A01 | Check one or more a well names to make sure they follow the... |
ArtifactGroupRefClass-class | An ArtifactGroup representation that subclasses from... |
ArtifactGroupRefClass_get_artifacts | Retrieve a list ArtifactRefClass objects |
ArtifactGroupRefNode_DELETE | DELETE is disallowed for ArtifactGroup |
ArtifactGroupRefNode_POST | POST is disallowed for artifact groups |
ArtifactGroupRefNode_PUT | PUT is disallowed for artifact groups |
ArtifactRefClass-class | An Artifact representation that sublcasses from NodeRefClass |
ArtifactRefClass_get_artifact_groups | Get the artifact groups associated with this artifact if any |
ArtifactRefClass_get_container | Get the artifact container as uri or NodeRefClass |
ArtifactRefClass_get_file_artifact | Retrieve the artifact's file artifact (if any) |
ArtifactRefClass_get_parent_process | Get the parent_process assocated with this artifact |
ArtifactRefClass_get_sample | Get the sample associated with this artifact |
ArtifactRefClass_get_samples | Get the samples associated with this artifact - useful for... |
ArtifactRefClass_get_wellname | Get the name of the well in the form A:1 |
ArtifactRefClass_location | Get a pretty string representing the location |
ArtifactRefClass_qc_flag | Get the qc flag |
ArtifactRefClass_working_flag | Get the working flag |
ArtifactRefNode_DELETE | DELETE is disallowed for artifacts |
ArtifactRefNode_POST | POST is disallowed for artifacts |
ArtifactRefNode_show | Show |
as_ascii | Sanitize a character vector to be UTF-8 ASCII |
batch_create | Create one or more nodes (Sample and Container only) |
batch_retrieve | Retrieve a batch resource |
batch_update | Update one or more XML::xmlNodes using batch resources |
build_config_path | Create a configuration file name in the form of... |
build_query | Prepares a contribution to a query list - see 'modify_url' |
check_type | Given a LIMS type code and value, cast the value to be LIMS... |
ContainerRefClass-class | A Container representation that subclasses from NodeRefClass |
ContainerRefClass_get_artifacts | Retrieve a named list ArtifactRefClass objects |
ContainerRefClass_get_placements | Retrieve a named vector of placements uri |
ContainerRefClass_get_samples | Retrieve a named list of artifact XML:xmlNode or... |
ContainerRefClass_get_type | Retrieve a named vector of container type attributes (uri and... |
ContainerRefClass_n_empty | Retrieve the empty well count |
ContainerRefClass_n_occupied | Retrieve the occupied well count |
ContainerRefClass_n_wells | Retrieve the well count (occupied + empty) |
ContainerRefClass_POST | POST is disallowed for containers |
ContainerRefClass_required_namespaces | Return a character vector of required namespace names |
ContainerRefClass_show | Show |
ContainerRefClass_well_occupied | Test if one or more wells are occupied |
ContainerTypeRefClass-class | A Containertype representation that subclasses from... |
cp_download | Download files using system cp |
create_artifacts_details | Create a artifacts details node assembled from one or more... |
create_artifacts_links | Create an artifacts links node from uris suitable for batch... |
create_container_node | Create a container XML::xmlNode suitable for POSTing |
create_containers_details | Create a containers details node assembled from one or more... |
create_exception_node | Create an exception node |
create_file_node | Create an unresolved file node |
create_iom_analyte | Create an 'input-output-map' node for Analyte - useful when... |
create_iom_resultfile | Create an 'input-output-map' node for a result file - useful... |
create_iom_shared_resultfile | Create an 'input-output-map' node for a shared result file -... |
create_lab_node | Create a lab/account XML::xmlNode suitable for POSTing |
create_process_node | Create a process node used for process creation |
create_project_node | Create a project XML::xmlNode suitable for POSTing |
create_researcher_node | Create a researcher XML::xmlNode suitable for POSTing |
create_routing | Create routing node |
create_routing_artifacts | Create or update an artifact routing map |
create_sample_node | Create a sample XML::xmlNode suitable for POSTing |
create_samples_details | Create a sample details node assembled from one or more... |
create_udf_node | Create a UDF XML::xmlNode and possibly add it to a parent... |
duck_download | Download a file using duck |
duck_upload | Upload a file using duck |
ExceptionRefClass-class | An Exception representation that sublcasses from NodeRefClass |
extract_udfs | Extract a named list of udf vectors from an xmlNode |
FieldRefClass-class | A User Defined Field configuration representation that... |
FieldRefClass_DELETE | DELETE is disallowed for field configuration |
FieldRefClass_get_type | Get the value of the Udf type |
FieldRefClass_POST | POST is disallowed for field configuration |
FieldRefClass_show | Show the contents |
FileRefClass-class | File.R A File representation that subclasses from... |
FileRefClass_download | Download the file identified in 'content-location' |
FileRefClass_show | Show |
genologicsr | genologicsr: R wrapper around the Genologics API |
get_childvalue | Retrieve the value of a child node(s) |
get_config | Retrieve a configuration value |
get_NSMAP | Retrieve the Genologics namespace map |
get_udfs | Retrieve the values of one or more udfs |
get_uri | Get a uri with option to depaginate |
has_duck | Test if duck is installed on the host platform See <URL:... |
has_rsync | Test if rsync is installed on the host platform Perhaps silly... |
has_scp | Test if scp is installed on the host platform Perhaps silly... |
InputOutputMapRefClass-class | An Input-Output-Map representation that subclasses from... |
InputOutputMapRefClass_DELETE | DELETE is disallowed for artifacts |
InputOutputMapRefClass_GET | GET is disallowed for input-output-map |
InputOutputMapRefClass_POST | POST is disallowed for input-output-map |
InputOutputMapRefClass_PUT | PUT is disallowed for input-output-map |
InputOutputMapRefClass_show | Show |
InstrumentRefClass_POST | POST is disallowed for instruments |
InstrumentRefClass_PUT | PUT is disallowed for instruments |
is_exception | Test XML::xmlNode or NodeRefClass is an exception |
is_xmlNode | Test if an object inherits from XML::XMLAbstractNode |
LabRefClass-class | A Lab/Account representation that subclasses from... |
Lims | Instantiate a LimsRefClass object |
LimsRefClass_ATTACH | ATTACH a file - not really a RESTful action but a combination... |
LimsRefClass_batchcreate | Create one or more Nodes (samples, containers only) |
LimsRefClass_batchretrieve | Get one or more nodes by uri by batch (artifacts, files,... |
LimsRefClass_batchupdate | Update one or more Nodes (artifacts, samples, containers... |
LimsRefClass_BROWSE | BROWSE a URI in a browser if in interactive session |
LimsRefClass_check | Verify a response and return xmlNode, possible an exception... |
LimsRefClass-class | Reference class for Lims instance |
LimsRefClass_create_exception | Create an exception node |
LimsRefClass_DELETE | DELETE a resource |
LimsRefClass_GET | GET a resource, a wrapper around get_uri |
LimsRefClass_get_artifactgroups | Get artifact group(s) in the system |
LimsRefClass_get_artifacts | Get one or more artifacts using queries on name, type,... |
LimsRefClass_get_byLimsid | Retrieve a resource by limsid |
LimsRefClass_get_containers | Get one or more containers by name, state, etc |
LimsRefClass_get_containertypes | Get the container type(s) in the system |
LimsRefClass_get_fields | Get one or more fields (UDF) as Nodes |
LimsRefClass_get_instruments | Retrieve a list of InstrumentRefClass or data.frame of the... |
LimsRefClass_get_labs | Get one or more Labs - does not leverage /batch/retrieve... |
LimsRefClass_get_max_requests | Retrieve the max requests value by name |
LimsRefClass_get_or_create_containers | Get or create containers by name and type |
LimsRefClass_get_processes | Get one or more Processes - does not leverage /batch/retrieve... |
LimsRefClass_get_processtypes | Get one or more process-types as Nodes |
LimsRefClass_get_projects | Get one or more Projects - does not leverage /batch/retrieve... |
LimsRefClass_get_researchers | Retrieve a list of ResearcherRefNodes or a data.frame of the... |
LimsRefClass_get_samples | Get one or more samples using queries on name, projectlimsid,... |
LimsRefClass_get_workflows | Retrieve a list of WorkflowRefClass |
LimsRefClass_LIST | LIST the URI's a resource with qualifiers |
LimsRefClass_name_host | Modify the URL provided to point to the named server |
LimsRefClass_POST | POST a resource |
LimsRefClass_PUSH | PUSH a file - not really a RESTful action but a combination... |
LimsRefClass_PUT | PUT a resource |
LimsRefClass_set_max_requests | Set the max requests value by name |
LimsRefClass_show-Sample | Print a pretty summary |
LimsRefClass_uri | Build a uri staring with the baseuri |
LimsRefClass_userpwd | Retrieve the user and password |
LimsRefClass_validate_session | Validate the session by testing the version |
list_resource | List URIs in a resource such as samples or containers. |
NodeRefClass_add_namespaces | Add namespaces to the XML::xmlNode as required - useful... |
NodeRefClass_ATTACH | ATTACH a file to this node |
NodeRefClass_BROWSE | BROWSE this node in a browser if in interactive session |
NodeRefClass-class | The root class that wraps XML::xmlNode |
NodeRefClass_DELETE | DELETE this node |
NodeRefClass_GET | GET an update of this node |
NodeRefClass_get_attached_files | Retrieve the attached file associated with an entity |
NodeRefClass_get_childv | Get the value of the value of a child or "" |
NodeRefClass_get_field | Get the contents of a UDF field |
NodeRefClass_get_limsid | Retrieve the limsid (if any) |
NodeRefClass_get_type | Get the value of the type field or "" |
NodeRefClass_get_udfs | Extract the UDFs into a list of udf vectors each with 'name',... |
NodeRefClass_has_child | Determine if this node has a child, test by name of... |
NodeRefClass_has_lims | Determine if http transactions (GET, PATCH, POST, HEAD, PUT,... |
NodeRefClass_new | Called when the object is instantiated. NodeRefClass is a... |
NodeRefClass_POST | POST this node |
NodeRefClass_PUT | PUT this node |
NodeRefClass_required_namespaces | Return a character vector of required namespace names |
NodeRefClass_set_udfs | Set the value of the value of one or more UDF children. If... |
NodeRefClass_show | Show the contents |
NodeRefClass_toString | Convert the XML node to string |
NodeRefClass_unames | Retrieve a vector of unique child names |
NodeRefClass_update | Update the node information |
parse_node | Convert a node to an object inheriting from NodeRefClass |
plural | Convert to plural from singular |
ProcessRefClass-class | An Process representation that sublcasses from NodeRefClass |
ProcessRefClass_date_run | Retrieve the date run as string or POSIXct |
ProcessRefClass_get_artifacts | Get either the input or the output artifacts (or both!) as... |
ProcessRefClass_get_file_artifacts | Retrieve file artifacts (either input, output or both) - very... |
ProcessRefClass_get_inputoutputmap | Get the input-output-maps as InputOutputMapRefClass or a... |
ProcessRefClass_get_parent_process | Get the parent_process assocated with this process |
ProcessRefClass_get_type | Retrieve the process type, overrides NodeRefClass_get_type |
ProcessRefClass_instrument | Retrieve instrument information (if any) |
ProcessRefClass_show | Show |
ProcessRefClass_technician | Retrieve the technican "First Last" name |
ProcessTypeRefClass-class | A Processtype representation that subclasses from... |
ProcessTypeRefClass_get_fields | Retrieve a named list of fields |
ProcessTypeRefClass_get_inputs | Retrieve a named list of process-inputs |
ProcessTypeRefClass_get_outputs | Retrieve a named list of process-output |
ProjectRefClass-class | A Project representation that subclasses from NodeRefClass |
ProjectRefClass_get_artifacts | Retrieve the artifacts associated with a project |
ProjectRefClass_get_containers | Retrieve the containers associated with a project |
ProjectRefClass_get_date | Retrieve a date "open", "close" or "invoice" |
ProjectRefClass_get_researcher | Retrieve the Researcher assigned to the project |
ProjectRefClass_get_samples | Retrieve the samples associated with a project |
ProjectRefNode_DELETE | DELETE is disallowed for Project |
ProjectRefNode_POST | POST is disallowed for projects - although see this... <URL:... |
ProjectsRefClass-class | A Projects representation that subclasses from NodeRefClass... |
ProjectsRefClass_DELETE | DELETE is disabled for ProjectsRefNodes |
ProjectsRefClass_get_projects | Retrieve a list of projects |
ProjectsRefClass_get_projects_uri | Retrieve a list of project uri |
ProjectsRefClass_PUT | PUT is disabled for ProjectsRefNodes |
ProtocolRefClass-class | A Protocol representation that sublcasses from NodeRefClass |
read_config | Read a configuration file |
ResearcherRefClass-class | A Researcher representation that sublcasses from NodeRefClass |
ResearcherRefClass_DELETE | Override the DELETE method to push user to use the GUI |
ResearcherRefClass_get_credentials | Get the credentials as a string. If the researcher is... |
ResearcherRefClass_get_lab | Get the lab uri or LabRefClass |
ResearcherRefClass_get_name | Get the user's First Last name (overrides... |
ResearcherRefClass_get_username | Get the user's username |
ResearcherRefClass_POST | Override the POST method to push user to use the GUI |
ResearcherRefClass_show | Show |
ResearcherRefClass_update | Update the object fields |
rsync_download | Download a file using rsync - rsync and then rename |
rsync_upload | Upload a local file using rsync. |
SampleRefClass-class | A Sample representation that subclasses from NodeRefClass |
SampleRefClass_get_all_artifacts | Get ALL associated artifacts. This can be painfully slow and... |
SampleRefClass_get_artifact | Get artifact as uri or Node. It is possible that... |
SampleRefClass_get_biosource | Get Biosource description |
SampleRefClass_get_container | Get the sample container as uri or NodeRefClass |
SampleRefClass_get_location | Get location as 'containerName_placement' |
SampleRefClass_get_project | Get project as uri or Node |
SampleRefNode_DELETE | DELETE is disallowed for samples |
SampleRefNode_POST | POST is disallowed for samples |
SampleRefNode_show | Show |
scp_download | Download a file using scp |
scp_upload | Upload a file using scp. |
set_udfs | Set one or more UDF fields in an xmlNode. |
singular | Convert to singular from plural |
split_vector | Split a vector into groups of MAX (or possibly fewer) |
StageRefClass-class | A Stage representation that sublcasses from NodeRefClass |
StageRefClass_get_protocol | Get the protocol as uri or Node |
StageRefClass_get_step | Get the Step as uri or Node |
StageRefClass_get_workflow | Get the workflow as uri or Node |
StepRefClass-class | A Step representation that sublcasses from NodeRefClass |
trimuri | Split a uri around the "?" or other character. For example,... |
try_GET | Get a uri with option to retry up to 'tries' times. Useful... |
udf_type2R | Retrieve a named vector of UDF types to R types |
unames | Return a vector of unique names from a objeect. The object... |
WorkflowRefClass-class | A Workflow representation that sublcasses from NodeRefClass |
WorkflowRefClass_get_protocols | Get one or more protocols |
WorkflowRefClass_get_stages | Get one or more stages |
xml_atts | Extract the attributes from a simple XML::xmlNode object |
xml_name | Extract the name from a simple XML::xmlNode object |
xml_string | Convert XML::xmlNode or NodeRefClass to character |
xmlString | Convert XML::xmlNode or NodeRefClass to character |
xml_value | Extract the value from a simple XML::xmlNode object |
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