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# BETYdb: Bulk Data Upload \label{sec:bulk_upload}  Currently the web interface does not support bulk data upload, although this is a planned feature for BETY 2.0.    There are three phases for a basic bulk upload of data :   \begin{enumerate}  \item Use the web interface   * to enter metadata (new sites, citations, treatments, managements);  * to obtain a template appropriate for your data set.  \item Fill in the template with your data. There are four templates to choose from:  \begin{itemize}  \item \href{https://docs.google.com/spreadsheets/d/1maK1uKr6i9KERaYdU5zSiXcBndQoiG4Vgn2DTnqdfbA/export?format=csv&gid=0}{yields.csv} Use this template if you are uploading yield data and you wish to specify the citation in the file by author, year, and title. If your data includes SE and cultivar information and you do not plan to add any additional information interactively, you will be able to use this template "as-is". Otherwise, you will need to delete one or more columns: (a) If your data has no SE information, delete both the `SE` and the `n` column. (b) If your data set has a single uniform value for the site, species, cultivar, treatment, access_level, or date, then these values may be entered interactively through the web interface; in this case you should delete the corresponding column(s) from the template. (c) Note that cultivar information can't be specified interactively unless species information is as well; delete the cultivar column if and only if either have not cultivar information or you are specifying both the species and the cultivar information interactively.  \item \href{https://docs.google.com/spreadsheets/d/1ExLosMvX05jHWO9UYVE4Dxcl2ZbUgPc0KYoUPruaOtM/export?format=csv&gid=0}{yields\_by\_doi.csv} Use this template if you are uploading yield data and you wish to specify the citation in the file by doi. Again, if you do not have data for all of the columns listed in the template, or if you plan to specify some of the data interactively, you will have to delete one or more columns. (You may also use this template if all of the data in your data set pertains to a single citation and you wish to specify that citation interactively. In this case, you must delete the `citation_doi` column.)  \item \href{https://docs.google.com/spreadsheets/d/1Bv4dAPKU6YDJ6yB0DC4bAmHoGxSLgKybMpTR7qBvCu0/export?format=csv&gid=0}{traits.csv} Use this template if you are uploading trait data and you wish to specify the citation in the file by author, year, and title. **This template must be modified before it can be used.** In particular, the column headings `[trait variable 1]` ... `[trait variable n]` must be replace by actual variable names that _exactly_ match names of variables in the database that have been marked to be recognized as trait variables. The number of these trait variable columns may need to be increased or decreased to accomodate the data set. Some trait variables allow or even require corresponding covariate information to be included. Again, the column headings `[covariate 1]` ... `[covariate n]` must be changed to actually covariate variable names, and the number of these columns may need to be increased or decreased to match the available information. As with the yield data templates, some columns may also need to be deleted. For a list of recognized trait variable names and their corresponding required and optional covariates, visit the trait variable/covariated list at www.betydb.org. [TO-DO: Make this Web page.]  \item \href{https://docs.google.com/spreadsheets/d/1Bv4dAPKU6YDJ6yB0DC4bAmHoGxSLgKybMpTR7qBvCu0/export?format=csv&gid=0}{traits\_by\_doi.csv} As with the corresponding yield data template, use this template if you are uploading trait data and you wish to specify the citation in the file by doi or if you plan to specify the citation interactively (in which case delete the `citation_doi` column). **Again, this template must be modified before it can be used.**  \end{itemize}  \item Use the web interface to upload your data set and insert it into the database.  \end{enumerate}  %% In what follows, the term "field" always refers either to a column name used in the heading of the uploaded CSV file or to an entry in that column in some particular row of the file. On the other hand, and the term "column" may either refer to a column of data in the uploaded CSV file or to an attribute of a trait or yield datum in the traits or yields table of the database.   %% ## **Detailed CSV Data File Specifications**  %% ### **Required fields**:  %% 1. For yields uploads, the only required field is a `yield` column.  %% 2. For trait uploads, there must be at least one column whose label exactly matches the variable name for the trait value being specified. (Leading and trailing spaces are permitted, but letter case must exactly match the name of the variable specified in the database.)  %% ### **Information that is required but that _may_ be specified interactively for the entire dataset.**  %% (Data values may be specified interactively only if there is a single value that pertains to the whole data set.)  %% #### **Information that references existing database entries**  %% 1. Citation  %% * If only one citation for the entire dataset exists, it may be specified  %% interactively by choosing a citation on the citations page instead of  %% including citation information in the CSV file.  %% * Otherwise, specify the citation in the CSV table, either by doi or by  %% author, year, and title.  %% * If a DOI is available for all citations in the data set, the citation  %% corresponding to each row may be specified in a `citation_doi` column. In  %% this case, the `citation_author`, `citation_year`, and `citation_title`  %% columns must not be in the column heading list. (If such information is  %% already included in the data set, to keep such columns for purely  %% informational purposes, the string `-ignore` may be appended to each of  %% these headings. One might want to do this, for example, to keep a visual  %% record of the author, year, and title even when it is the citation doi  %% that is being used to determine how the data will associated with a  %% citation in the database.) Each value in the `citation_doi` column must  %% exactly match the `doi` attribute of some row in the `citations` except  %% that case and leading and trailing spaces are ignored.  %% * Conversely, if a DOI is not available for all citations in the data set,  %% or if it is preferred to specify the citation by author, year, and title,  %% then the `citation_doi` column should _not_ be included and the columns  %% `citation_author`, `citation_year`, and `citation_title` must all be  %% present. (Again, if some DOI information is already included and you wish  %% to retain it for purely informational purposes, simply give the column  %% some descriptive name other than `citation_doi` and it will be ignored by  %% the upload code.)  %% 2. Site  %% * If all of the data in the data set pertains to a single site, that site  %% may be specified interactively.  %% * Otherwise, a `site` column is required. The value must match an existing  %% `sitename` column value in the `sites` table of the database. (Letter  %% case, leading and trailing spaces, and extra internal spaces are ignored  %% when searching for a match.)  %% 3. Species  %% * If all of the data in the data set pertains to a single species, that  %% species may be specified interactively.  %% * Otherwise, the `species` column is required. The value must match an  %% existing `scientificname` column value in the `species` table of the  %% database. (Again, letter case, leading and trailing spaces, and extra  %% internal spaces are ignored when searching for a match.)  %% 4. Treatment  %% * If a single treatment and a single citation applies to all of the data in  %% the data set, the treatment may be specified interactively provided that  %% the citation is specified interactively as well.  %% * Otherwise, a `treatment` column is required. The value must match an  %% existing `name` column value in the `treatments` table of the database.  %% (Again, letter case, leading and trailing spaces, and extra internal  %% spaces are ignored when searching for a match.)  %% #### **Other information**    %% 1. Date  %% * If a single date applies to all of the data in the data set, the date may be specified interactively.  %% * Otherwise, a `date` column is required.  %% * Date values must be in one of the forms "2003-07-25", "2003-07", or "2003".  %% 2. Rounding  %% * The amount of rounding for numerical data can only be specified  %% interactively. Any value from 1 to 4 significant digits may be chosen.  %% The amount of rounding for the standard error SE (if present) may be  %% specified separately from the amount of rounding for yield and for trait  %% variables and their covariates.  %% * By default, all numerical data is rounded to three significant digits.  %% For example, with this default in place, 999.1 will be rounded to 999 and  %% 1001.1 will be rounded to 1000.  %% ### Other information that is _never_ specified interactively  %% #### **Data for Yields**   %% 1. Yield  %% * Every yield data upload file must have a `yield` column. The data in  %% this column must always be a parsable non-negative number and must never  %% be blank. Scientific notation is not currently supported. As noted  %% above, the number given in the file is subject to rounding before being  %% inserted into the database.  %% 2. Sample Size  %% * An `n` column is required if and only if an `SE` column is included. The value must always be an integer greater than 1.  %% 3. Standard Error  %% * An `SE` column is required if and only if an `n` column is included;  %% this datum will be inserted into the stat column of the yields table,  %% and the statname column value will be set to "SE".  %% #### **Data for Traits**  %% 1. Trait variable values  %% * Every trait data upload file must have at least one column whose heading  %% matches the name of some recognized trait variable. A list of  %% recognized trait variables is listed on the BetyDB web site. If  %% multiple trait variable columns are used, each row in the CSV file will  %% produce one row in the `traits` table for each trait variable column.  %% (These resulting rows will be effectively _grouped_ by assigning them a  %% unique entity id. Said another way, there is a one-to-one  %% correspondence between rows in the CSV file and resultant rows in the  %% `entities` table, the table that keeps track of this grouping.) As with  %% yield numbers, the data in this column must always be a parsable number,  %% and is subject to rounding before being inserted into the database. In  %% addition, it must conform to any range restrictions on the value of the  %% variable.  %% * The template for traits uploads provides dummy column headings `[trait  %% variable 1]`, `[trait variable 2]`, etc., which must be changed to  %% actual variable names before data can be uploaded.  %% 2. Covariate values  %% * If any of the included trait variables has a required covariate, there  %% must be a column corresponding to that covariate.  %% * For any of the included trait variables has an optional covariate, a  %% column corresponding to that covariate _may_ be included.  %% * The template for traits uploads provides dummy column headings  %% `[covariate 1]`, `[covariate 2]`, etc., which must be changed to actual  %% variable names before data can be uploaded.  %% 3. Sample Size and Standard Error  %% * To enter n and SE, add additional columns `[trait variable 1] n` and  %% `[trait variable 1] SE`, etc. as needed.    %% ### **Optional data**:  %% 1. Sample Size and Standard Error  %% * As noted above, these are both optional, but if one of these is  %% included, the other must be included as well. In other words, the  %% column heading list must include both of `n` and `SE` or neither.  %% Note that if `n` and `SE` are not given fields of the uploaded CSV  %% file, the value of the `n` column of the traits or yields table will  %% default to 1 and the `stat` and `statname` column values will default  %% to NULL.  %% 2. Cultivar  %% * If a uniform value for the species is provided interactively when  %% uploading the data set, the cultivar may be specified this way as  %% well provided that it also has a uniform value for the whole data  %% set.  %% * Otherwise, to include cultivar information in the upload file, both a  %% `species` and a `cultivar` column must be included. The values in  %% the `cultivar` column are allowed to be blank (in which case a value  %% of NULL is inserted into the `cultivar_id` column for the given row);  %% but if provided, they must match the value of the `name` column in  %% some row of the `cultivars` table, and moreover, this row must be a  %% row associated with the species corresponding to the value given in  %% the `species` column. Again, matching is case insensitive, and  %% leading, trailing, and excess internal whitespace is ignored.  %% 3. Notes  %% * To include notes, use a `notes` column. There is no restriction on  %% what can be included in this column, but leading and trailing space  %% will be stripped before insertion into the database. Non-ascii  %% characters entered in the file in UTF-8 encoding are allowed. If  %% there is no `notes` column, each row inserted into the `traits` or  %% `yields` table will use the empty string as the value for the `notes`  %% column.