biolink append

biolink append bhandle label ?property value?...

j.append({?property:value,?...})

j.append(?property,value,?...)

Standard data manipulation command for appending property data. It is explained in more detail in the section about setting property data.

The command returns the first data value.

biolink defined

biolink defined bhandle label property

j.defined(property)

This command checks whether a property is defined for the biolink. This is explained in more detail in the section about property validity checking. Note that this is not a check for the presence of property data! The biologics valid command is used for this purpose.

The command returns a boolean status value.

biolink delete

biolink delete bhandle ?label?...

biolink delete bhandle all

j.delete()

Biolink.Delete(bref,?jlabel/jref/jrefsequence?,...)

Biolink.Delete(jref,...)

Biolink.Delete(bref,“all”)

Delete zero or more biolinks. The bioitems the links connect remain intact.

The special biolink label all requests deletion of all links.

The return value of the command is the number of deleted biolinks.

Example:

biolink delete $bhandle 1

This command is one of few biolink subcommands which do not require an biolink label. If no label is given, the command does nothing. This is useful for list expansions where the list might be empty:

eval biolink delete $bhandle $dellinklist

biolink delete $bhandle {*}$dellinklist

biolink dget

biolink dget bhandle label propertylist ?filterset? ?parameterdict?

j.dget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the biolink get command. The difference between biolink get and biolink dget is that the latter does not attempt computation of property data, but rather initializes the property values to the default and return that default if the data is not yet available. For data already present, biolink get and biolink dget are equivalent.

biolink exists

biolink exists bhandle label ?filterlist?

b.exists(?filters=?)

Biolink.Exists(bref,label,?filters=?)

Check whether this biolink exists. Optionally, a filter list can be supplied to check for the presence of specific features. The command returns 0 if the biolink does not exist, or fails the filter, and 1 in case of successful testing.

Example:

biolink exists $bhandle 99

biolink fill

biolink fill bhandle label ?property value?...

j.fill({property:value,...})

j.fill(?property,value?,...)

Standard data manipulation command for setting data, ignoring possible mismatches between the lengths of the lists of objects associated with the property and the value list. It is explained in more detail in the section about setting property data.

biolink filter

biolink filter bhandle label filterlist

j.filter(filters)

Check whether a biolink passes a filter list. The return value is boolean 1 for success and 0 for failure.

biolink get

biolink get bhandle label propertylist ?filterset? ?parameterdict?

j.get(property=,?filters=?,?parameters=?)

j[property]

j.property

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For the use of the optional property parameter list argument, refer to the documentation of the ens get command.

Variants of the biolink get command are biolink new, biolink dget, biolink nget, biolink show, biolink sqldget , biolink sqlget, biolink sqlnew and biolink sqlshow.

biolink index

biolink index bhandle label

j.index()

Get the index of the bioitem. The index is the position in the biolink list of the biologics object. The first position is index 0.

biolink items

biolink items bhandle label ?filterset? ?filtermode?

j.items(?filters=?,?mode=?)

Standard cross-referencing command to obtain the labels or references of the bioitems which are connected by the biolink. This is explained in more detail in the section about object cross-references.

biolink bioitems is a command alias.

biolink jget

biolink jget bhandle label propertylist ?filterset? ?parameterdict?

j.jget(property=,?filters=?,?parameters=?)

This is a variant of biolink get which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

biolink jnew

biolink jnew bhandle label propertylist ?filterset? ?parameterdict?

j.jnew(property=,?filters=?,?parameters=?)

This is a variant of biolink new which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

biolink jshow

biolink jshow bhandle label propertylist ?filterset? ?parameterdict?

j.jshow(property=,?filters=?,?parameters=?)

This is a variant of biolink show which returns the result data as a JSON formatted string instead of Tcl or Python interpreter objects.

biolink link

biolink link bhandle label

Biolink.Ref(bref,identifier)

Return the biolink label stored in property J_LABEL ( Tcl ) , or a minor object reference ( Python ). This is useful in case the label used in the command is not a straightforward numerical label or reference but some other item identification format.

biolink biolink is an alias.

biolink new

biolink new bhandle label propertylist ?filterset? ?parameterdict?

j.new(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the biolink get command. The difference between biolink get and biolink new is that the latter forces the re-computation of the property data, regardless whether it is present and valid, or not.

biolink nget

biolink nget ehandle label propertylist ?filterset? ?parameterdict?

j.nget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the biolink get command. The difference between biolink get and biolink nget is that the latter always returns numeric data, even if symbolic names for the values are available.

biolink ref

Biolink.Ref(bref,identifier)

Python only method to get a biolink reference. See biolink link command.

biolink set

biolink set bhandle label ?property value?...

j.set(?property,value?,...)

j.set({property:value,...})

j.property = value

j[property] = value

Standard data manipulation command. It is explained in more detail in the section about setting property data.

biolink show

biolink show bhandle label propertylist ?filterset? ?parameterdict?

j.show(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the biolink get command. The difference between biolink get and biolink show is that the latter does not attempt computation of property data, but raises an error if the data is not present and valid. For data already present, biolink get and biolink show are equivalent.

biolink sqldget

biolink sqldget bhandle label propertylist ?filterset? ?parameterdict?

j.sqldget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the biolink get command. The differences between biolink get and biolink sqldget are that the latter does not attempt computation of property data, but initializes the property value to the default and returns that default, if the data is not present and valid; and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

biolink sqlget

biolink sqlget bhandle label propertylist ?filterset? ?parameterdict?

j.sqlget(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the biolink get command. The difference between biolink get and biolink sqlget is that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

biolink sqlnew

biolink sqlnew bhandle label propertylist ?filterset? ?parameterdict?

j.sqlnew(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the biolink get command. The differences between biolink get and biolink sqlnew are that the latter forces re-computation of the property data, and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

biolink sqlshow

biolink sqlshow bhandle label propertylist ?filterset? ?parameterdict?

j.sqlshow(property=,?filters=?,?parameters=?)

Standard data manipulation command for reading object data. It is explained in more detail in the section about retrieving property data.

For examples, see the biolink get command. The differences between biolink get and biolink sqlshow are that the latter does not attempt computation of property data, but raises an error if the data is not present and valid, and that the SQL command variant formats the data as SQL values rather than for Tcl or Python script processing.

biolink subcommands

biolink subcommands

dir(Biolink)

Lists all subcommands of the biolink command. Note that this command does not require a biologics handle, or a biolink label.