deletions | additions       diff --git a/bulk upload.md b/bulk upload.md  index ff88184..4cbcc3f 100644  --- a/bulk upload.md  +++ b/bulk upload.md 
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1. Use the web interface   * to enter metadata (new sites, citations, treatments, managements);  * to obtain a template appropriate for your data set._[Decide whether to really do this. A draft template would simply be a header line with all possible fields. Users would be instructed to remove the fields they don't need.]_  2. Fill in the template with your data. There are four templates to choose from:  * [yields.csv](https://docs.google.com/spreadsheets/d/1maK1uKr6i9KERaYdU5zSiXcBndQoiG4Vgn2DTnqdfbA/export?format=csv&gid=0) 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.  * [yields\_by\_doi.csv](https://docs.google.com/spreadsheets/d/1ExLosMvX05jHWO9UYVE4Dxcl2ZbUgPc0KYoUPruaOtM/export?format=csv&gid=0) 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.) 
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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 references existing database entries and is required but  that _may_ be specified globally 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 using table,  either (doi) by doi  or (author, by  author,  year, first 20 or more characters of (title)) _[Currently, the full title must be specified.]_ and title.  * If a `citation_doi` 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 all not  be deleted. (Alternatively, 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 `citation_doi` 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 deleted included  and the columns  `citation_author`, `citation_year`, and `citation_title` must all be entered. 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, the 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  * use name   5. date: require one If a single treatment and a single citation applies to all  of the forms "2003-07-25", "2003-07", or "2003".  Of these, data in  the citation, site, species, treatment, and access_level data set, the treatment  may be specified interactively when uploading the dataset (if they are uniform for provided that  the whole set) rather than appearing citation is specified interactively  as well.  * Otherwise,  a field or set of fields `treatment` column is required. The value must match an  existing `name` column value in the `treatments` table  of the CSV file. As noted above, database.  (Again, letter case, leading and trailing spaces, and extra internal  spaces are ignored when searching  for citations, this is done outside a match.)  #### **Other information**    1. Date  * If a single date applies to all  of the upload wizard by choosing a citation on data in  the citations page.   ## **Data for Yields**   1. mean: data set, the date may be specified interactively.  * Otherwise, a `date` column is required.  * Date values  must be in  one of the fields forms "2003-07-25", "2003-07", or "2003".  2. Rounding  * The amount  of the CSV table, though rounding  for uploads numerical data can only be specified  interactively. Any value from 1 to 4 significant digits may be chosen.  The amount  of yields data, we will by 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 call 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 field "yield" 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 provided templates file is subject to rounding before being  inserted into the database.  2. n: Sample Size  * An `n` column is  required if and only if an SE `SE`  column is given included. The value must always be an integer greater than 1.  3. SE: Standard Error  * An `SE` column is  required if and only if an n `n`  column is given; included;  this datum will be inserted into the stat column, column of the yields table,  and the statname column value  will be set to "SE" access_level   ## "SE".  ####  **Data for Traits** 1. \, \, ... \:   These Trait variable values  * Every trait data upload file must have at least one  column names should 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 replaced 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 values from \ref{tab:traits} (or see yield numbers,  the [variables table](https://www.betydb.org) for data in this column must always be  a comprehensive listing).  2. \, \, ... \  these columns should 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 replaced with changed to  actual variable names before data can be uploaded.    2. Covariate  values from \ref{tab:covariates}. * 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 "\ n" `[trait variable 1] n`  and "\ SE" `[trait variable 1] SE`, etc.  as needed.   ## ###  **Optional fields**: 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.  1. n and SE: as noted above, if one of these is present, the other must be as well; if SE is given, the value will go into the stat column of the yields table, and the statname column will be set to "SE"   2. cultivar: use name; defaults to NULL (for the cultivar_id column) if not provided   3. notes: defaults to the empty string if not provided   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. If n and SE are not given fields of the uploaded CSV file, the value of the n column of the yields table will default to 1 and the stat and statname column values will default to NULL.