Metadata-Version: 2.1
Name: scingestor
Version: 0.12.0
Summary: Scientific Catalog Tools
Home-page: http://github.com/jkotan/scingestor
Author: ('Jan Kotanski',)
Author-email: jankotan@gmail.com
Maintainer: Jan Kotanski
Maintainer-email: jankotan@gmail.com
License: GNU GENERAL PUBLIC LICENSE, version 3
Description: # Scicat Dataset Ingestor
        
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        The `scingestor` python package provides a support for scripts which ingest Datasets and OrigDatablocks into the SciCat metadata server.
        
        ## scicat_dataset_ingestor
        SciCat Dataset ingestor server ingests scan metadata just after a scan is finished. It can be executed by
        
        ```
        scicat_dataset_ingestor -c ~/.scingestor.yaml
        ```
        ### Configuration variables
        The configuration written in YAML can contain the following variables
        * **scicat_url** *(str)* , default: `"http://localhost:3000/api/v3"`
        * **ingestor_credential_file** *(str)* , default: `None`
        * **beamtime_dirs** *(list\<str\>)* , default: `[]`
        * **beamtime_base_dir** *(str)* , default: `""`
        * **ingestor_var_dir** *(str)* , default: `""`
        * **ingestor_username** *(str)* , default: `"ingestor"`
        * **dataset_pid_prefix** *(str)* , default: `""`
        * **dataset_update_strategy** (`"no"`, `"patch"`, `"create"`, `"mixed"`) , default: `"patch"`
        * **relative_path_in_datablock** *(bool)* , default: `False`
        * **scandir_blacklist** *(list\<str\>)* , default: `["/gpfs/current/scratch_bl", "/gpfs/current/processed", "/gpfs/current/shared"]`
        * **beamtimeid_blacklist_file** *(str)* , default: `None`
        * **beamtime_type_blacklist** *(list\<str\>)* , default: `["P"]`
        * **chmod_json_files** *(str)* , default: `None`
        * **max_scandir_depth** *(int)*, default: `-1`
        * **oned_in_metadata** *(bool)* , default: `False`
        * **force_measurement_keyword** *(bool)* , default: `True`
        * **max_oned_size** *(int)* , default: `None`
        * **scan_metadata_postfix** *(str)* , default: `".scan.json"`
        * **datablock_metadata_postfix** *(str)* , default: `".origdatablock.json"`
        * **attachment_metadata_postfix** *(str)* , default: `".attachment.json"`
        * **metadata_in_var_dir** *(bool)* , default: `False`
        * **use_corepath_as_scandir** *(bool)* , default: `False`
        * **beamtime_filename_postfix** *(str)* , default: `"beamtime-metadata-"`
        * **beamtime_filename_prefix** *(str)* , default: `".json"`
        * **datasets_filename_pattern** *(str)* , default: `"scicat-datasets-{beamtimeid}.lst"`
        * **ingested_datasets_filename_pattern** *(str)* , default: `"scicat-ingested-datasets-{beamtimeid}.lst"`
        * **file_dataset_metadata_generator** *(str)* , default: `"nxsfileinfo metadata -k4  -o {metapath}/{scanname}{scanpostfix}  -b {beamtimefile} -p {beamtimeid}/{scanname}  -w {ownergroup} -c {accessgroups} {mastefile}"`
        * **dataset_metadata_generator** *(str)* , default: `"nxsfileinfo metadata -k4  -o {metapath}/{scanname}{scanpostfix}  -c {accessgroups} -w {ownergroup} -b {beamtimefile} -p {beamtimeid}/{scanname}"`
        * **datablock_metadata_generator** *(str)* , default: `"nxsfileinfo origdatablock  -s *.pyc,*{datablockpostfix},*{scanpostfix},*~  -p {pidprefix}{beamtimeid}/{scanname}  -w {ownergroup} -c {accessgroups} -o {metapath}/{scanname}{datablockpostfix} "`
        * **datablock_metadata_stream_generator** *(str)* , default: `"nxsfileinfo origdatablock  -s *.pyc,*{datablockpostfix},*{scanpostfix},*~  -w {ownergroup} -c {accessgroups} -p {pidprefix}{beamtimeid}/{scanname} "`
        * **datablock_metadata_generator_scanpath_postfix** *(str)* , default: `" {scanpath}/{scanname} "`
        * **attachment_metadata_generator** *(str)* , default: `"nxsfileinfo attachment  -w {ownergroup} -c {accessgroups} -o {metapath}/{scanname}{attachmentpostfix} {plotfile} "`
        * **metadata_generated_callback** *(str)* , default: `"nxsfileinfo groupmetadata  {lastmeasurement} -m {metapath}/{scanname}{scanpostfix} -d {metapath}/{scanname}{datablockpostfix} -a {metapath}/{scanname}{attachmentpostfix} -p {beamtimeid}/{lastmeasurement} -f -k4 "`
        * **metadata_group_map_file** *(str)* , default: `""`
        * **raw_metadata_callback** *(bool)* , default: `False`
        * **skip_multi_datablock_ingestion** *(bool)* , default: `False`
        * **skip_multi_attachment_ingestion** *(bool)* , default: `False`
        * **skip_scan_dataset_ingestion** *(bool)* , default: `False`
        * **call_metadata_generated_callback** *(bool)* , default: `False`
        * **metadata_group_map_file_generator_switch** *(str)* , default: `" --group-map-file {groupmapfile} "`
        * **raw_metadata_callback_switch** *(str)* , default: `" --raw "`
        * **execute_commands** *(bool)* , default: `False`
        * **plot_file_extension_list** *(list\<str\>)* , default: `["png", "nxs", "h5", "ndf", "nx", "fio"]`
        * **master_file_extension_list** *(list\<str\>)* , default: `["nxs", "h5", "ndf", "nx", "fio"]`
        * **chmod_generator_switch** *(str)* , default: `" -x {chmod} "`
        * **relative_path_generator_switch** *(str)* , default: `" -r {relpath} "`
        * **oned_dataset_generator_switch** *(str)* , default: `" --oned "`
        * **max_oned_dataset_generator_switch** *(str)* , default: `" --max-oned-size {maxonedsize} "`
        * **override_attachment_signals_generator_switch** *(bool)* , default: `" --override "`
        * **hidden_attributes_generator_switch** *(str)* , default: `" -n {hiddenattributes} "`
        * **hidden_attributes** *(str)* , default: `"nexdatas_source,nexdatas_strategy,units"`
        * **attachment_signals_generator_switch** *(str)* , default: `" -s {signals} "`
        * **attachment_axes_generator_switch** *(str)* , default: `" -e {axes} "`
        * **attachment_frame_generator_switch** *(str)* , default: `" -m {frame} "`
        * **attachment_signal_names** *(str)* , default: `""`
        * **attachment_axes_names** *(str)* , default: `""`
        * **attachment_image_frame_number** *(str)* , default: `""`
        * **ingest_dataset_attachment** *(bool)* , default: `False`
        * **override_attachment_signals** *(bool)* , default:`False`
        * **retry_failed_dataset_ingestion** *(bool)* , default:`False`
        * **retry_failed_attachement_ingestion** *(bool)* , default:`False`
        * **log_generator_commands** *(bool)* , default: `False`
        * **add_empty_units_generator_switch** *(str)* , default: `" --add-empty-units "`
        * **add_empty_units** *(bool)* , default: `True`
        * **metadata_copy_map_file** *(str)* , default: `None`
        * **metadata_copy_map_file_generator_switch** *(str)* , default: `" --copy-map-file {copymapfile} "`
        * **inotify_timeout** *(float)* , default: `0.1`
        * **get_event_timeout** *(float)* , default: `0.01`
        * **ingestion_delay_time** *(float)* , default: `5.0`
        * **max_request_tries_number** *(int)* , default: `100`
        * **recheck_dataset_list_interval** *(int)* , default: `1000`
        * **recheck_beamtime_file_interval** *(int)* , default: `1000`
        * **request_headers** *(dict\<str,str\>)* , default: `{"Content-Type": "application/json", "Accept": "application/json"}`
        * **scicat_datasets_path** *(str)* , default: `"Datasets"`
        * **scicat_proposals_path** *(str)* , default: `"Proposals"`
        * **scicat_datablocks_path** *(str)*, default: `"OrigDatablocks"`
        * **scicat_attachments_path** *(str)*, default: `"Datasets/{pid}/Attachments"`
        * **scicat_users_login_path** *(str)*, default: `"Users/login"`
        * **owner_access_groups_from_proposal** *(bool)*, default: `False`
        * **metadata_fields_without_checks** *(list\<str\>)*, default: `["techniques", "classification", "createdBy", "updatedBy", "datasetlifecycle", "numberOfFiles", "size", "createdAt", "updatedAt", "history", "creationTime", "version", "scientificMetadata", "endTime"]`
        
        e.g.
        ```
        beamtime_dirs:
          - "{homepath}/gpfs/current"
          - "{homepath}/gpfs/commissioning"
        scicat_url: http://localhost:3000/api/v3
        ingestor_credential_file: "{homepath}/gpfs/pwd"
        ```
        
        ### Pattern keywords for configuration variables
        
        The  **datasets_filename_pattern**, **ingested_datasets_filename_pattern**  and **ingestor_var_dir** can contain the *{beamtimeid}* and *{hostname}* keywords,  e.g. `"scicat-ingested-datasets-{beamtimeid}.lst"` or `"scicat-ingested-datasets-{hostname}-{beamtimeid}.lst"` which is instantiated during the ingestor execution.
        
        The  **beamtime_dirs**, **beamtime_base_dir**, **ingestor_var_dir**, **ingestor_credential_file**, **scandir_blacklist** can contain the *{homepath}* keyword.
        
        Similarly, **file_dataset_metadata_generator**, **dataset_metadata_generator**, **datablock_metadata_generator**,  **datablock_metadata_stream_generator**, **datablock_metadata_generator_scanpath_postfix**, **attachment_metadata_generator**, **chmod_generator_switch**, **relative_path_generator_switch** can contain the following keywords: *{beamtimeid}* , *{scanname}*, *{chmod}*, *{scanpath}*, *{metapath}*, *{relpath}*, *{beamtimeid}*, *{beamline}*, *{pidprefix}*, *{beamtimefile}*, *{scanpostfix}*, *{datablockpostfix}*, *{ownergroup}*, *{accessgroups}*, *{hostname}*, *{homepath}*, *{hiddenattributes}*, *{ext}*, "{masterfile}", "{plotfile}", "{masterscanname}", "{entryname}"
        
        The "{masterfile}" is either equal to   "{scanpath}/{scanname}.{ext}" or "{scanpath}/{scanname}/{scanname}.{ext}". Also
        the "{plotfile}" is either equal to  "{scanpath}/{scanname}.{plotext}" or "{scanpath}/{scanname}/{scanname}.{plotext}".
        
        
        ## scicat_dataset_ingest
        
        Re-ingestion script for SciCat Datasets and OrigDatablocks is usually launched at the end of the beamtime.
        ```
        scicat_dataset_ingest -c ~/.scingestor.yaml
        ```
        Its configuration written YAML like for `scicat_dataset_ingestor`
        
        
        ## scicat_ingest
        
        General ingestion script for SciCat Models could be used for manual scicat model ingestion, e.g. Sample, Instrument or DerivedDataset.
        ```
        scicat_ingest  -m Samples  -c ~/.scingestor.yaml  ./metadata.json
        ```
        Its configuration written YAML like for `scicat_dataset_ingestor`
        
        ## Installation
        
        ### Required packages
        
        * python3 >= 3.7
        * nxstools >= 3.38.0
        * inotifyx (python3 version)
        * requests
        * setuptools
        * pyyaml
        * pytest (to run tests)
        * sphinx (to build the documentation)
        
        
        ### Install from sources
        
        The code from https://github.com/jkotan/scingestor can be built with
        
        ```
        python3 setup.py install
        ```
        
        
        To build the documentation use
        
        ```
        python3 setup.py build_sphinx
        ```
        
        The resulting documentation can be found below `build/sphinx/html` in the root
        directory of the source distribution.
        
        Finally, the package can be tested using
        
        ```
        python3 -m pytest test
        ```
        
        ### Install in conda or pip environment
        
        The code can be installed in your conda environment by
        ```
        conda create -n myenv python=3.9
        conda activate myenv
        
        pip install inotifyx-py3
        pip install scingestor
        ```
        
        or in your pip environment by
        ```
        python3 -m venv myvenv
        . myvenv/bin/activate
        
        pip install inotifyx-py3
        pip install scingestor
        ```
        
        
        ### Debian and Ubuntu packages
        
        Debian  `bookworm`, `bullseye`, `buster`  or Ubuntu  `lunar`, `jammy`, `focal` packages can be found in the HDRI repository.
        
        To install the debian packages, add the PGP repository key
        
        ```
        sudo su
        curl -s http://repos.pni-hdri.de/debian_repo.pub.gpg  | gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/debian-hdri-repo.gpg --import
        chmod 644 /etc/apt/trusted.gpg.d/debian-hdri-repo.gpg
        ```
        
        and then download the corresponding source list, e.g.
        for `bookworm`
        
        ```
        cd /etc/apt/sources.list.d
        wget http://repos.pni-hdri.de/bookworm-pni-hdri.list
        ```
        
        or `jammy`
        
        ```
        cd /etc/apt/sources.list.d
        wget http://repos.pni-hdri.de/jammy-pni-hdri.list
        ```
        respectively.
        
        Finally,
        
        ```
        apt-get update
        apt-get install python3-scingestor
        ```
        
        ## Dataset list file content
        
        The scicat ingestor triggers its actions on append a new line in the dataset list file.
        The dataset list file is located in the scan directory and its filename is defined
        by **datasets_filename_pattern** variable, i.e. by default "scicat-datasets-{beamtimeid}.lst".
        
        By default the scan dataset metadata are fetched from the corresponding the master file with its filename given by \<scanname\>.\<ext\> where usually \<ext\> is `nxs` or `fio`. The detector files related to the particular scan are placed in the \<scanname\> subdirectory and they are added to the scan origindatablock.
        
        A separete line in the dataset list file may contain
        * scanname to ingest e.g.  `myscan_00012`
        * scanname to re-ingest with a unique identifier (timestamp), e.g. `myscan_00012:1702988846.0770347`
        * scanname and additional detector subdirectories to ingest, e.g.  `myscan_00012 pilatus1 lambda`
        * string with a  base master filename, a NXentry NeXus path and a scanname representing scan metadata from the multi-scan nexus file to ingest, e.g.  `myscan::/scan12;myscan_00012`
        * command to start a measurement with a given name which groups related scans,  e.g. `__command__ start mycalib6`
        * command to stop a measurement which groups related scans,  e.g. `__command__ stop`
        
        
        ## Measurment Datasets which group scan metadata
        
        The `__command__ start \<measurement\>` and `__command__ stop` allow to pass information to scicat ingestor which scan datasets should be grouped into the measurement dataset, i.e. by default of scan datasets between start and stop commands are grouped to the one measurement.
        
        ### Sardana Measurement macros
        
        The config/scmacros.py module provides sardana macros which help to start/stop the measurement
        * **start_measurement \<measurement\>** starts a new measurment with the given name
        * **make_measurement \<measurement\>** starts a new measurment with the given name and adds to the measurement the last scan
        * **update_measurement** updates the current measurement dataset in the SciCat database
        * **stop_measurement** updates the current measurement dataset in the SciCat database and stops the  measurement
        * **show_measurement** shows the current measurement name
        
        ### Sardana Measurement with SciCatAutoGrouping
        
        Setting the **SciCatAutoGrouping** sardana environment variable to `False` we can switch on the autogrouping mode. In this mode scan metadata is grouped automatically into the measurement dataset and the measurement dataset updated after each scan. The name of measurement is taken from the base scanname after removing ScanID, e.g. for `<scanname>` = "mycalib2_00012" the measurement name is "mycalib2"
        
Keywords: metadata catalog tools metadata photon science
Platform: Linux
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Description-Content-Type: text/markdown
