deletions | additions
diff --git a/bulk upload.tex b/bulk upload.tex
index d160ee7..be2cb06 100644
--- a/bulk upload.tex
+++ b/bulk upload.tex
...
%% \begin{itemize}
%% \item If all of the data in the data set pertains to a single site, that site
%% may be specified interactively.
%% \item Otherwise, a
`site` \verb|site| column is required. The value must match an existing
%%
`sitename` \verb|sitename| column value in the
`sites` \verb|sites| table of the database. (Letter
%% case, leading and trailing spaces, and extra internal spaces are ignored
%% when searching for a match.)
%% \end{itemize}
...
%% \begin{itemize}
%% \item If all of the data in the data set pertains to a single species, that
%% species may be specified interactively.
%% \item Otherwise, the
`species` \verb|species| column is required. The value must match an
%% existing
`scientificname` \verb|scientificname| column value in the
`species` \verb|species| table of the
%% database. (Again, letter case, leading and trailing spaces, and extra
%% internal spaces are ignored when searching for a match.)
%% \end{itemize}
...
%% \item 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.
%% \item Otherwise, a
`treatment` \verb|treatment| column is required. The value must match an
%% existing
`name` \verb|name| column value in the
`treatments` \verb|treatments| table of the database.
%% (Again, letter case, leading and trailing spaces, and extra internal
%% spaces are ignored when searching for a match.)
%% \end{itemize}
\end{enumerate}
%% #### **Other information** \subsubsubsection{Other information}
%% 1. \begin{enumerate}
\item Date
%% * \begin{itemize}
\item If a single date applies to all of the data in the data set, the date may be specified interactively.
%% * \item Otherwise, a
`date` \verb|date| column is required.
%% * \item Date values must be in one of the forms "2003-07-25", "2003-07", or "2003".
%% 2. \end{itemize}
\item Rounding
%% * \begin{itemize}
\item 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.
%% * \item 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.
\end{itemize}
\end{enumerate}
%% ### Other information that is _never_ specified interactively
%% #### **Data for Yields**
%% 1. Yield
%% * Every yield data upload file must have a
`yield` \verb|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` \verb|n| column is required if and only if an
`SE` \verb|SE| column is included. The value must always be an integer greater than 1.
%% 3. Standard Error
%% * An
`SE` \verb|SE| column is required if and only if an
`n` \verb|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".
...
%% 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` \verb|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` \verb|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 \verb|[trait
%% variable
1]`, `[trait 1]|, \verb|[trait variable
2]`, 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
...
%% * 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]`, \verb|[covariate 1]|, \verb|[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 \verb|[trait variable 1]
n` n| and
%%
`[trait \verb|[trait variable 1]
SE`, 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` \verb|n| and
`SE` \verb|SE| or neither.
%% Note that if
`n` \verb|n| and
`SE` \verb|SE| are not given fields of the uploaded CSV
%% file, the value of the
`n` \verb|n| column of the traits or yields table will
%% default to 1 and the
`stat` \verb|stat| and
`statname` \verb|statname| column values will default
%% to NULL.
%% 2. Cultivar
%% * If a uniform value for the species is provided interactively when
...
%% 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` \verb|species| and a
`cultivar` \verb|cultivar| column must be included. The values in
%% the
`cultivar` \verb|cultivar| column are allowed to be blank (in which case a value
%% of NULL is inserted into the
`cultivar_id` \verb|cultivar_id| column for the given row);
%% but if provided, they must match the value of the
`name` \verb|name| column in
%% some row of the
`cultivars` \verb|cultivars| table, and moreover, this row must be a
%% row associated with the species corresponding to the value given in
%% the
`species` \verb|species| column. Again, matching is case insensitive, and
%% leading, trailing, and excess internal whitespace is ignored.
%% 3. Notes
%% * To include notes, use a
`notes` \verb|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` \verb|notes| column, each row inserted into the
`traits` \verb|traits| or
%%
`yields` \verb|yields| table will use the empty string as the value for the
`notes` \verb|notes|
%% column.
