require.js:1154 check require.js:925 enable require.js:1112 bind require.js:129 emit require.js:1155 each require.js:57 emit require.js:1154 check require.js:925 enable require.js:1112 bind require.js:129 emit require.js:1155 MetadataView.js:527:25 ```
Response from the view service ```xml
National Center for Ecological Analysis and Synthesis and Wolkovich E. 2012. NECTAR: Network of Ecological and Climatological Timings Across Regions Download

General

nceas.988.17

The Network of Ecological and Climatological Timings Across Regions (NECTAR) database was designed to bring together species-rich plant phenology with a focus on non-clonal, non-cultivated species observations of natural communities. Towards this goal, in October 2009, we reviewed the literature for ground (not herbarium) observational studies of species phenology, searching ISI for topic: (plant phenolog*) and Topic: (observat*) and Topic: (time-series OR long-term). Combined with personal knowledge, we identified 61 datasets. Of these we gained access to 26 datasets (23 with raw data, 4 with only mean phenological values---derived data) and merged these into a common format for the raw and derived data. Further details regarding NECTAR development can be found in the Supplementary materials here: Wolkovich, E.M., B.I. Cook, J.M. Allen, T.M. Crimmins, J.L. Betancourt, S.E. Travers, S. Pau, J. Regetz, T.J. Davies, N.J.B. Kraft, T.R. Ault, K. Bolmgren, S.J. Mazer, G.J. McCabe, B.J. McGill, C. Parmesan, N. Salamin, M.D. Schwartz, and E.E. Cleland, 2012: Warming experiments underpredict plant phenological responses to climate change. Nature, doi:10.1038/nature11014. AND here: Cook, Benjamin; Wolkovich, Elizabeth; Davies, Jonathan; Ault, Toby; Betancourt, Julio; Allen, Jenica; Bolmgren, Kjell; Cleland, Elsa; Crimmins, Theresa; Kraft, Nathan; Lancaster, Lesley; Mazer, Susan; McCabe, Gregory; McGill, Brian; Parmesan, Camille; Pau, Stephanie; Regetz, James; Salamin, Nicholas; Schwartz, Mark; Travers, Steven. Sensitivity of spring phenology to warming across temporal and spatial climate gradients in two independent databases. Ecosystems, in press.

None

Keyword Type
plant phenology
2012-07-04

People and Associated Parties

National Center for Ecological Analysis and Synthesis
Elizabeth Wolkovich
University of British Columbia

Vancouver, BC V6T1Z4 Canada
wolkovich@biodiversity.ubc.ca
Elizabeth Wolkovich
University of British Columbia

Vancouver, BC V6T1Z4 Canada
wolkovich@biodiversity.ubc.ca
Elizabeth Wolkovich
AssociatedParty
Benjamin Cook
Custodian/Steward
James Regetz
Custodian/Steward
Elizabeth Wolkovich

Geographic Region

Northern hemisphere
9.0000  degrees
67.0000  degrees
20.0000  degrees
-107.0000  degrees

Temporal Coverage

1739-03-04
2010-04-20

Methods & Sampling

Step 1
General disclaimer for all datasets, especially LTER datasets

Please note that we provide information on how we obtained data here without all explicit references to the underlying data usage policies. Data users should consult all data usage notes, expected acknowledgements etc. when obtaining the data! We provide notes on main data collectors/curators and usage statements when possible, but this is not an exhaustive list.

Remember, only you can prevent data fires!

Step 2
Obtain dataset: Chinnor (Fitter) data

Fitter data (Chinnor, UK ) available with Fitter & Fitter 2002 Science publication. We downloaded data 20 November 2009 from:

http://www.sciencemag.org/cgi/content/full/sci;296/5573/1689/DC1

Thanks to R. S. R. Fitter and A. Fitter for posting data with their publication.

Step 3
Obtain dataset: Harvard Forest LTER data

We downloaded Harvard Forest LTER 'Phenology of Woody Species' data on 2 May 2010. The following file was used:

hf003_03ObsPhenSpringPhen.csv

Data can be downloaded from Harvard Forest LTER data webportal: harvardforest.fas.harvard.edu/data/archive.html

Special thanks to John O'Keefe for posting data.

Step 4
Obtain dataset: Hubbard Brook LTER data

We downloaded 'Routine Phenology Measurements' from Hubbard Brook LTER at: http://www.hubbardbrook.org/data/dataset_search.php

on 30 April 20120, using the file phn.txt. Thanks to Amey Bailey for data collection.

Step 5
Obtain dataset: Konza data

We downloaded data for Konza collected by volunteers:

http://keep.konza.ksu.edu/Plant%20List.htm

on 30 Nov 2009.

Step 6
Obtain dataset: Luquillo LTER data

We downloaded Luquillo LTER 'Phenologies for the Tabonuco Forest trees and shrubs' data including the following files:

Lfdp1-BisleyPhenology.txt

Lfdp1-ElVerdePhenology.txt

Lfdp2-ElVerdePhenology.txt

on 13 May 2010. Data available through Luquillo Data server: http://luq.lternet.edu/data/datacatalog

Thanks to Jess Zimmerman for data.

Step 7
Obtain dataset: Niwot LTER data

We downloaded the Niwot Ridge LTER 'Individual plant phenology in nodal plots' data on 2 May 2010 from Niwot LTER datasite:

http://culter.colorado.edu/NWT/data/datmansearch.html

Using the file: Walker_IndPhenology.txt

Many thanks to Marilyn Walker for collecting data. Please note the required data statement:

Logistical support and/or data were provided by the NSF supported Niwot Ridge Long-Term Ecological Research project and the University of Colorado Mountain Research Station

The user of NWT LTER data agrees to provide proper acknowledgment with each usage of the data. Citation of the name(s) of the investigator(s) responsible for the data set, in addition to the generic statement above, constitute proper acknowledgment. Author(s) (including NWT investigators) of published material that makes use of previously unpublished NWT data agree to provide the NWT data manager with four (4) copies (preferably reprints) of that material for binding as soon as it becomes available. The user of NWT data agrees not to resell or redistribute shared data. The user of these data should be aware that, while efforts have been taken to ensure that these data are of the highest quality, there is no guarantee of perfection for the data contained herein and the possibility of errors exists.

Step 8
Obtain datasets: Sevilleta LTER data (core and transects)

We used two different datasets from Sevilleta LTER, first what we called 'sevtrans' is the 'Plant Phenology Transects' and includes:

sev048_1995_data.dbf

sev048_1994_data.dbf

sev048_1993_data.dbf

sev048_1991_data.dbf

The other is 'Core Site Phenology' data and includes:

sev137_data.dbf

Both datasets use the species file: sev048_1991_meta.dbf and were downloaded on 13 May 2010). Thanks to Kirstin Vanderbilt for data and answering many of our questions. Data were obtained directly from the KNB: http://knb.ecoinformatics.org/

Note the following:

The Data User should acknowledge any institutional support or

specific funding awards referenced in the metadata accompanying this dataset in any

publications where the Data Set contributed significantly to its content.

Acknowledgements should identify the supporting party, the party that received the

support, and any identifying information such as grant numbers. For example:

Data sets were provided by the Sevilleta Long Term Ecological Research (LTER)

Program. Significant funding for collection of these data was provided by the National

LTER Home | UNM Sevilleta Field Station Home | Webmail

Home » Information Management Overview

‹ Information Management Overview up Data Collection and Submission

Science Foundation Long Term Ecological Research program (NSF Grant numbers BSR

88-11906, DEB 9411976, DEB 0080529 and DEB 0217774).

5 ) Notification. The Data User will notify the Data Set Contact

Step 9
Obtain dataset: Mikesell data

'Mikesell phenological data from Wauseon, Ohio, USA, 1883-1912' data obtained from M. Lechowicz and now publically available at: knb.ecoinformatics.org/knb/metacat/wolkovich.33/knb

Step 10
Additional datasets (in progress)

The following datasets are part of NECTAR:

(1) Concord, Massachusetts - 1851 to 2006 (shared courtesy of Richard Primack)

Notes: Please contact Abraham Miller-Rushing (aberushing@alumni.grinnell.edu) or Richard Primack (primack@bu.edu) before using these data.

For supporting information, please see Miller-Rushing and Primack (2008).

The 2003 flowering data is not accurate estimates of first flowering as we were learning the locations of plant species and often found species when they were in full flower or even past full flower.

Cite data as: Miller-Rushing, A.J. and R.B. Primack. 2008. Global warming and flowering times in Thoreau's Concord: a community perspective. Ecology 89: 332-341.

(2) First-flowering dates of plants in the Northern Great Plains (1910-1961 and 2007-2012)

Earlier data published at Ecological Archives (Ecology 90:2332): E090-162-D1 by Steven E. Travers and Kelsey L. Dunnell in 2009.

(3) Data collected by David Inouye in Gothic, Colorado (1975-2009). See:

Inouye, D. W. Effects of climate change on phenology, frost damage, and floral abundance of montane wildflowers. Ecology 89(2), 353–362 (2008).

(4) First flowering dates recorded by farmer Gunnar Johansson between 1934-2006

25 species growing in and around his garden (About half of the species are wild and the other half considered garden plants). The data has been transformed to Julian days and entered by Kjell Bolmgren.

(5) Marsham data (1736-1958). See:

Sparks, T. H. and Carey, P. D. The responses of species to climate over two centuries - an analysis of the Marsham phenological record, 1736-1947. Journal of Ecology 83(2), 321–329 (1995).

(6) Data from Mohonk Lake, New York (1928-2002).

All records listed in Table I were digitized from notecard observations taken by observers at Mohonk Lake over the years. Observations were made along predetermined routes and at specific locations. This methodology helped reduce observer bias or error. Following digitizing, the original notecard records were rechecked and problematic observations were dropped if they clearly exceeded the range of phenological variability of the species in question (the 3-sigma rule). Finally, for this analysis, we also only retained records for which at least 24 observations (years) were available to ensure a reasonable level of significance in our statistical analysis.

See also:

Cook, B. I., Cook, E. R., Huth, P. C., Thompson, J. E., Forster, A., and Smiley, D. Across-taxa phenological dataset from Mohonk Lake, NY and its relationship to climate. International Journal of Climatology 28(10), 1369–1383 (2008).

(7) Data from University of Milwaukee Field Station (2000-2009, courtesy of M. D. Schwartz)

UWMFS location: 43.387 °N, 88.023 °W

Web page: http://www4.uwm.edu/fieldstation/

Event codes:

bb50mdoy is mean day of year among the individuals of that species that 50% of buds on the tree that have broken open, revealing leaves.

l75mdoy is the mean day of year among the individuals of that species that 75% of leaves on the tree are at least 75% of their total size.

l95mdoy is the mean day of year among the individuals of that species that 95% of leaves on the tree are at least 95% of their total size.

See also:

Schwartz, M. D. and Hanes, J. M. Intercomparing multiple measures of the onset of spring in eastern North America. International Journal of Climatology 30(11), 1614–1626 (2010).

(8) Spring flowering records from Washington, DC area.

Data available at: http://botany.si.edu/dcflora/springflowers/index.htm

And additionally extracted from: Abu-Asab, M. S., Peterson, P. M., Shetler, S. G., and Orli, S. S. Earlier plant flowering in spring as a response to global warming in the Washington, DC, area. Biodiversity and Conservation 10(4), 597–612 (2001).

Step 11
Taxa scrubbing

Taxon scrubbing of species names occurs with using file: TS_AllTaxa.csv, which was originally an MS Access database file called 'TS_taxonomy_IPNI_1.0.mdb' (unzipped 2006-08-24 16:01) by J. Regetz. Contact J. Regetz for access to this file.

Step 12
Merge datasets in R

After obtaining all datasets they can be merged in R using the mergenectar.R file provided. This file should run (outside of taxonomy scrubbing) as long as the structure of the underlying datasets remains unchanged from 2010.

Data Table, Image, and Other Data Details

Species list for Harvard Forest data
species list to convert codes for Harvard Forest data, extracted from metadata of HF003 'Phenology of Woody Species'
specieslist_bylizzie.csv
ecogrid://knb/wolkovich.36.1
864 byte
Number of Header Lines 1
Record Delimiter #x0A
Attribute Orientation column
Simple Text
Field Delimeter ,
38

Attribute Information

Variables
code
genusspecies
code
PLACEHOLDER
 
taxa code
 
nominal
Definition species code is comprised of the first two letters of the genus plus the first two letters of the species
 
 
 
 
 
genusspecies
PLACEHOLDER
 
latin binomial
 
nominal
Definition latin binomial (genus species)
 
 
 
 
 
Luquillo species translation file
File needed to translate Luquillo species codes
Luquillo_species_JD.txt
ecogrid://knb/wolkovich.37.1
9660434 byte
Number of Header Lines 1
Record Delimiter #x0A
Attribute Orientation column
Simple Text
Field Delimeter #x09
125021

Attribute Information

Variables
DATE
BASKET
SPECIES
CODE
NUMBER
Genus
Species
Family
site
DATE
PLACEHOLDER
 
Date of observation
 
dateTime
Format MM/DD/YYYY
Precision 0
 
 
 
 
 
BASKET
PLACEHOLDER
 
Litter trap basket ID
 
nominal
Definition Codes for litter trap baskets
 
 
 
 
 
SPECIES
PLACEHOLDER
 
codes for species
 
nominal
Definition Codes for species names
 
 
 
 
 
CODE
PLACEHOLDER
 
NA
 
nominal
Definition See metadata of Luquillo phenology data for more information
 
 
 
 
 
NUMBER
PLACEHOLDER
 
NA
 
nominal
Definition See metadata for Luquillo phenology data for more information
 
 
 
 
 
Genus
PLACEHOLDER
 
Genus name
 
nominal
Definition Genus name
 
 
 
 
 
Species
PLACEHOLDER
 
Species epithet
 
nominal
Definition Species epithet
 
 
 
 
 
Family
PLACEHOLDER
 
family
 
nominal
Definition family
 
 
 
 
 
site
PLACEHOLDER
 
site
 
nominal
Definition site
 
 
 
 
 
mergenectar.R
Data Object Type: Other
R code to merge public data
Physical Structure Description:
mergenectar.R
22929 byte
Format Name text/plain
ecogrid://knb/wolkovich.38.3
NECTAR taxa scrubbing
File showing original species name, whether they matched to IPNI and any adjustments made
nectarnames_all.csv
ecogrid://knb/wolkovich.39.1
66441 byte
Number of Header Lines 1
Record Delimiter #x0A
Attribute Orientation column
Simple Text
Field Delimeter ,
1160

Attribute Information

Variables
site
genus
species
scrub
genus.prescrub
species.prescrub
ipni
site
PLACEHOLDER
 
site of data
 
nominal
Definition Site names
 
 
 
 
 
genus
PLACEHOLDER
 
genus, as given in NECTAR
 
nominal
Definition genus, after cleaning, as given in NECTAR
 
 
 
 
 
species
PLACEHOLDER
 
species epithet, as given in NECTAR
 
nominal
Definition species epithet, after cleaning, as given in NECTAR
 
 
 
 
 
scrub
PLACEHOLDER
 
how many times a name was cleaned (adjusted), this was all done by hand
 
ratio
Unit dimensionless
Type integer
 
 
 
 
 
genus.prescrub
PLACEHOLDER
 
genus from original data source
 
nominal
Definition genus from original data source
 
 
 
 
 
species.prescrub
PLACEHOLDER
 
species epithet, from original data source
 
nominal
Definition species epithet, from original data source
 
 
 
 
 
ipni
PLACEHOLDER
 
International Plant Names Index -- whether species name was accepted, not-accepted or not found in our IPNI list (unmatched)
 
nominal
Definition Species name matching to International Plant Names Index
 
 
 
 
 
nectarpheno_raw.csv
NECTAR raw, collated data
nectarpheno_raw.csv
ecogrid://knb/wolkovich.40.2
1709107 byte
Number of Header Lines 1
Record Delimiter #x0A
Attribute Orientation column
Simple Text
Field Delimeter ,
23105

Attribute Information

Variables
site
plot
event
year
doy
date
genus
species
scrub
varetc
cult
site
PLACEHOLDER
 
site name
 
nominal
Definition site name
 
 
 
 
 
plot
PLACEHOLDER
 
plot, Plot means a couple things that factor into first-events calculations so be careful: For the `network' sites (washdc) I put station id info in the plot column. For washdc we take ffd by the entire site, so plot for washdc is basically just an FYI of the spatial location the ffd happened. For Fargo, the site variable given in the raw data was transferred to the plot column. We give ffd by site alone. Thus, as for washdc, the plot column just tells you where the ffd happened. I also used plot in its more traditional ecological sense: as a small plot of land (or transect of land), or an area of plots and transects (something akin to a block), given in the raw data by the researchers for: Sevilleta (core and trans: each maintains the LTER plot info like: cresote site, blue gamma dominated site etc.), Niwot, Luquillo (3 forests) and for all these we take site x plot.
 
nominal
Definition plot, varies by site
 
 
 
 
 
event
PLACEHOLDER
 
phenological event
 
nominal

Enumerated Domain

Code Definition Source
ffd irst flowering date (either data was taken only as first flowering date or we condensed monitoring data into estimates of first flowering dates)
 
 
 
 
 
year
PLACEHOLDER
 
year
 
ratio
Unit nominalYear
Type natural
 
 
 
 
 
doy
PLACEHOLDER
 
day of year (0 to 366)
 
ratio
Unit nominalDay
Type natural
 
 
 
 
 
date
PLACEHOLDER
 
date
 
dateTime
Format YYYY-MM-DD
Precision
 
 
 
 
 
genus
PLACEHOLDER
 
genus
 
nominal
Definition genus
 
 
 
 
 
species
PLACEHOLDER
 
species epithet
 
nominal
Definition species epithet
 
 
 
 
 
scrub
PLACEHOLDER
 
was taxa name scrubbed and how many times
 
ratio
Unit dimensionless
Type whole
 
 
 
 
 
varetc
PLACEHOLDER
 
taxonomic classification below species: variety, subspecies etc.
 
nominal
Definition taxonomic classification below species: variety, subspecies etc.
 
 
 
 
 
cult
PLACEHOLDER
 
cultivated, was observation of cultivated species -- NA means not cultivated
 
nominal
Definition cultivated, was observation of cultivated species -- NA means not cultivated
 
 
 
 
 

Data Set Usage Rights

no restrictions

Access Control

knb
allowFirst
Permission Principal
[all] uid=nceasadmin,o=NCEAS,dc=ecoinformatics,dc=org
[all] cn=knb-prod,o=NCEAS,dc=ecoinformatics,dc=org
[all] cn=esa-moderators,dc=ecoinformatics,dc=org
[read] [write] uid=wolkovich,o=NCEAS,dc=ecoinformatics,dc=org
[read] public
```
robyngit commented 4 months ago

Branch: bugfix-2403-view-service-response