From d258d070c16aa75a36c1141640688323959a7100 Mon Sep 17 00:00:00 2001 From: wow-such-code Date: Wed, 30 Oct 2024 21:08:06 +0100 Subject: [PATCH] upate readme, rename property files, provide examples --- README.md | 30 ++++++++- dataset_type_to_asset_type.properties | 3 + experiment_type_to_assay_class.properties | 2 + experiment_type_to_assay_type.properties | 1 + openbis_datatype_to_seek_attributetype.xml | 64 +++++++++++++++++++ .../qbic/model/OpenbisSeekTranslator.java | 4 +- 6 files changed, 101 insertions(+), 3 deletions(-) create mode 100644 dataset_type_to_asset_type.properties create mode 100644 experiment_type_to_assay_class.properties create mode 100644 experiment_type_to_assay_type.properties create mode 100644 openbis_datatype_to_seek_attributetype.xml diff --git a/README.md b/README.md index 460a317..eedc8cc 100644 --- a/README.md +++ b/README.md @@ -183,7 +183,7 @@ address) and their password, have to be provided. In order to interact with openBIS (transfer of data and metadata), the respective credentials need to be provided, as well. -**Everything but the passwords can be provided via the config file (config.txt):** +**Everything but the passwords can be provided via the config file (e.g. config.txt):** * as=https://my-openbis-instance.de/openbis/openbis * dss=https://my-openbis-instance.de/datastore_server @@ -204,6 +204,34 @@ section **Transferring Sample Types to SEEK**). * seek_openbis_sample_title=openBIS Name +In order to create certain objects in SEEK, user-provided mappings need to be provided via property +files placed in the same folder as the .jar. These are: + +**experiment_type_to_assay_class.properties** + +Here, openBIS experiment type codes are mapped to the assay class needed to create assay objects in +SEEK. Example entries: + + PARAMETER_ESTIMATION=EXP + MASS_SPECTROMETRY_EXPERIMENT=EXP + +**experiment_type_to_assay_type.properties** + +Here, openBIS experiment type codes are mapped to the assay type property needed to create assay +objects in SEEK. Example entry: + + MASS_SPECTROMETRY_EXPERIMENT=http://jermontology.org/ontology/JERMOntology#Proteomics + +Other fitting assay types can be found using the JERM ontology browser: +https://bioportal.bioontology.org/ontologies/JERM/?p=classes&conceptid=http%3A%2F%2Fjermontology.org%2Fontology%2FJERMOntology%23Experimental_assay_type&lang=en + +**dataset_type_to_asset_type.properties** + +Here, openBIS dataset type codes are mapped to the asset type created in SEEK. Example entries: + + SOURCE_CODE=documents + UNKNOWN=data_files + Refer to the help of the respective command or the examples below for more details. ### Transferring Sample Types to SEEK diff --git a/dataset_type_to_asset_type.properties b/dataset_type_to_asset_type.properties new file mode 100644 index 0000000..44bb45f --- /dev/null +++ b/dataset_type_to_asset_type.properties @@ -0,0 +1,3 @@ +SOURCE_CODE=documents +UNKNOWN=data_files +TEST_DAT=data_files diff --git a/experiment_type_to_assay_class.properties b/experiment_type_to_assay_class.properties new file mode 100644 index 0000000..a37900e --- /dev/null +++ b/experiment_type_to_assay_class.properties @@ -0,0 +1,2 @@ +PARAMETER_ESTIMATION=EXP +MASS_SPECTROMETRY_EXPERIMENT=EXP diff --git a/experiment_type_to_assay_type.properties b/experiment_type_to_assay_type.properties new file mode 100644 index 0000000..5ee82f3 --- /dev/null +++ b/experiment_type_to_assay_type.properties @@ -0,0 +1 @@ +MASS_SPECTROMETRY_EXPERIMENT=http://jermontology.org/ontology/JERMOntology#Proteomics diff --git a/openbis_datatype_to_seek_attributetype.xml b/openbis_datatype_to_seek_attributetype.xml new file mode 100644 index 0000000..0a29815 --- /dev/null +++ b/openbis_datatype_to_seek_attributetype.xml @@ -0,0 +1,64 @@ + + + + 4 + Integer + Integer + + + 8 + String + String + + + 7 + Text + Text + + + 3 + Real number + Float + + + 1 + Date time + DateTime + + + 16 + Boolean + Boolean + + + 8 + String + String + + + 8 + String + String + + + 8 + String + String + + + 7 + Text + Text + + + 5 + Web link + String + + + 2 + Date time + Date + + + diff --git a/src/main/java/life/qbic/model/OpenbisSeekTranslator.java b/src/main/java/life/qbic/model/OpenbisSeekTranslator.java index 7ae298b..482cf23 100644 --- a/src/main/java/life/qbic/model/OpenbisSeekTranslator.java +++ b/src/main/java/life/qbic/model/OpenbisSeekTranslator.java @@ -138,9 +138,9 @@ public SeekStructure translateForRO(OpenbisExperimentWithDescendants experiment, */ private void parseConfigs() throws IOException, ParserConfigurationException, SAXException { final String dataTypeToAttributeType = "openbis_datatype_to_seek_attributetype.xml"; - final String datasetToAssaytype = "dataset_type_to_assaytype.properties"; + final String datasetToAssaytype = "dataset_type_to_asset_type.properties"; final String experimentTypeToAssayClass = "experiment_type_to_assay_class.properties"; - final String experimentTypeToAssayType = "openbis_experiment_type_to_seek_assaytype.properties"; + final String experimentTypeToAssayType = "experiment_type_to_seek_assay_type.properties"; this.experimentTypeToAssayType = PropertyReader.getProperties(experimentTypeToAssayType); this.datasetTypeToAssetType = PropertyReader.getProperties(datasetToAssaytype); this.experimentTypeToAssayClass = PropertyReader.getProperties(experimentTypeToAssayClass);