Common DFOS tools:
Documentation

make printable	new:	see also:
		OCA syntax
	v3.6.4: - DRS_TYPE=INT supported (internal parallelization, MUSE pipeline) (see here)	createAB wrapped into autoDaily, processPreImg, calChecker more reading: AB concepts, events and rules, AB structure
	v3.6.8: - OBS.START recognized just like TPL.START and ARCFILE (if used for file grouping: suppressed in PARAMS section of ABs)	databases obs_metadata..data_products for file statistics; sched_rep for SM/VM flag dfos tools uses ABbuilder; filterRaw ; related tools: processAB, updateAB, extractAB, getStatusAB output ABs in $DFO_AB_DIR; AB_list in $DFO_MON_DIR upload/download none
topics: description | fits files vs headers | incremental mode | completeness check | AB re-creation | architecture | assoc logs and ATAB files | output | usage | configuration | cascade | workflow | operations

createAB

Description

This tool creates association information and stores it in Association Blocks (ABs). It forms the central part of the daily workflow. Find its place in the workflow here. Find a general description of the Association Block concepts here.

The tool uses ABbuilder as central association engine. That tool uses the OCA framework, which is software developed by SEG for the purpose of Organization, Classification and Association of data. Other dfos tools making use of this framework are filterRaw and calChecker.

The tool works on a pool of raw hdr data defined by <DATE> and expected to be found under $DFO_HDR_DIR/$DATE.

It has two fundamental modes:
   - CALIB for calibration data,
   - SCIENCE for science data.

createAB is executed on a selected DATE. It also has an incremental mode working for an incomplete date, used for the incremental processing scheme implemented with autoDaily. More about operational modes here.

Apart from ABs, createAB also creates a text file AB_list_<MODE>_<DATE> under $DFO_MON_DIR. This is the list of created ABs, sorted by the proper execution sequence. That list is fundamental for the daily workflow steps following createAB.

The tool has three TOOL_MODES:

• AUTO (no interaction required); this is the standard mode
• WARN (asks for interaction when a warning is found); this mode is useful for command-line execution
• INTER (fully interactive).

The option -a can be used to override the configured value and enforce running in AUTO mode, which is useful if createAB itself is wrapped in automatic control tools like autoDaily or processPreImg.

Per configuration, the filter tool filterRaw can be called (in mode FILTER) before ABs are created. All filtered files will be hidden before AB creation. So they won't spoil your VCAL list, nor produce any AB. If required, they can be inspected under ${HIDE_DIR}/<date>.

Fits files vs. headers. Historically, the tool was executed on fits files. The entire information needed for ABs is available in the headers of these files. With the implementation of the on-line data transfer, all header and fits files were delivered incrementally. In this situation the execution of createAB on fits files became obsolete, and hence has been terminated at the end of 2012.

Incremental mode. This option is designed for the fast data transfer. It is triggered by the option -i and available for mode=CALIB. If set, the tool will first look for already existing CALIB ABs for the specified date. Under certain conditions, it will then move all raw header files listed in these ABs (RAWFILE section) to a temporary directory, and will associate only the remaining headers. The conditions are:

• TRY_AGAIN_INCOMPLETE=YES: headers listed in complete ABs are not associated again
• TRY_AGAIN_FAILED=YES: headers listed in successfully executed ABs are not associated again

In other words, usually only new headers, and headers from incomplete or failed ABs, will be exposed to createAB, all others will not create again (and not process either). If the above configuration keys are set to NO, only new headers will be used for AB creation. Thereby AB creation and processing can be triggered once per hour, minimizing processing delays and avoiding unnecessary multiple AB creation. Using this option in routine operations requires a properly configured autoDaily (ENABLE_INCREM=YES).

No VCALs. With the option -N, the tool uses only certified and renamed master calibrations (MCALs) for association, no virtual calibrations (VCALs). It is available for mode=SCIENCE only. This is a stronger association constraint than the configurable flag SCI_VIRT_MCAL which gives only a warning in case of VCALs being associated. It is available on the command-line or by configuration of the dfoMonitor (CREATEAB_VCAL=YES).

Completeness checks

In mode SCIENCE, a completeness check is made between the raw files as extracted from the science ABs, and the science raw files as extracted from data_products. In case of a difference, it raises an alert (email and command-line).That difference would have the consequence that the corresponding science ABs could not be harvested. It would be caused by an OCA configuration inconsistency or incompleteness.

Re-creation of ABs. The tool offers support for the re-creation of ABs. This might become of interest if

• virtual calibration products required for an AB did not process well, hence that AB failed but could be saved with another association (use case "failed")
• virtual calibration products required for an AB were rejected, hence that AB is invalid and must be created again with another association (use case "invalid")
• the association rules, or recipe parameters, must be modified for an AB, hence that AB must be processed again (use case "OCA")

For AB re-creation the tool is called with option -r (recreate, or reprocess). Before calling, the user has to prepare the environment. The exact measures depend on the use case:

• clean up VCAL directory, to get rid of associations to unwanted virtual products. This step is offered within certifyProducts if an AB is rejected, but not if an AB failed: then the user must take care of deletion (use cases failed, invalid).
• hide a bad raw file header, to avoid unwanted associations: if a certain raw file is part of the cascade, it would create unwanted ABs and unwanted virtual calibrations as soon as createAB is called again. Either you hide a header manually (move it somewhere else and move it back later), or use filterRaw and hideFrames to do it in the proper way (use cases failed, invalid).
• clean up MCAL directory and NGAS: this is necessary if an unwanted real product has already been certified, moved, renamed and archived. This might happen if a quality issue is detected at some later point. These steps are not supported by dfos tools, except for NGAS deletion with cdbDelete (use case invalid).
• If you want to create and process all ABs for a given date, you actually do not need the re-creation mode since it is designed for interactive AB selection (use case OCA).

In re-creation mode the tool goes through the standard workflow but has certain additional parts with dialogues marked by "[RECREATE]". These are interactive by design. For better distinction, you may want to call the option '-a' in addition, thereby forcing the tool to be interactive only in the re-creation parts. You can do the call on the command line, or use the interactive call on the AB monitor ("recreate ABs") which is more comfortable.

After having created all ABs for the specified date and mode, a window pops up with the complete AB list and you are prompted for the AB selection. This is an editor session, with your favorite editor as configured in config.createAB, in the key RECREATE_EDITOR. Mark your selection by a leading 'R<blank>', e.g.:

You do not need to care about hidden dependencies, just select the ABs you know you want to reprocess. Next, the tool analyses dependencies. Dependent ABs are those that are using products from a selected one. The tool displays all selections and dependencies in a second interactive editor session:

At that stage you could also remove selections or dependencies, but removing dependencies usually makes no sense.

After the prompt, the tool creates a new AB list called AB_list_<mode>_<date>_recreate. As the last step, createAB then calls createJob (this step is different from normal execution!) because this needs to be done with a special syntax: createJob -m <mode> -d <date> -r <job_ID> where job_ID is <mode>_<date>_recreate, thereby creating the usual job files execAB etc. with suffix _recreate, containing only the selected ABs. This is a mechanism to protect any standard job file which might exist and contain the complete list. These job files are written into the standard JOBS_NIGHT, at which point the tool stops, leaving the execution of JOBS_NIGHT to the user. The jobs will execute as normal and will deliver the usual products which are then available for review together with any other pre-existing products.

[click to enlarge]

Architecture. The tool is a shell-script wrapper calling the DFS tool ABbuilder. createAB provides all functionality which is specific to DFO while ABbuilder is the central engine largely independent of DFO-specific settings. Strictly speaking ABbuilder again is a shell-script wrapper around a central java application:

Association logs. createAB displays the association log to the console, and also into separate text files. These come per AB, have the same root name and the extension .alog, and are found under $DFO_AB_DIR. In particular they contain all associated MCALIBs/MASSOCs, their DELTA_T values, the configured DELTA_T values (validity), plus warnings: warnings if the configured threshold value has been violated, warnings if a required mcalib could not be found, and warnings if a SCIENCE AB has virtual calibrations associated (if keys SCI_VIRT_MCAL | SCI_VIRT_MASS configured as YES). These entries are scanned by the AB monitor tool getStatusAB and get displayed.

ATAB files (or tab files). These are text files with one line in tabular form (hence their name). Their name is <AB_ROOT>.tab. They contain the complete information about a particular AB as displayed on the AB monitor. It has 33 entries, like e.g. processing status, display color, execution time, HC flag, name of processing log, score results. Each of these ATAB files is generated by createAB, and then updated throughout the workflow by the various tools (processAB, processQC, certifyProducts, harvestAB). At any stage in the workflow, the tool getStatusAB can read the tabular information and transform it directly into HTML code, without further queries for information. This is a very fast way for displaying the actual AB monitor, and very efficient since information is only updated when needed, not every time when the tool getStatusAB is called.

ATAB files are created and maintained in $DFO_AB_DIR along with the ABs, and then move to their final destination $DFO_LOG_DIR/$DATE. They are not exported to qcweb since their only value is technical (speed up the AB monitor). They do not contain any information beyond the ABs and format information for the AB monitor.

Output

The tool creates the following output:

• ABs under $DFO_AB_DIR (extension .ab)
• AB logs under $DFO_AB_DIR (extension .alog)
• a list of ABs, $DFO_MON_DIR/AB_list_<MODE>_<DATE>, read by other tools supporting ABs

How to use

Type createAB -h | -H | -v for on-line help about createAB / ABbuilder, and version,

createAB -m CALIB -d 2006-12-30

to create ABs for mode CALIB and date 2006-12-30;

createAB -m SCIENCE -d 2006-10-30 -c test_config.createAB

to create ABs for mode SCIENCE and date 2006-10-30, with a non-standard config file test_config.createAB (mcalib pool is defined by $N_MCAL_LIST and the latest date in $DFO_CAL_DIR, which usually is the one from -d or a few days later);

createAB -m SCIENCE -d 2006-10-30 -D 2006-11-02

to create ABs these ABs with a pool of mcalib files starting at date 2006-11-02 and going backwards by $N_MCAL_LIST days as configured;

createAB -m CALIB -d 2010-09-30 -i

to create CALIB ABs incrementally, i.e. only if they are did not exist before;

createAB -m CALIB -d 2010-09-30 -r [ -a ]

for re-creation of selected ABs.

Status

The tool writes the status values cal_AB or sci_AB into DFO_STATUS. It also writes a timestamp into each created AB, and creates association log files under $DFO_AB_DIR which are scanned by getStatusAB and distributed together with the ABs.

Configuration files

The tool has a configuration which is somewhat more complex than for most other DFOS tools. All relevant configuration is kept under $DFO_CONFIG_DIR/OCA/:

• config.createAB which has the createAB tool configuration
• OCA_macro.h: general macros
• <instr>_macro.h: instrument specific macros ( <instr> is short for $DFO_INSTRUMENT)
• log4j.cf which is a java logging configuration file
• a set of config files in OCA syntax:
  • <instr>_classification.h : all classification configuration
  • <instr>_organisation.h: all organization configuration
  • <instr>_association.h: all association configuration
  • <instr>.h: all include information (auto-created by the tool, listed here for completeness

Find here more details about the OCA syntax.

The user may want to specify a non-standard config file by using the -c option (the standard one being config.createAB), e.g. to handle pre-imaging association in addition to standard DFO association. That file must also reside under $DFO_CONFIG_DIR/OCA.

The DFOS configuration file config.createAB has the following structure:

Cascade configuration

The configuration of the cascade follows the matrix scheme which has from left to right all raw types in their logical sequence, and from top to bottom the process flow from raw to product, involving the grouping rule, the recipe, the required input mcalibs and the predicted products. The classification defines the raw types and is configured in <instr>_classification.h. The grouping rules are configured in <instr>_organisation.h. The association rules are configured in <instr>_association.h.

There are currently the following cascade types supported by createAB:

• classical "simple" cascade: one raw_type, one action
• cascade with multiple actions: one raw_type, two actions
• cascade with parent-child actions: one raw_type triggers one action, second action is triggered by products of the first action (not by a raw_type)

Not supported types are e.g. cascades with raw data from different nights or different OBs.

Simple cascade: one action per raw_type

The classical cascade is configured by one entry block per raw_type, in each of the OCA config files. The sequence of raw_type definition is evaluated by the tool and should reflect the processing sequence (left to right ordering).

Cascade with multiple actions

An example for that type could be jittered science observations: create and process an AB per single raw file first, e.g. in order to derive QC information. Then create and process an AB per TPL set, in order to create the de-jittered product. Both actions are triggered by the same raw_type.

That cascade is configured in the same way as the simple cascade. In addition, the second action for a given raw_type is entered by additional blocks in the OCA config files.

Cascade with step1-step 2 ABs ("parent-child ABs")

In step1, all raw input STD files create corresponding ABs (step1 or parent ABs). The products of those (here called 'single_zp', typically all per setup from the night) are then combined in another (step2, child) AB which has no input raw files and produces a single night_zp product.

That case cannot be handled in the classical, raw-type driven way. It is configured in config.createAB using the PROD_STEP2 key. The second action is then entered as corresponding blocks in the OCA config files.

If PROD_STEP2 is set, the tool calls ABbuilder twice:

• first, it calls ABbuilder with the purpose to create the parent (step1) ABs and from them the virtual calibration products (single_zp in the above example). These are then copied into $RAW_DIR, with extension .HDR. Thereby they become 'pseudo-raw files' which the tool then can handle in the standard way.
• second, it calls ABbuilder in the usual way. Now the input directory contains all input file information (raw and pseudo-raw) and can create both parent and child ABs.

The HDR files are deleted afterwards. This mechanism works both for hdr and fits input files.

Workflow description

1. Filter input data pool
- if FILTER_RAW=YES: call filterRaw -m FILTER -H, to remove the found files from further processing. Corresponding headers are also moved, but moved back to their original folder at the end.

2. Pre-compile all OCA configuration files into a final <instr>.RLS file (using gcc)

3. Prepare links under $DFO_CAL_DIR/MCAL to all mcalibs as defined by $N_MCAL_LIST and the latest date in $DFO_CAL_DIR. If option -D <SCANDATE> has been set, the set is defined by this start date instead. Supported are both fits and hdr files in $DFO_CAL_DIR.

4. Only if PROD_STEP2 is set:

4.1 call ABbuilder to create virtual product headers; call PGI_PREPROC if configured
4.2 copy the virtual product headers as .HDR files into RAW_DIR; no ABs are created at that step

5. Only with option -i (incremental) and mode=CALIB:

5.1 check for pre-existing ABs
5.2 move their headers to temporary space, unless INCOMPLETE (if TRY_AGAIN_INCOMPLETE=YES) or FAILED (if TRY_AGAIN_FAILED=YES)
5.3 have only new headers in input data pool, plus the ones from step 5.2

6. Call ABbuilder:

6.1 Classify input data pool
- read fits keys as defined in <instr>_classification.h to classify each raw file into RAW_TYPE | DO_CLASS. (Note: PACK_DIR is obsolete and can be removed.)

6.2 Organize input data into groups
- get raw match keys from <instr>_organisation.h
- get grouping rules (e.g. SINGLE, TPL_A, TPL_D etc.)

6.3 Find association per group, reading rules in <instr>_association.h
- evaluate MCALIB file match keys to find all calibration products required for processing
- evaluate MASSOC match keys to find additional mcalib files (if any) useful for packing
- evaluate RASSOC match keys to find associated raw files (if any) useful for packing
- find recipe, recipe parameter
- find WAITFORs for CONDOR (from associated virtual calibrations)
- set the AB status to 'created'

6.4 Create the ABs in a work directory ($DFO_AB_DIR/TMP)
- call PGI_PREPROC if configured

6.5 Add virtual calibrations as predicted from the ABs to $DFO_CAL_DIR/VCAL

7A. (normal operations, including incremental mode):
Verify the ABs (ordered in a cascade as configured in <instr>_classification.h)

- scan for COMPLETE/INCOMPLETE flag
- create and display the association log (includes all found MCALIB/MASSOC with their DELTA_T values, and all missing ones)
- create the .tab files for speedy AB monitor page
- edit the RAW_MATCHKEY section to suppress UNDEFINED entries (typical of mutually exclusive keys e.g. in VIMOS or FORS2)
- for SCIENCE only: check if MCALIBs and MASSOCs have VIRTUAL calibrations (flag as *NOK)
- if configured (TOOL_MODE=INTER/WARN), ask the user what to do in case of incomplete ABs
- creates the list of all created ABs
-
- move ABs and AB logs to $DFO_AB_DIR

7B. (RECREATE=YES): same as 7A, plus

- offer the created ABs and let the user decide which ones to select
- create the list of ABs on the selected ones and the ones depending on them
- move only those to $DFO_AB_DIR, the other ones are deleted

8A. (normal operations) After AB creation:

- if step 5 was applied (incremental mode), move all headers back to $DFO_HDR_DIR/$DATE
- apply PGI_POSTPROC if configured
- create directories in $DFS_PRODUCT
- manage the set of virtual calibrations (headers in $DFO_CAL_DIR/VCAL): remove outdated ones (defined by $N_VCAL_LIST)
- move back hidden headers to $DFO_HDR_DIR/$DATE

8B. (RECREATE=YES): same as 8A, plus

- call createJob and create the job files for the selected set of ABs (the job files come with suffix _recreate)

9. call PGI_FINAL if configured

Operational hints

• The incremental mode is the standard mode for calibrations of all instruments
• It complies with other parallel activities like e.g. scheduled jobs in JOBS_NIGHT (inc. processing other ABs, QC reporting etc.). This just increases the load on the machine but does not break anything.
  
• In MODE=SCIENCE, all files with OBS_PROG_ID starting with 60. or 060. are filtered (not accepted) (unless ACCEPT_060=YES).
• You can use CAL_N_MCAL_LIST to have different calibration memory depths for CALIB and for SCIENCE (which may make sense but is normally not required)
  
• You can call three plugins, one (PGI_PREPROC) directly after calling ABbuilder (works in the temporary AB directory, used e.g. to edit setup keys), one (PGI_POSTPROC) on the final ABs (after editing them and moving them to $DFO_AB_DIR), one (PGI_FINAL) just at the end. All plugins are optional. If defined, they must exist in $DFO_BIN_DIR.