From 525d6fd85ec87e6c7fc9456b327b7221d8775130 Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Tue, 22 Sep 2020 13:42:08 -0700 Subject: [PATCH 01/13] SFTP files --- workflows/pi_correspondence/final_review_checklist.Rmd | 3 +++ 1 file changed, 3 insertions(+) diff --git a/workflows/pi_correspondence/final_review_checklist.Rmd b/workflows/pi_correspondence/final_review_checklist.Rmd index 2f6b71b7..d15ff86f 100644 --- a/workflows/pi_correspondence/final_review_checklist.Rmd +++ b/workflows/pi_correspondence/final_review_checklist.Rmd @@ -61,3 +61,6 @@ Included lines for FAIR: - Granted access to PI using `set_rights_and_access()` + make sure it is `http://` (no s) - **note** if it is a part of portals there might be specific access requirements for it to be visible using `set_access()` + +### SFTP Files +- if there are files transferred to us via SFTP, delete those files when the ticket is resolved From 510ea89f3578c2717bbe3eb0a6b78980b54d9149 Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Tue, 22 Sep 2020 14:13:38 -0700 Subject: [PATCH 02/13] fix broken link for chapter 4.11 --- workflows/edit_eml/set_coverages.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/edit_eml/set_coverages.Rmd b/workflows/edit_eml/set_coverages.Rmd index 51c52528..35e75f92 100644 --- a/workflows/edit_eml/set_coverages.Rmd +++ b/workflows/edit_eml/set_coverages.Rmd @@ -38,4 +38,4 @@ coverage <- EML::set_coverage(beginDate = '2012-01-01', doc$dataset$coverage$geographicCoverage <- list(geocov1, geocov2) ``` -For arctic circle geographic coverage, we only have the starting vertical line of the circle shown in the projection. Here is an example with arctic circle geographic coverage. +For arctic circle geographic coverage, we only have the starting vertical line of the circle shown in the projection. Here is an example with arctic circle geographic coverage. From f6e02135cc2d3c1c85971c143e69525f7fded48f Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Wed, 23 Sep 2020 12:37:45 -0700 Subject: [PATCH 03/13] add eval=F and fix indent --- workflows/explore_eml/navigate_through_eml.Rmd | 2 +- workflows/pi_correspondence/final_review_checklist.Rmd | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/explore_eml/navigate_through_eml.Rmd b/workflows/explore_eml/navigate_through_eml.Rmd index bff5142a..5fc4fe7a 100644 --- a/workflows/explore_eml/navigate_through_eml.Rmd +++ b/workflows/explore_eml/navigate_through_eml.Rmd @@ -7,7 +7,7 @@ library(dataone) library(EML) ``` -```{r} +```{r, eval = F} # Need to be in this member node to explore file cn_staging <- CNode('STAGING') adc_test <- getMNode(cn_staging,'urn:node:mnTestARCTIC') diff --git a/workflows/pi_correspondence/final_review_checklist.Rmd b/workflows/pi_correspondence/final_review_checklist.Rmd index d15ff86f..481a9efa 100644 --- a/workflows/pi_correspondence/final_review_checklist.Rmd +++ b/workflows/pi_correspondence/final_review_checklist.Rmd @@ -11,8 +11,8 @@ the format ids are correct ### General EML Included lines for FAIR: ```{r eval=F} - doc <- eml_add_publisher(doc) - doc <- eml_add_entity_system(doc) +doc <- eml_add_publisher(doc) +doc <- eml_add_entity_system(doc) ``` ### Title From 8bf1c4b9054e8ab155336222c3416e8513679eab Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Wed, 23 Sep 2020 14:11:02 -0700 Subject: [PATCH 04/13] note on how to copy and paste code in slack and github --- training/01_introduction.Rmd | 2 ++ 1 file changed, 2 insertions(+) diff --git a/training/01_introduction.Rmd b/training/01_introduction.Rmd index c1d96b47..f916fc6b 100644 --- a/training/01_introduction.Rmd +++ b/training/01_introduction.Rmd @@ -67,6 +67,8 @@ How to generate a reprex: 3. fix until everything runs smoothly 4. copy the result to ask your question +When copy and paste code slack message or github issues, use three backticks for code blocks and two backticks for a small piece of code will prevent issues with slack formats quotation. + For more information and examples check out more of Jenny Bryan's [slides](https://speakerdeck.com/jennybc/reprex-help-me-help-you) or watch the [video](https://vimeo.com/208749032) starting at about the 10 min mark. From 860949be0aef96427feb558f72c833d3219baac7 Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Wed, 23 Sep 2020 14:11:44 -0700 Subject: [PATCH 05/13] delete useless lines --- workflows/edit_eml/edit_attributelists.Rmd | 3 --- 1 file changed, 3 deletions(-) diff --git a/workflows/edit_eml/edit_attributelists.Rmd b/workflows/edit_eml/edit_attributelists.Rmd index 05269a56..8810b4bc 100644 --- a/workflows/edit_eml/edit_attributelists.Rmd +++ b/workflows/edit_eml/edit_attributelists.Rmd @@ -95,7 +95,6 @@ new_attribute <- datamgmt::edit_attribute(doc$dataset$dataTable[[1]]$attributeLi doc$dataset$dataTable[[1]]$attributeList$attribute[[1]] <- new_attribute ``` -<<<<<<< HEAD ### Edit custom units @@ -140,8 +139,6 @@ Custom units are then added to `additionalMetadata` using the following command: unitlist <- set_unitList(custom_units, as_metadata = TRUE) doc$additionalMetadata <- list(metadata = list(unitList = unitlist)) ``` -======= ->>>>>>> 9f923bd81a51f2f7215cd9e1881ac8d79c60ad24 ### Edit factors From e44969fd965811b6a036faa38e09fb6202e7bc87 Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Wed, 23 Sep 2020 14:12:00 -0700 Subject: [PATCH 06/13] fix personnel typo --- workflows/edit_eml/set_project.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/edit_eml/set_project.Rmd b/workflows/edit_eml/set_project.Rmd index d0b91981..f9e113e8 100644 --- a/workflows/edit_eml/set_project.Rmd +++ b/workflows/edit_eml/set_project.Rmd @@ -1,10 +1,10 @@ ## Set the Project section -The project section in an EML document is automatically filled out by the metacatUI editor. It sets the project title and project personell to the submission's title and creators. Most of the time at least some of this information is incorrect and we need to update it. +The project section in an EML document is automatically filled out by the metacatUI editor. It sets the project title and project personnel to the submission's title and creators. Most of the time at least some of this information is incorrect and we need to update it. -Start by searching for the funding information using NSF's award search. This will give us the project title, abstract, and personell - along with some additional metadata. +Start by searching for the funding information using NSF's award search. This will give us the project title, abstract, and personnel - along with some additional metadata. -Using this information we will set the title, personell, and funding number. For NSF funded projects prepend the funding number with "NSF". If there are multiple awards associated with one dataset then additional `funding`, `title`, and `personell` elements should be added to reflect the additional awards. +Using this information we will set the title, personnel, and funding number. For NSF funded projects prepend the funding number with "NSF". If there are multiple awards associated with one dataset then additional `funding`, `title`, and `personnel` elements should be added to reflect the additional awards. ``` From 2f6252eb3cf21d200fe9742987dae68387507de8 Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Wed, 23 Sep 2020 14:12:28 -0700 Subject: [PATCH 07/13] add semantic annotation checking --- workflows/pi_correspondence/final_review_checklist.Rmd | 1 + 1 file changed, 1 insertion(+) diff --git a/workflows/pi_correspondence/final_review_checklist.Rmd b/workflows/pi_correspondence/final_review_checklist.Rmd index 481a9efa..5810ccd4 100644 --- a/workflows/pi_correspondence/final_review_checklist.Rmd +++ b/workflows/pi_correspondence/final_review_checklist.Rmd @@ -34,6 +34,7 @@ doc <- eml_add_entity_system(doc) - **Variables** match what is in the file - **Measurement domain** - if appropirate (ie dateTime correct) - **Missing Value Code** - accounted for if applicable +- **Semantic Annotation** - if applicable ### People - complete information for each person in each section From cdab75db6997c6c2ad9733c02ae43ddfed998449 Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Wed, 23 Sep 2020 14:12:53 -0700 Subject: [PATCH 08/13] change temporal into spatial --- workflows/pi_correspondence/initial_review_checklist.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/pi_correspondence/initial_review_checklist.Rmd b/workflows/pi_correspondence/initial_review_checklist.Rmd index c41df407..4b4a7dc6 100644 --- a/workflows/pi_correspondence/initial_review_checklist.Rmd +++ b/workflows/pi_correspondence/initial_review_checklist.Rmd @@ -30,7 +30,7 @@ Before responding to a new submission use this checklist to review the submissio * Coverages + Includes coverages that make sense - Start date BEFORE end date - - Temporal coverage matches geographic description (check hemispheres) + - Spatial coverage matches geographic description (check hemispheres) - Geographic description is from the local to state or country level, at the least - Taxonomic coverage if appropriate * Project Information From 983a02a41597af5582eef32f40e913d6f7f002ff Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Thu, 24 Sep 2020 14:35:55 -0700 Subject: [PATCH 09/13] add commonly used custom units --- workflows/edit_eml/edit_custom_units.Rmd | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/workflows/edit_eml/edit_custom_units.Rmd b/workflows/edit_eml/edit_custom_units.Rmd index 1b671fc0..8967d9d1 100644 --- a/workflows/edit_eml/edit_custom_units.Rmd +++ b/workflows/edit_eml/edit_custom_units.Rmd @@ -21,12 +21,12 @@ To manually generate the custom units list, create a dataframe with the fields m ```{r, eval = FALSE} custom_units <- data.frame( - id = c('siemensPerMeter', 'decibar'), - unitType = c('resistivity', 'pressure'), - parentSI = c('ohmMeter', 'pascal'), - multiplierToSI = c('1','10000'), - abbreviation = c('S/m','decibar'), - description = c('siemens per meter', 'decibar'), + id = c('partsPerThousand', 'decibar', 'wattsPerSquareMeter', 'micromolesPerGram', 'practicalSalinityUnit'), + unitType = c('dimensionless', 'pressure', 'power', 'amountOfSubstanceWeight'， 'dimensionless'), + parentSI = c(NA, 'pascal', 'watt', 'molesPerKilogram'， NA), + multiplierToSI = c(NA, '10000', '1', '1000000000', NA), + abbreviation = c('ppt', 'decibar', 'W/m^2', 'umol/g', 'PSU'), + description = c('parts per thousand', 'decibar', 'watts per square meter', 'micro moles per gram', 'used to describe the concentration of dissolved salts in water, the UNESCO Practical Salinity Scale of 1978 (PSS78) defines salinity in terms of a conductivity ratio'), stringsAsFactors = FALSE) ``` From 8655493ac86603068173bcf1c3e121ae7b87a7e4 Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Thu, 24 Sep 2020 14:36:25 -0700 Subject: [PATCH 10/13] adjust exercise 3a --- training/04_editing_eml.Rmd | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/training/04_editing_eml.Rmd b/training/04_editing_eml.Rmd index f685e60a..768f1842 100644 --- a/training/04_editing_eml.Rmd +++ b/training/04_editing_eml.Rmd @@ -39,8 +39,10 @@ Add the following lines to all of your data processing scripts. The metadata for the dataset created earlier in Exercise 2 was not very complete. Here we will add a attribute and physical to our entity (the csv file). * Make sure your package from [before](#exercise-2) is loaded into R. +* Convert `otherEntity` into `dataTable`. * Replace the existing `dataTable` with a new `dataTable` object with an `attributelist` and `physical` section you write in R using the above commands. -* We will continue using the objects created and updated in this exercise in 3b +* Add semantic annotations for attribute area. +* We will continue using the objects created and updated in this exercise in 3b. ```{r, child = '../workflows/edit_eml/edit_spatialdata.Rmd'} ``` From eb11cbf9a80e67f94986acf2a891f362275baf57 Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Mon, 28 Sep 2020 09:10:00 -0700 Subject: [PATCH 11/13] add email template --- .../email_templates/A_initial_email_template.Rmd | 4 ++++ .../email_templates/B_final_email_templates.Rmd | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/workflows/pi_correspondence/email_templates/A_initial_email_template.Rmd b/workflows/pi_correspondence/email_templates/A_initial_email_template.Rmd index 50503d6d..91177aef 100644 --- a/workflows/pi_correspondence/email_templates/A_initial_email_template.Rmd +++ b/workflows/pi_correspondence/email_templates/A_initial_email_template.Rmd @@ -62,6 +62,10 @@ File contents and relationships among files are clear > Could you provide a short description of the files submitted? Information about how each file was generated (what software, source files, etc.) will help us create more robust metadata for long term use. +Data layout + +> Would you be able to clarify how the data in your files is laid out? Specifically, what do the rows and columns represent? + We try not to prescribe a way the researchers must format their data as long as reasonable. However, in extreme cases (for example Excel spreadsheets with data and charts all in one sheet) we will want to kindly ask them to reformat. > We would like to suggest a couple of modifications to the structure of your data. This will others to re-use it most effectively. [DESCRIBE WHAT MAY NEED TO BE CHANGED IN THE DATA SET]. Our data submission guidelines page (https://arcticdata.io/submit/) outlines what are best practices for data submissions to the Arctic Data Center. Let us know if you have any questions or if we can be of any help. diff --git a/workflows/pi_correspondence/email_templates/B_final_email_templates.Rmd b/workflows/pi_correspondence/email_templates/B_final_email_templates.Rmd index 5717f819..e7d3b8ef 100644 --- a/workflows/pi_correspondence/email_templates/B_final_email_templates.Rmd +++ b/workflows/pi_correspondence/email_templates/B_final_email_templates.Rmd @@ -25,7 +25,7 @@ > https://doi.org/10.18739/A20X0X -> Please let us know if you need any further assistance. +> Please let us know if you need any further assistance. However, any further changes to the dataset will result in a new DOI. If you would like to maintain the same DOI please let us know. *New Submission: Abstract, methods, excel to csv, and attributes* > Thank you for your submission to the Arctic Data Center. From my preliminary examination of your dataset a few fields need to be updated before we can assign a DOI. From e6a48bbc551f6a7837fc238f8b49e4b3db166af2 Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Mon, 28 Sep 2020 09:10:13 -0700 Subject: [PATCH 12/13] fix link --- training/09_first_ticket.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/training/09_first_ticket.Rmd b/training/09_first_ticket.Rmd index a9290b28..eb94ff95 100644 --- a/training/09_first_ticket.Rmd +++ b/training/09_first_ticket.Rmd @@ -14,7 +14,7 @@ Before opening a R script first look over the initial checklist first to identif We have developed some partially filled R scripts to get you started on working on your first dataset. They outline common functions used in processing a dataset. However, it will differ depending on the dataset. -You can use this template where you can [fill in the blanks](data/dataset_processing_example_blanks.R) to get familiar with the functions we use and workflow at first. We also have a more minimal example [A filled example](dadataset_processing_example_skeleton.R_.R) as a intermediate step. You can look at the [filled example](data/dataset_processing_example_filled.R) if you get stuck or message the #datateam. +You can use this template where you can [fill in the blanks](data/dataset_processing_example_blanks.R) to get familiar with the functions we use and workflow at first. We also have a more minimal example [A filled example](data/dataset_processing_example_skeleton.R) as a intermediate step. You can look at the [filled example](data/dataset_processing_example_filled.R) if you get stuck or message the #datateam. Once you have updated the dataset to your satisfaction and reviewed the Final Checklist, post the link to the dataset on #datateam for peer review. From dde6c8805933ba7b3da381a156e5d8b2a4a46b0d Mon Sep 17 00:00:00 2001 From: Kelly Wang Date: Mon, 28 Sep 2020 09:11:15 -0700 Subject: [PATCH 13/13] add more context to shiny attributeList --- workflows/edit_eml/edit_attributelists.Rmd | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/edit_eml/edit_attributelists.Rmd b/workflows/edit_eml/edit_attributelists.Rmd index 896d7ac9..494927e1 100644 --- a/workflows/edit_eml/edit_attributelists.Rmd +++ b/workflows/edit_eml/edit_attributelists.Rmd @@ -81,7 +81,8 @@ data <- read.csv(text=rawToChar(getObject(adc_test, pkg$data))) EML::shiny_attributes(data = data) # From an existing attribute table -EML::shiny_attributes(attributes = attributes) +attributeList <- get_attributes(doc$dataset$dataTable[[i]]$attributeList) +EML::shiny_attributes(data = NULL, attributes = attributeList$attributes) # From scratch atts <- EML::shiny_attributes()