Scott Rohde save point  over 9 years ago

Commit id: b6f87ab90d98813fa4d528ffba40a0d84c0f258f

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the upload code.)  \end{itemize}  %% \item Site%%  \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 \verb|site| column is required. The value must match an existing%%  \verb|sitename| column value in the \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}%%  \item Species%%  \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 \verb|species| column is required. The value must match an%%  existing \verb|scientificname| column value in the \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 Treatment%%  \begin{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 \verb|treatment| column is required. The value must match an%%  existing \verb|name| column value in the \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} 

\end{enumerate}  %% ### Other \subsubsection{Other  information that is _never_ \textit{never}  specified interactively  %% #### **Data interactively}  \subsubsubsection{Data  for Yields**   %% 1. Yields}  \begin{enumerate}  \item  Yield%% *  Every yield data upload file must have a \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. \item  Sample Size%% *  An \verb|n| column is required if and only if an \verb|SE| column is included. The value must always be an integer greater than 1. %% 3. \item  Standard Error%% *  An \verb|SE| column is required if and only if an \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". %% #### **Data \end{enumerate}  \subsubsubsection{Data  for Traits**  %% 1. Traits}  \begin{enumerate}  \item  Trait variable values %% * \begin{itemize}  \item  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 \verb|traits| table for each trait variable column.%%  (These resulting rows will be effectively _grouped_ \textit{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%%  \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. %% * \item  The template for traits uploads provides dummy column headings \verb|[trait%%  variable 1]|, \verb|[trait variable 2]|, etc., which must be changed to%%  actual variable names before data can be uploaded. %% 2. \end{itemize}  \item  Covariate values %% * \begin{itemize}  \item  If any of the included trait variables has a required covariate, there%%  must be a column corresponding to that covariate. %% * \item  For any of the included trait variables has an optional covariate, a%%  column corresponding to that covariate _may_ \textit{may}  be included. %% * \item  The template for traits uploads provides dummy column headings%%  \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 \verb|[trait variable 1] n| and  %% \verb|[trait variable 1] SE|, etc. as needed. \end{itemize}    \item Sample Size and Standard Error  To enter n and SE, add additional columns \verb|[trait variable 1] n| and  \verb|[trait variable 1] SE|, etc. as needed.  %% ### **Optional data**:  %% 1. \end{enumerate}  \subsubsection{Optional data}:  \begin{enumerate}  \item  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 \verb|n| and \verb|SE| or neither.%%  Note that if \verb|n| and \verb|SE| are not given fields of the uploaded CSV%%  file, the value of the \verb|n| column of the traits or yields table will%%  default to 1 and the \verb|stat| and \verb|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%%  \verb|species| and a \verb|cultivar| column must be included. The values in%%  the \verb|cultivar| column are allowed to be blank (in which case a value%%  of NULL is inserted into the \verb|cultivar_id| column for the given row);%%  but if provided, they must match the value of the \verb|name| column in%%  some row of the \verb|cultivars| table, and moreover, this row must be a%%  row associated with the species corresponding to the value given in%%  the \verb|species| column. Again, matching is case insensitive, and%%  leading, trailing, and excess internal whitespace is ignored.%%  3. Notes%%  * To include notes, use a \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 \verb|notes| column, each row inserted into the \verb|traits| or%%  \verb|yields| table will use the empty string as the value for the \verb|notes|%%  column. \end{enumerate}