Available from: BaseSpace Clarity LIMS v5.1.x

When the Template File Generator generates the file, it creates a log file and attaches it to the step in the LIMS.

If the file generation process encounters errors, these error conditions appear in the log file.

If the file generation process completes successfully, the log file contents resemble the following example:

When troubleshooting Template File Generator issues, you will find detailed information in the Automation Worker log files.

Available from: BaseSpace Clarity LIMS v4.2.x

The Template File Generator is a file-generation solution that allows Clarity LIMS admins, such as lab managers, to produce custom template files without requiring scripting or development knowledge or resources.

At run time, the Template File Generator uses a script (driver_file_generator) and the supplied template file to generate a file. This may be a simple file that includes a subset of LIMS data, or a more complex sample sheet file for upload to the sequencing instrument to start a run.

The format of a template file is typically a comma-delimited CSV file. However, the following file formats are also supported: .bak, .groovy, .md5, .tsv, .txt, .xml.

How the Template File Generator Works

1. In Clarity LIMS:

   • An automation is configured and enabled on a step.

   • The driver_file_generator script is triggered from the automation command line.

2. The script uses the template file to generate a file, the contents of which are based on the specifications provided in the template.

3. The script extracts data from the LIMS via the API, based on tokens defined within the template file.

4. The script parses the template file and processes the sections, metadata, and tokens it contains. Sections may include header block, header, data, and footer, each of which is enclosed inside tags.

For example:

<HEADER_BLOCK> 
    Header block entry one, two, three 
    More information
</HEADER_BLOCK>
<DATA>
    Data row entry
    Data row entry
</DATA>

For details on template sections and the tokens you can use in your template files, see Creating Template Files article.

This article describes the metadata, tokens, and special characters that you can include in your custom template files for use with the Template File Generator.

Available from: BaseSpace Clarity LIMS v5.1.x

Metadata

The following table lists and describes the metadata elements that you can include in your template files.

• Unless otherwise specified, metadata elements are optional. In some cases, a metadata element must be used in conjunction with another element. For example, ILLEGAL.CHARACTERS must be used with ILLEGAL.CHARACTER.REPLACEMENTS.

• Unless otherwise specified, metadata elements can appear multiple times in the template. However, if they are paired with values, only the first occurrence is used. The other lines are silently ignored.

• Unless otherwise specified, if a metadata element requires a single value, any additional values are ignored when the file is generated. For example, suppose you include the OUTPUT.TARGET.DIR <path> metadata in your template file and provide more than one value for <path>. The script will process only the first (valid) path value and will ignore all other values.

• Unless "metadata syntax must match exactly" is specified, metadata elements are detected and used even if there is text appended before or after them. For example the following expressions are equivalent:

  Copy

  LIST.SEPARATOR, COMMA
  This-expression-is-equivalent-LIST.SEPARATOR-to-the-one-above, COMMA

For more information on metadata and how to use metadata elements in your template files, see Metadata in Creating Template Files article.

Tokens

A token is a placeholder variable that is replaced with unique data at run time. You can include tokens in automation command lines, in scripts, and in template files.

For example, suppose you include the INPUT.CONTAINER.NAME token in a template file generated by a step. At run time, this token is replaced with the name of the container that was input to the step.

All tokens included in a template file must appear in the following form: ${TOKEN}, for example - ${INPUT.CONTAINER.NAME}.

Input and Output Tokens

For steps with ResultFile inputs or outputs, refer to the following entries in the Metadata table:

• INCLUDE.INPUT.RESULTFILES

• INCLUDE.OUTPUT.RESULTFILES

Process Tokens

Submitted Sample Tokens

Other Tokens

Special Characters

CSV and template file generation special characters have substitution symbols within templates.

Available from: BaseSpace Clarity LIMS v4.2.x

You can create template files that the Template File Generator script (driver_file_generator) will use to generate custom files for use in your lab.

This article provides details on the following:

• The parameters used by the script.

• The sections of the template file—these define what is output in the generated file.

• Sorting logic—options for sorting the data in the generated file.

• Rules and constraints to keep in mind when creating templates and generating files.

• Examples of how you can use specific tokens and metadata in your template files.

For a complete list of the metadata elements and tokens that you can include in a template file, see Template File Contents.

Script Parameters

Upgrade Note: process vs step URIs The driver_file_generator script now uses steps instead of processes for fetching information. When a process URI is supplied, the script detects it and automatically switches it to a step URI. (The PROCESS.TECHNICIAN token, which is only available on 'process' in the API, is still supported.) The behavior of the script has not changed, except that the long form -processURI parameter must be replaced by -stepURI in configuration. The -i version of this parameter remains supported and now accepts both process and step URI values. If your configuration is using -processURI or --processURI, replace each instance with -i (or -stepURI/--stepURI).

The following table defines the parameters used by the driver_file_generator script.

Command-line example:

bash -l -c "opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar script:driver_file_generator -i {stepURI:v2} -u {username} -p {password} -t /opt/gls/clarity/customextensions/InfiniumHT/driverfiletemplates/NextSeq.csv-o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}"

Command-line example using -quickAttach and -destLIMS:

bash -l -c "/opt/gls/clarity/bin/java -cp /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar script:driver_file_generator -i {stepURI:v2} -u {username} -p {password} -t /opt/gls/clarity/customextensions/Robot.csv -quickAttach true -destLIMSID {compoundOutputFileLuid0} -o extended_driver_x384.csv -l {compoundOutputFileLuid2}"

See also the Examples section.

Data Source

The input-output-maps of the step (defined by the -stepURI parameter) are used as the data source for the content of the generated file.

If they are present, input-output-maps with the attribute output-generation-type=PerInput are used. Otherwise, all input-output-map items are used.

By default, the data source entries are sorted alphanumerically by LIMS ID. You can modify the sort order by using the SORT.BY and SORT.VERTICAL metadata elements (see Metadata section of the Template File Contents article).

Template Sections

The content of the generated file is determined by the sections defined in the template. Content for each section is contained within xml-like opening and closing tags that are structured as follows:

<SECTION>
    section content
</SECTION>

Most template files follow the same basic structure and include some or all the following sections (by convention, section names are written in capital letters, but this is not required):

<HEADER_BLOCK>
<HEADER>
<DATA>
<FOOTER>

The order of the section blocks in the template does not affect the output. In the output file, blocks will always be in the order shown.

The area outside of the sections can contain metadata elements (see Metadata section of the Template File Contents article). Anything else outside of the section tags is ignored.

The <PLACEMENT> and <TOKEN FORMAT> sections are not part of the list and do not create distinct sections in the generated file. Instead, they alter the formatting of the generated output.

HEADER_BLOCK

The header block section may include both plain text and data from the LIMS. It consists of information that does not appear multiple times in the generated file—ie, the information is not included in the data rows (see DATA section)

Tokens in the header block always resolve in the context of the first input and first output available. For example, suppose the INPUT.CONTAINER.TYPE token is used in the header block:

• If there is only one type of input container present in the data source, that container type will be present in the output file.

• If multiple input container types are present in the data source, only the first one encountered while processing the data will be present in the output file.

For this reason, we recommend against using tokens that will resolve to different values for different samples - such as SAMPLE.NAME. If one of these tokens is encountered, a warning is logged and the first value retrieved from the API is used. (Note that you may use.ALL tokens, where available.)

To include a header block section in a template, enclose it within the <HEADER_BLOCK> and </HEADER_BLOCK> tags.

HIDE feature: If one of the tokens of a line is empty and is part of a HIDE statement, that line will be removed entirely. See Using HIDE to Exclude Empty Columns and Using HIDE to Exclude Empty HEADER rows examples.

HEADER

The header section describes the header line of the data section (see DATA section). A simple example might be "Sample ID, Placement".

The content of this section can only include plain text and is output as is. Tokens are not supported.

To include a header section in a template, enclose it within the <HEADER> and </HEADER> tags.

HIDE feature: See 'Hide feature' in DATA section. Also note:

• If multiple <HEADER> lines are present, at least one must have the same number of columns as the <DATA> template line.

• <HEADER> lines that do not match the number of columns are unaffected by the HIDE feature.

DATA

Each data source entry creates a data row for each template line in the section. All entries are output for the first template line, then the next template line runs, and so on.

The data section allows tokens and text entries. All tokens are supported.

Note the following:

• Duplicated rows are eliminated, if present. A row is considered duplicated if its content (after all variables and placeholders have been replaced with their corresponding values) is identical to a previous row. Tokens must therefore provide distinctive enough data (ie, something more than just CONTAINER.NAME) if all of the input-output entry pairs are desired in the generated file.

• By default, the script processes only sample entries. However, there are metadata options that allow inclusion of result files/measurements and exclusion of samples.

• Metadata sorting options are applied to this section of the template file only.

• By default, pooled artifacts are treated as a single input artifact. They can be demultiplexed using the PROCESS.POOLED.ARTIFACTS metadata element.

• If there is at least one token relevant to the step inputs or outputs, this section will produce a row for each PerInput entry in the step input-output-map. If no PerInput entries are present in the step input-output-map, the script will attempt to add data rows for PerAllInputs entries.

• Input and output artifacts are always loaded if a <DATA> section is present in the template file, due to the need to determine what type of artifacts the script is dealing with.

To include a data section in a template, enclose it within the <DATA> and </DATA> tags.

HIDE feature: If the token in a given column is empty for all lines and that token is part of a HIDE statement, that column (including the matching <HEADER> columns) will be removed entirely. There can only be one <DATA> template line present when using the HIDE feature. See Using HIDE to Exclude Empty Columns and Using HIDE to Exclude Empty HEADER rows examples.

FOOTER

The content of this section can only include plain text and is output as is. Tokens are not supported.

To include a footer section in a template, enclose it within the <FOOTER> and </FOOTER> tags.

PLACEMENT

This section contains groovy code that controls the formatting of PLACEMENT tokens (see the PLACEMENT tokens in Template File Contents article Tokens table).

Within the groovy code, the following variables are available:

Note the following:

• The script must return a string, which replaces the corresponding <PLACEMENT> tag in the template.

• Logic within the placement tags can be as complex as needed, provided it can be compiled by a groovy compiler.

• If an error occurs while running formatting code, the original location value is used.

To include a placement section in a template, enclose it within the <PLACEMENT> and </PLACEMENT> tags.

Placement Example: Container Type

In the following example:

• If the container type is a 96 well plate, sample placement A1 will return as "A_1"

• If the container type is not a 96 well plate, sample placement A1 will return as "A:1"

<PLACEMENT>
// The inputs to this segment are: String row, String column, Node containerTypeNode
if (containerTypeNode.@name == "96 well plate") return row + "_" + column
else return row + ":" + column
</PLACEMENT>

Placement Example: Zero Padding

<PLACEMENT>
// The inputs to this segment are: String row, String column, Node containerTypeNode
String zeroPad (String entry) {
if (entry.isNumber() && entry.size() == 1) return "0" + entry
return entry
}
return zeroPad(row) + ":" + zeroPad(column)
</PLACEMENT>

TOKEN FORMAT

This section defines logic to be applied to specific tokens to change the format in which they appear in the generated file.

Special formatting rules can be defined per token using the following groovy syntax:

${token.identifier}
…groovy code…
// or 
${token.identifier##Name}
…groovy code…

Within the groovy code, the variable 'token' refers to the original value being transformed by the formatting code. The logic replaces all instances of that token with the result.

${token.identifier} marks the beginning of the token formatting code and the end of the previous token formatting code (if any).

• You can define multiple formatting logic rules for a given token, by assigning a name to the formatting section (named formatters are called 'variations'). This is done by appending “##” after the token name (eg “${token.identifier##formatterName}”).

• Using the named formatter syntax without giving a name (“${token.identifier##}”) will abort the file generation.

• If an error occurs while running formatting code, the resulting value will be blank.

• If a named formatter is used but not defined, the value is used as is.

To include a placement section in a template, enclose it within the <TOKEN_FORMAT> and </TOKEN_FORMAT> tags.

TOKEN FORMAT Example: Technician Name

In this example, a custom format is defined for displaying the name of the technician who ran a process (step).

The name of the token appears at the beginning of the groovy code that will then be applied. In this code, the variable 'token' refers to the token being affected. The return value is what will replace all instances of this token in the file.

<TOKEN_FORMAT>
${PROCESS.TECHNICIAN}
def name = token.split(" ")
return "First name: " + name[0] + ", Last name: " + name[1]
</TOKEN_FORMAT>

TOKEN FORMAT Example: Appending a String to Container Name or Sample Name

In this second example, when special formatting is required for two tokens, the logic for both appear inside the same set of tags.

The example appends a string to the end of the input container name or a prefix to the beginning of the submitted sample name.

<TOKEN_FORMAT>
${INPUT.CONTAINER.NAME}
return token + "-PlateName"
${SAMPLE.NAME}
return "SN-" + token
</TOKEN_FORMAT>

Metadata

Metadata provides information about the template file that is not retrieved from the API — such as the file output directory to use, and how the data contents should be grouped and sorted.

Metadata is not strictly confined to a section, and is not designated by opening and closing tags. However, each metadata entry must be on a separate line.

Metadata entries can be anywhere in the template, but the recommended best practice is to group them either at the top or the bottom of the file.

For a list of supported metadata elements, rules for using them, and examples, see Template File Contents, Metadata section.

Sorting Logic

Sorting in the generated file is done either alphanumerically or by vertical placement information, using the SORT.BY. and SORT.VERTICAL metadata elements.

Sorting must be done using a combination of sort keys - provided to SORT.BY. as one or more ${token} values, each of which always produces a unique value in the file. For example, sorting by just OUTPUT.CONTAINER.NAME would work for samples placed in tubes, but would not work for samples in 96 well plates. Sorting behavior on nonunique combinations is not guaranteed to be predictable.

To sort vertically:

Include the SORT.VERTICAL metadata element in the template file. In addition, the SORT.BY.${token}, ${token} metadata must also be included, as follows:

SORT.BY.${OUTPUT.CONTAINER.ROW}${OUTPUT.CONTAINER.COLUMN}

Any SORT.BY. tokens will be sorted using the vertical sorter instead of the alphanumeric sort.

To apply sorting to samples in 96 well plates:

You could narrow the sort key to a unique combination such as:

SORT.BY.${OUTPUT.CONTAINER.NAME}${OUTPUT.CONTAINER.ROW}${OUTPUT.CONTAINER.COLUMN}

See also SORT.VERTICAL and SORT.BY. in the Template File Contents article.

Rules and Constraints

The template must adhere to the following rules:

• Metadata entries must each appear on a new line and be the only entry on that line.

• Metadata entries must not appear inside tags.

• Opening and closing section tags must appear on a new line and as the only entry on that line.

• Each opened tag must be closed, otherwise it is skipped by the script.

• Any sections (opening tag + closing tag combination) can be omitted from the template file.

• Entries that are separated by commas in the template will be delimited by the metadata-specified separator (default: COMMA) in the template file.

• White space is allowed in the template. However, if there is a blank line inside a tag, it will also be present in the template file produced.

• If an entry in the template is enclosed in double quotes it will be imported as a single entry and written to the template file as such, even if it has commas inside.

• To include double-quotes or single-quotes in the template file, use the escape character: Example: \" or \'

• To include an escape character in the template file, use two escape characters inside double-quotes. For example, if you want to see \\Share\Folder\Filename.txt use "\\\\Share\\Folder\\Filename.txt" as the token.

If any of the following conditions is not met - the tag, and everything inside it, is ignored by the script and a warning displays in the log file:

• Except for the metadata, all template sections must be enclosed inside tags.

• Each tag must have its own line, and must be the only tag present on that line.

• No other entries, even empty ones, are allowed.

• All opened tags must be closed.

• Custom field names must not contain periods.

Examples

Illumina Instrument Sample Sheets

The LIMS provides configuration to support generation of sample sheets that are compatible with some Illumina instruments. For details, see the Illumina Instrument Sample Sheets documentation.

Generating Sample Sheets for QC Instruments

The LIMS provides configured automations that generate sample sheets compatible with a number of QC instruments. The default automation command lines are provided below.

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -u {username} -p {password} \
script:driver_file_generator \
-i {processURI:v2} \
-t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/bioA_driver_file_template.csv \
-o {compoundOutputFileLuid0}.csv \
-l {compoundOutputFileLuid1} \
&& /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \
script:addBlankLines \
-i {stepURI:v2} \
-f {compoundOutputFileLuid0}.csv \
-l {compoundOutputFileLuid1} \
-sep COMMA \
-b ',False,' \
-h 1 \
-c LIMSID \
-pre 'Sample '"

INCLUDE.OUTPUT.RESULTFILES
<HEADER_BLOCK>
</HEADER_BLOCK>
<HEADER>
"\"Sample Name\",\"Sample Comment\",\"Rest. Digest\",\"Observation\""
</HEADER>
<DATA>
${OUTPUT.LIMSID},,False,
</DATA>
<FOOTER>
Ladder,,False,"\"Chip Lot #\",\"Reagent Kit Lot #\",
\"QC1 Min [%]\",\"QC1 Max [%]\",\"QC2 Min [%]\",\"QC2 Max [%]\"
,,,
\"Chip Comment\”
"
</FOOTER>

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -u {username} -p {password} \
script:driver_file_generator \
-i {processURI:v2} \
-t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/nd_driver_file_template.csv \
-o {compoundOutputFileLuid0}.csv \
-l {compoundOutputFileLuid1}"

INCLUDE.OUTPUT.RESULTFILES
<HEADER_BLOCK>
</HEADER_BLOCK>
<HEADER>
"Well Location, Sample Name"
</HEADER>
<DATA>
${INPUT.CONTAINER.PLACEMENT},${INPUT.CONTAINER.NAME}_${INPUT.CONTAINER.PLACEMENT}_${INPUT.NAME}
</DATA>

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -u {username} -p {password} \
script:driver_file_generator \
-i {processURI:v2} \
-t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/tapestation_driver_file_template.csv \
-o {compoundOutputFileLuid0}.csv \
-l {compoundOutputFileLuid1}"

INCLUDE.OUTPUT.RESULTFILES
SORT.BY.${INPUT.LIMSID}
<DATA>
${OUTPUT.LIMSID}_${INPUT.NAME}
</DATA>

bash -c "/opt/gls/clarity/bin/java -cp /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar driver_file_generator \
-i {processURI} -u {username} -p {password} -t /opt/gls/clarity/extensions/conf/driverfiletemplates/GenomeStudioGeneExpressionTemplate.csv \
-o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}.html"

INCLUDE.OUTPUT.RESULTFILES
OUTPUT.SEPARATOR,COMMA
LIST.SEPARATOR,";"
ILLEGAL.CHARACTERS,COMMA
ILLEGAL.CHARACTER.REPLACEMENTS,_SORT.BY.${INPUT.CONTAINER.NAME}${INPUT.CONTAINER.ROW}${INPUT.CONTAINER.COLUMN}
<HEADER_BLOCK>
[HEADER]Investigator Name ${PROCESS.TECHNICIAN}
Project Name, ${SAMPLE.PROJECT.NAME.ALL}
Experiment Name
Date, ${DATE}
[Manifests]
${PROCESS.UDF.Manifest A}
</HEADER_BLOCK>
<HEADER>
[DATA]
Sample_Name,Sample_Well,Sample_Plate,Pool_ID,Sentrix_ID,Sentrix_Position
</HEADER>
<DATA>
${INPUT.NAME},,,,${INPUT.CONTAINER.NAME},${INPUT.CONTAINER.PLACEMENT}
</DATA>
<PLACEMENT>
// inputs to this section are String row, String column, Node containerTypeNode
int convertAlphaToNumeric(String letters) {
    int result = 0
    letters = letters.toUpperCase()
    for (int i = 0; i < letters.length(); i++) {
        result += (letters.charAt(i).minus('A' as char) + 1) * (26 ** (letters.length() - i - 1))
    }
    return result
}
int SENTRIX_POS_THRESHOLD = 12
int WELL_PLATE_SIZE_96 = 96
int xSize = containerTypeNode.'x-dimension'.size.text().toInteger()
int ySize = containerTypeNode.'y-dimension'.size.text().toInteger()
int containerSize = xSize * ySize
boolean xIsAlpha = containerTypeNode.'x-dimension'.'is-alpha'.text().toBoolean()
boolean yIsAlpha = containerTypeNode.'y-dimension'.'is-alpha'.text().toBoolean()
if (containerSize <= SENTRIX_POS_THRESHOLD && (xIsAlpha || yIsAlpha)) {
    return row
}
// R001_C001 for 96 well plate, r01c01 for other container types
if (containerSize == WELL_PLATE_SIZE_96) {
    def numFormat = java.text.NumberFormat.getNumberInstance() numFormat.setMinimumIntegerDigits(3)
    String xStr = numFormat.format(column.isInteger() ? column as int : convertAlphaToNumeric(column))
    String yStr = numFormat.format(row.isInteger() ? row as int : convertAlphaToNumeric(row))
    // Row is mapped to x coordinate, while column is mapped to y.
    // When creating an array type of size 96, swap the row and column dimension.
    // e.g 12 x 8 array should be mapped as an 8 x 12 array
    //
    // This mapping has been in RI for a while.
    // In AddIlluminaArraysStep, all 2D Illumina arrays added have a dimension of 8 x 12.
    // This driver file template then converts it back to 12 x 8.
    // This logic is now corrected to follow other arrays to make sure the driver file.
    // generated is compatible with existing arrays and software.
    return "R"+xStr+"_C"+yStr
} else {
    def numFormat = java.text.NumberFormat.getNumberInstance()
    numFormat.setMinimumIntegerDigits(2)
    String xStr = numFormat.format(column.isInteger() ? column as int : convertAlphaToNumeric(column))
    String yStr = numFormat.format(row.isInteger() ? row as int : convertAlphaToNumeric(row))
    // row is mapped to y, column is mapped to x
    return "r"+yStr +"c"+xStr
}
</PLACEMENT>

Renaming Generated Files

In the template file, the following OUTPUT.FILE.NAME metadata element renames the generated template file 'NewTemplateFileName':

OUTPUT.FILE.NAME, NewTemplateFileName.csv

In the automation command line, the following will attach the generated file to the {compoundOutputFileLuid0} placeholder, with the name defined by the OUTPUT.FILE.NAME metadata element.

bash -c "/opt/gls/clarity/bin/java -cp /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar \
script:driver_file_generator \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-t /opt/gls/clarity/customextensions/Robot.csv \
-q true -destLIMSID {compoundOutputFileLuid0} \
-o extended_driver_x384.csv \
-l {compoundOutputFileLuid2}"

• If the quickAttach parameter is provided without destLIMSID parameter, the script logs an error and stops execution.

• If destLIMSID is provided without using quickAttach, it is ignored.

Using Token Values In File Names

The OUTPUT.FILE.NAME and OUTPUT.TARGET.DIR metadata elements support token values. This allows you to name files based on input / output values of the step - the input or output container name, for example.

The following tokens are supported for this feature:

• PROCESS.LIMSID

• PROCESS.UDF.<UDF NAME>

• PROCESS.TECHNICIAN

• DATE

• INPUT.CONTAINER.NAME

• INPUT.CONTAINER.TYPE

• INPUT.CONTAINER.LIMSID

• OUTPUT.CONTAINER.NAME

• OUTPUT.CONTAINER.TYPE

• OUTPUT.CONTAINER.LIMSID

Rules and Constraints

When using token values in file names, the following rules and constraints apply:

• Container-related functions will return the value from a single container, even if there are multiple containers.

• Other tokens will function, but will only return the value for the first row of the file (first input or output).

• If the OUTPUT.FILE.NAME specified does not match the LIMS ID of the file, the output file will not be attached in the LIMS user interface. To ensure that the file is attached, include the quickAttach and destLIMSID parameters in the command-line string.

• It is highly recommended that you do not use SAMPLE.PROJECT.NAME.ALL or SAMPLE.PROJECT.CONTACT.ALL, because the result is prone to surpassing the maximum length of a file name. There are similar issues with other SAMPLE tokens when dealing with pools.

• Only the following characters are supported in the file name. Any other characters will be replaced by an _ (underscore) by default. This replacement character can be configured with the OUTPUT.FILE.NAME.ILLEGAL.CHARACTER.REPLACEMENT metadata element.

  • a-z

  • A-Z

  • 0–9

  • _ (underscore)

  • - (dash)

  • . (period)

Defining a Project Name for Control Samples

You can use the CONTROL.SAMPLE.DEFAULT.PROJECT.NAME metadata element to define a project name for control samples. The value specified by this token will be used when determining one or more values for the SAMPLE.PROJECT.NAME and SAMPLE.PROJECT.NAME.ALL tokens.

Example:

CONTROL.SAMPLE.DEFAULT.PROJECT.NAME, My Control Sample Project

Rules and Constraints

• If the token is found in the template, but with no value then no project name will be given for control samples.

• If the token is not found in the template, then no project name will be given for control samples.

• If multiple values are provided, the first one will be used.

• The SAMPLE.PROJECT.NAME.ALL list will include the control project name.

Using HIDE to Exclude Empty Columns

You can use tthe HIDE metadata element to optionally hide a column if it contains no data. The following lines in the metadata will hide a data column when empty:

HIDE, ${OUTPUT.UDF.SAMPLEUDF}, IF, NODATA

Assuming ${OUTPUT.UDF.SAMPLEUDF} is one of the data columns specified in the template, then that column will be hidden whenever there is no data to show in the output file. If a list of fields is provided, then any empty ones will be hidden:

HIDE, ${OUTPUT.UDF.SAMPLEUDF},${PROCESS.TECHNICIAN}, ${PROCESS.LIMSID}, IF, NODATA

You may also hide only one representation of a specific column or field:

HIDE, ${PROCESS.TECHNICIAN##FirstName}, IF, NODATA

Using HIDE to Exclude Empty HEADER rows

You can also use the HIDE metadata element with tokens in the header section. If one or more tokens are used for a header key value pair, and there are no values for any of the tokens, the entire row will be hidden.

Assuming ${OUTPUT.UDF.SAMPLEUDF} is one of the rows specified in the template header section, that header row will be hidden whenever there is no data to display in the output file.

If a list of tokens is provided for the value, the row will only be shown if one or more of the tokens resolves to a value:

HIDE, ${OUTPUT.UDF.SAMPLEUDF},${PROCESS.TECHNICIAN}, ${PROCESS.LIMSID}, IF, NODATA

Generating Multiple Files

If you would like to generate multiple files, you can use the following GROUP.FILES.BY metadata elements:

• GROUP.FILES.BY.INPUT.CONTAINERS

• GROUP.FILES.BY.OUTPUT.CONTAINERS

These elements allow a file to be created per instance of the specified element in the step, for example, one file per input or per output container. Step level information appears in all files, but sample information is specific to the samples in the given container.

For example, suppose that a step has two samples - each in their own container - with a template file calling for information about process UDFs and sample names. Using this metadata will produce two files, each of which will contain:

• One sample entry

• The same process UDF information

As a best practice, we recommend storing a copy of generated files in the LIMS. To do this, you must use the quickAttach script parameter. This parameter must be used with the destLIMSID parameter, which tells the Template File Generator script which file placeholder to use. (For details, see Script Parameters.)

Naming The Files

When generating multiple files, the script gathers them all into one zip file so only one file placeholder is needed regardless of how many containers are in the step.

The zip file name may be provided in the metadata as follows:

GROUP.FILES.BY.INPUT.CONTAINERS,<zip file name>

GROUP.FILES.BY.OUTPUT.CONTAINERS,<zip file name>

Inside the zip file, include any paths specified for where files should be written. An example final structure inside the zip, where the subfolders are specified using the container name token, could be as follows:

GROUP.FILES.BY.INPUT.CONTAINERS,MyZip.zip
MyZip.zip\
      \-- Container1\
              \-- SampleSheet.csv\
      \-- Container2\
              \-- SampleSheet.csv

The file naming, writing, and uploading process works as follows:

• The outputPath parameter element is required for the script. You can use this parameter to specify the path to which the generated files will be written and/or the name to use for the file. Use this in the following scenarios:

  • When the target path/name is constant OR

  • When the target path/name includes something that can only be passed to the script via the command line - for example, if you want to include the value of a {compoundOutputFileLuidN} in the path.

• The OUTPUT.TARGET.DIR metadata element overrides any path provided by outputPath, but does not change the file name. Use this:

  • When the target path includes something that can only be accessed with token templates - for example, the name of the user who ran the step.

• The OUTPUT.FILE.NAME metadata element overrides any value provided by outputPath entirely. This token determines the name of the files that are produced for each container - for example, SampleSheet.csv. It may also contain tokens to access information, such as the container name, and it may also contain a path.

If you provide all three of outputPath, OUTPUT.TARGT.DIR, and OUTPUT.FILE.NAME, the result is that outputPath is ignored and the path specified by OUTPUT.TARGET.DIR is used as the parent under which OUTPUT.FILE.NAME is created, even if OUTPUT.FILE.NAME includes a path in addition to the file name.

If you wish to only attach files to placeholders in the LIMS and do not wish to also write anything to disk, then omit OUTPUT.TARGET.DIR and provide the outputPath parameter value as ".". This will cause files to only be written to the temporary directory that is cleaned up after the automation completes.

To produce the example of MyZip.zip, you could use the following:

Script parameters:

-outputPath SampleSheet.csv
-q 'true'
-destLIMSID {compoundOutputFileLuid0}

Template:

GROUP.FILES.BY.OUTPUT.CONTAINERS,MyZip.zip
OUTPUT.TARGET.DIR,${OUTPUT.CONTAINER.NAME}

Rules and Constraints

• You can only use one GROUP.FILES.BY metadata element in each template file.

• To attach the files in the LIMS as a zip file, you must provide the quickAttach parameter along with the destLIMSID.

• The zip file name may optionally be specified with the GROUP.FILES.BY metadata.

• If quickAttach is used and no zip name is specified in the template, the zip will be named using the destLIMSID parameter value.

• The zip file name, file paths, and file names should not contain characters that are illegal for directories and files on the target operating system. Illegal characters will be replaced with underscores.

• If a file name is not unique to the target directory, e.g., if multiple SampleSheet.csv files are being written to /my/target/path, an error will be thrown and no files written.

• When specifying the OUTPUT.TARGET.DIR metadata element, if a token is used that may resolve to multiple values for a single path (for example, using INPUT.NAME in the path when it will resolve to multiple sample names), one value will be chosen arbitrarily for the path. For example, you may end up with /Container1/Sample1/myfile.csv when there are two samples in the container.