| 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... |
| 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. |
| make_remote_directory | Make a remote directory specified by a URL using 'cp', 'scp'... |
| 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...... |
| 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 |
| remote_directory_exists | Test if a remote directory exists |
| 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 |
