Known issues

isatools v0.7 package

  • Issues #101, #153 are still outstanding, as per below
  • SRA/ENA importer and Biocrates importer relies on XSLT2 processing only available with SAXON and requires .jar file to run

isatools v0.6 package

  • Issues #146, #101, #153 are still outstanding, as per below
  • SRA/ENA importer and Biocrates importer relies on XSLT2 processing only available with SAXON and requires .jar file to run
  • We are aware that there may be some performance issues when loading and writing ISA-Tab documents with several thousand samples. This has been worked on and there is ongoing efforts to improve on the current performance of ISA-Tab I/O

isatools v0.5 package

  • All issues inherited from v0.4 (see below)
  • Currently only Python 3.4 and 3.5 is supported. Python 2.7 support is present in the py2 source branch on Github.

isatools v0.4 package

  • For certain of ISA-Tab table files, the ISA-Tab parser cannot disambiguate between process instances where a Name column is required to qualify a Protocol REF has been left blank. Utility functions have been written to detect these anomalies and to assist in correcting them, in the isatools.utils package. #146 (see detail after bullet points)
  • When converting to ISA JSON in using UUID or counter Identifier Types, some elements are not detected, such as Array_Design_REF #101
  • The ISA-Tab parser does not support reading Protein Assignment File, Peptide Assignment File, Post Translational Modification Assignment File columns, and therefore the isatab2* converters also do not support these #174
  • The SRA/ENA importer in sra2isatab relies on XSLT2 processing functionality only available with SAXON, so you must provide the JAR file yourself to use this
  • sra2isatab converter does not support SRA pools #153
  • The legacy functionality (marked in the documentation) relies on Java 1.6

To check for possible erroneous pooling events in an ISA-Tab archive, you can try something like:

>>> from isatools import utils
>>> utils.detect_isatab_process_pooling('tests/data/tab/MTBLS1/')
INFO: Converting ISA-Tab to ISA JSON...
INFO: Converting ISAtab to ISAjson for tests/data/tab/MTBLS1/
INFO: ... conversion finished.
Checking s_MTBLS1.txt
Checking a_mtbls1_metabolite_profiling_NMR_spectroscopy.txt
Possible process pooling detected on:  #process/Extraction1
Possible process pooling detected on:  #process/ADG_normalized_data.xlsx
[{'a_mtbls1_metabolite_profiling_NMR_spectroscopy.txt': ['#process/Extraction1', '#process/ADG_normalized_data.xlsx']}]
>>>

In this case, #process/Extraction1 is the pooling that we did not expect. This is a pooling on a single Extraction. From manual inspection of the ISA-Tab file a_mtbls1_metabolite_profiling_NMR_spectroscopy.txt we can

then confirm that values are entirely missing from Extract Name, causing the parser to think the experimental graph
converges on one process node. To rectify this, individual values should be put into this Name column. We can try

fix erroneous pooling by filling out an empty Name column with a corresponding Protocol REF by doing the following:

>>> utils.insert_distinct_parameter(open('tests/data/tab/MTBLS1/a_mtbls1_metabolite_profiling_NMR_spectroscopy.txt', 'r+'), 'Extraction')
Are you sure you want to add a column of hash values in Extract Name? Y/(N)
>? Y

If successful, this will fill out the empty column with 8 character-long UUIDs (e.g. 4078cb03).

Please be aware that these utility functions detect_isatab_process_pooling() and insert_distinct_parameter() are there to help you manually fix your ISA-Tabs, not to automatically fix them for you. We wil address this issue in more depth in following releases.

isatools v0.3 package

  • required constraints on JSON schemas causes validation failure for @id objects, meaning some constraints using JSON schemas cannot be used for validation #108
  • Chained processes (i.e. a process followed by another process without any intermediate inputs and outputs, in ISAtab a Protocol REF columns followed by another Protocol REF columns without any materials in between) are not currently supported. It is not recommended to attempt to use such patterns with this version of the isatools package #111
  • When converting to ISA JSON in using UUID or counter Identifier Types, some elements are not detected, such as Array_Design_REF #101
  • The SRA/ENA importer in sra2isatab relies on XSLT2 processing functionality only available with SAXON, so you must provide the JAR file yourself to use this
  • The legacy functionality (marked in the documentation) relies on Java 1.6

isatools v0.2 package

  • required constraints on JSON schemas causes validation failure for @id objects, meaning some constraints using JSON schemas cannot be used for validation #108
  • When converting to ISA JSON in using UUID or counter Identifier Types, some elements are not detected, such as Array_Design_REF #101
  • Protocol REF columns must be present in order for the ISA-Tab to JSON conversion to pick up processes in the process sequences #111
  • Characteristics and Factor Values declared in assay tables in ISAtab are associated to Sample objects only. This means that when writing from Python objects, or converting from ISA JSON, to ISAtab these columns appear at the study table.
  • Chained processes (i.e. a process followed by another process without any intermediate inputs and outputs, in ISAtab a Protocol REF columns followed by another Protocol REF columns without any materials in between) are not currently supported. It is not recommended to attempt to use such patterns with this version of the isatools package #111
  • For experimental graph patterns to work, should follow relatively simple patterns. e.g. Straight Sample -> ... -> Materials -> ... -> Data paths (per assay), or simple splitting and pooling. See test package code for examples of what works.
  • No ISA JSON configurations have been included that correspond with the following default XML configurations: clinical_chemistry.xml and most are as yet untested.

isatools v0.1 package

  • Characteristics and Factor Values declared in assay tables in ISAtab are associated to Sample objects only. This means that when writing from Python objects, or converting from ISA JSON, to ISAtab these columns appear at the study table.
  • Chained processes (i.e. a process followed by another process without any intermediate inputs and outputs, in ISAtab a Protocol REF columns followed by another Protocol REF columns without any materials in between) are not currently supported. It is not recommended to attempt to use such patterns with this version of the isatools package #111
  • For experimental graph patterns to work, should follow relatively simple patterns. e.g. Straight Sample -> ... -> Materials -> ... -> Data paths (per assay), or simple splitting and pooling. See test package code for examples of what works.

For a full up-to-date list of issues, or to report an issue or ask a question, please see the issue tracker.