UCBG reports

Owned by Chris Hoffman
Last updated: Apr 23, 2013Version comment
7 min read

Documenting more information about the reports listed in the document.

Note: must be able to export these to Excel and to save as a PDF.  This might be handled by using campus-licensed software and reasonable workflows.

Accession Report (three versions run from within CSpace: cataloging, group-PDF, group-Excel)

  • User-entered range of accession numbers or list of accession numbers
  • Sort by accession number; resort by taxon
  • Named Business Objects report: Accession Report revisedbk.rep
  • Layout: Not tabular
  • Fields
    • Source
    • Requested by
    • Accession number
    • Accession date
    • Scientific name (with author)
    • Dead flag
    • Family name
    • Material type
    • Field collection place (or taxonomic range?)
    • Collector
    • Collection date
    • Collector number
    • Accession notes

Notes

Three reports developed.  All run from within CollectionSpace though from different records

Status

4/23/2013: Three versions (cataloging and group-PDF and group-Excel) installed on botgarden.

  • Run from Cataloging/collection object - Accession report for a single specimen (PDF) (ucbgAccessionReport.jrxml)
  • Run from Group record - Accession report for a group of specimens (PDF) (ucbgAccessionGroupReport.jrxml)
  • Run from Group record - Accession report for a group of specimens (Excel) (ucbgAccessionGroupExcel.jrxml)

Accession History report (from CSpace cataloging record)

  • Shows versions of Current Location (movement records) for a particular accession record.
  • Layout: tabular
  • Fields
    • Accession number
    • Scientific name (with author)
    • Action date
    • Action
    • Label requested
    • Label count
    • Label size
    • Label type
    • Previous location
    • New location

Notes

Status

2/27/2013: Installed on botgarden-dev

  • Run from CollectionSpace Cataloging record - Accession History for a single specimen (PDF) (ucbgAccessionHistory.jrxml)

Label Order Report (from CSpace cataloging record)

  • Automatically queued in system when user indicates label requested on Current Location (movement) records
  • Sort by bed number, then latin name
  • Named Business Objects report: Rh._label_revisedbk.rep
  • Layout: Not tabular
  • Fields
    • Bed number
    • Family
    • Accession number
    • Label count
    • Label size
    • Label type
    • Common name
    • Scientific name (no author name preferred)
    • Section name (taxon rank between genus and species)
    • Subsection name (ditto)
    • Red Dot (when rare = Yes)
    • Accession notes

Notes

  • Run from CollectionSpace Cataloging record - Creates Label Order report for all queued Plant Location records (PDF) (ucbgLabelOrder.jrxml)

Status

2/27/2013: Installed on botgarden-dev

Functions that find section or subsection ancestor records in Taxonomy currently only find those that are immediate parents of the primary determination, so the functions need to be expanded to look at the rank of any higher level taxonomy record.

Voucher Label report (run iReport ucbgVoucherLabel.jrxml)

  • Prints a voucher label similar to the existing voucher label:

Notes

Produce voucher labels where label requested = yes. This should run from within CSpace but the barcode library is not recognized when run from the server.

Status

2/27/2013: iReport version ready.

  • Run from CollectionSpace Cataloging record - Produce voucher labels where label requested = yes (PDF) (ucbgVoucherLabel.jrxml)

Bed List Report (http://dev.cspace.berkeley.edu/cgi-bin/cswaMain.py?webapp=ucbgBedListV321)

  • User supplies a range of bed numbers (garden locations), get accessions that have a current location in a matching bed
  • Results sorted by garden location, then scientific name with option to change to accession number
  • Named Business Objects report: Sagebedlist_hf.rep
  • Layout: Tabular, grouped by garden location, with group header and footer
  • Group header fields
    • Garden location type (bed, section)
    • Garden location
  • Detail fields
    • Data quality
    • Accession number
    • Taxonomic name
    • Family
  • Group footer:
    • number of accessions
    • number of unique scientific names
    • number of unique families

Notes

Possible alternatives:

  • Build sortable Storage Location field; add Storage Location range search, denormalize current locations, use iReport.

Status

4/23/2013: Web app at http://dev.cspace.berkeley.edu/cgi-bin/cswaMain.py?webapp=ucbgBedListV321

User enters a Garden Location and selects from list. Click Search to find locations at that location or within that location. De-select any locations you do not want to include. Click Produce Bed List button.

Location Report (http://dev.cspace.berkeley.edu/cgi-bin/cswaMain.py?webapp=ucbgLocationReportV321)

  • User supplies a taxonomic name, typically genus or list of genera but can also be by family or division
  • Query gets living accessions at that name or below (hierarchical search)
  • Results sorted by latin name, accnmb, bed number
  • Not a canned report
  • Layout: Tabular with counts at end
  • Detail fields:
    • Accession number
    • Scientific name without authors (ask if Full Name is acceptable)
    • Short storage location name
    • Field collection place (or range?)
  • Footer:
    • Count of unique accession numbers
    • Count of unique scientific names
    • Total count of records returned

Notes

Initial implementation: Web app.

Other possible implementations:

  • By genus - iReport: User enters a scientific name; query performs like '%name%' on scientific taxonomy though this will get the term if it's part of a species or subspecies name.
  • By genus - iReport: User enters a scientific name; query gets list of this genus plus all children of this genus; but we'd need an index similar to the one Glen created for PAHMA.
  • By list of genera: ?
  • By family or division - iReport: User supplies a family name; query gets list of this genus plus all children of this genus; but we'd need an index similar to the one Glen created for PAHMA.

Status

4/23/2013 Web application at http://dev.cspace.berkeley.edu/cgi-bin/cswaMain.py?webapp=ucbgLocationReportV321

User enters a scientific name and selects from list. Click Search. (Instructions not complete)

Dead Report (run iReport ucbgDeadReportRange.jrxml)

  • User supplies a range of dates (date accession marked dead, i.e. no locations extant)
  • Sort by accnmb only
  • Named Business Objects report: new dead list.rep
  • Layout: tabular, but date range visible in header
  • Fields
    • Accession number
    • Scientific name

Notes

Possible implementations:

  • Within CSpace: User performs advanced search, date range on Dead Date, adds to group, runs report (dead dates however not visible)
  • Within CSpace: User runs a report "Dead within last one month", "Dead within last one year"
  • iReport: User supplies begin date and end date; report produced.

Status

4/23/2013: Run iReport ucbgDeadReportRange.jrxml

Report prompts user for begin date and end date. Enter in format yyyy-MM-dd.

List of Living Accessions (run iReport ucbgListofLivingAccessions.jrxml)

  • All living accessions
  • Sort alpha by genus (scientific name)
  • Named report: living_list_by_genus_rev.rep
  • Layout: Tabular but many fields are set to not repeat
  • Fields
    • Full no author name (don't repeat)
    • Family (don't repeat)
    • Accession number (don't repeat)
    • Full location name
    • Data quality

Notes

Implementation: Should be able to run from within CSpace or iReport, but run from iReport because this produces a very large report.

Status

Run iReport ucbgListofLivingAccessions.jrxml

No parameters required.

Taxonomic Holdings Report (on hold currently due to overlap with Location Report)

  • This report is very similar to the Location Report (above) but it has the full name (with author) and more information about the garden location (short name plus parent location)
  • User supplies a taxonomic name, typically genus or list of genera but can also be by family or division
  • Query gets living accessions at that name or below (hierarchical search)
  • Results sorted by latin name, accnmb, bed number
  • Not a canned report
  • Layout: Tabular with counts at end
  • Title/header: like "UCBG Ferns, October 2011" (customizable)
  • Detail fields:
    • Accession number
    • Full scientific name (with authors)
    • Short storage location name
    • Field collection place (or range?)
    • Parent location name
  • Footer:
    • Count of unique accession numbers
    • Count of unique scientific names
    • Total count of records returned

Notes

Implementation should follow Location Report.

Status

Still under development as webapp.

Voucher Report (query by family: run iReport ucbgVoucherFamily.jrxml; query by genus, run ucbgVoucherGenus.jrxml)

  • Typically query by genus, but also should be by family, or by range of accession numbers (different versions of report?)
  • Report returns list of vouchers for specimens (hierarchical search, family search, or accession range search)
  • Sort alpha by latin name and alternatively by accnmb
  • Layout: Tabular with count at the end
  • Fields
    • Accession number
    • Full scientific name (with authors)
    • Voucher institution
    • Hort/Wild code
  • Footer: Count of unique accession numbers returned

Notes

Possible implementations

  • Accession number range: Could be run from CSpace - Advanced search on range of accession numbers; add to group; run to report
  • Genus: Hierarchical search - either by like %term% (could be in iReport) or through taxonomic hierarchy (would require a hierarchical index and/or web app)
  • Family: Because Family will be on the taxonomy vocabulary record, this might be possible to do in iReport.

Status

Query by family: run iReport ucbgVoucherFamily.jrxml

  • Report prompts user for family name. Use form %FAMILYNAME% (e.g., %CACTACEAE%)

Query by genus: run iReport ucbgVoucherGenus.jrxml

  • Report prompts user for genus name. Use form: %Genusname% (e.g., %Armatocereus%)

Rare Status Report (query by family: run iReport ucbgRareStatusFamily.jrxml; query by genus, run ucbgRareStatusGenus.jrxml)

  • Query by division, family, or genus
  • Return living accessions that are rare
  • Sort alpha by latin name
  • Layout: Tabular with count at end
  • Fields
    • Accession number
    • Full scientific name (with author)
    • Family
    • Garden location
    • Skip this field for now: What is: "1" Plant... (Is this count of planted out specimens of this accession?)
    • Data Quality
    • Field collection place or geographic range (locality)
  • Footer: Count of unique scientific names (in second iteration of report)

Notes

Possible implementation: This could be functionality added into the Location report, a web app, modified to filter for rare plants only.  In the meantime, two iReports will be developed -- one by Family and one by Genus. 

  • Genus: Hierarchical search - either by like %term% (could be in iReport) or through taxonomic hierarchy (would require a hierarchical index and/or web app)
  • Family: Because Family will be on the taxonomy vocabulary record, this might be possible to do in iReport.
  • Family or Division search: Taxonomic hierarchy (would require a hierarchical index and/or web app)

Status

Query by family: run iReport ucbgRareStatusFamily.jrxml

  • Report prompts user for family. Use form %FAMILYNAME% (e.g., %ARAUCARIACEAE%)

Query by genus: run iReport ucbgRareStatusGenus.jrxml

  • Report prompts user for genus. Use form %Genus% (e.g., %Agathis%)

Accession Count (run iReport ucbgAccessionCount.jrxml)

  • Number of living accessions
  • This report produces a list of all unique, living accession numbers, plus a count of unique accession numbers at the end.  Normally, Holly is looking for the count, and the detail helps with analysis.
  • Layout: Tabular plus count at end
  • Sort by Accession number
  • Fields:
    • Accession Number
  • Footer: Count of unique accession numbers

Notes

Possible implementation: Need to learn more about this report.

Status

Run iReport ucbgAccessionCount.jrxml (no parameters)

Taxon Count (run iReport ucbgTaxonCount.jrxml)

  • Number of living taxa
  • Sort alpha by taxonomic name
  • Layout: Tabular plus count at end.
  • Fields:
    • Accession Number
    • Scientific Name
  • Footer: Count of unique taxonomic names

Notes

Implementation: iReport

Status

Run iReport ucbgTaxonCount.jrxml (no parameters)

Collection Holdings by collection (http://dev.cspace.berkeley.edu/cgi-bin/cswaMain.py?webapp=ucbgCollHoldingsV321)

  • Takes a geographic name as input (and this might require searching different things – the Business Object reports is doing Geographic Location like '%California%' OR State='California')
  • e.g. California Area and by other geographic levels
  • Sort alpha by latin name
  • Fields
    • Accession number
    • Scientific name (no author though probably flexible)
    • Garden location (short though probably flexible)

Notes

Possible implementation: Need to learn more about this report.

The Business Object reports is doing Geographic Location like '%California%' OR State='California'

Questions: Should we use field collection place and geographic range, or just field collection place?  Field collection place is hierarchical so searching for California and children would not get Baja California.

Status

Run web app at http://dev.cspace.berkeley.edu/cgi-bin/cswaMain.py?webapp=ucbgCollHoldingsV321

Duplicate accession number (from CSpace cataloging record)

  • Returns a list of accession numbers that appear more than once
  • Includes determination and collector to help disambiguate records

Notes

  • When no duplicates found, you just get an empty page
  • This version is copied from that used in UCJEPS.  Worked without modification.

Status

Run from CollectionSpace Cataloging record (PDF) (duplicateobjectnumber.jrxml)

Propagation reports

  • Though not defined, we know there is a propagation summary report in SAGE that should be replicated.

Plant Sales pot tag extract

  • Data needed by TaggitPro provided by a view in nuxeo: utils.plantsalespottags
  • Usually performed by volunteers and volunteer coordinator at Bot Garden
  • Fields:
    • label_id
    • accession_number
    • taxon_data (taxonomic name plus family name)
    • common_name
    • country_name
    • label_data
    • quantity
    • label_req_flag
    • staff_logon
    • date_entered
    • last_change_staff_logon
    • last_change_date

Notes

  • Report runs in CSpace in pot tag procedure, where label requested is yes
  • Produces a data file named ucbgPlantSalesPotTags.csv

Status

View, utils.plantsalespottags, used by TaggitPro labels.