From 839a63983c7c3a4f6cbf20b98deea7999b08cde8 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 4 May 2021 13:19:53 +0200 Subject: [PATCH 1/3] fix and complete metadata setting docs --- docs/_writing_tool_metadata.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/_writing_tool_metadata.rst b/docs/_writing_tool_metadata.rst index 57cb2a2a4..59104b407 100644 --- a/docs/_writing_tool_metadata.rst +++ b/docs/_writing_tool_metadata.rst @@ -42,10 +42,11 @@ Examples of tools using ``new_primary_dataset`` entries: The ``type`` of an entry may also be ``dataset``. In this case the metadata descriptions describe an explicit output (one with its own corresponding ``output`` -element definition). In this case, an entry called ``dataset`` should appear in +element definition). In this case, an entry called ``dataset_id`` should appear in the dictionary (in lieu of ``filename`` above) and should be the database id of the output dataset. Such entries may contain all of the other fields described above except -``metadata``. +``metadata``. Note that the output needs to set ``format="auto"`` in order to set the +format. Example tool using a ``dataset`` entry: From 69fb86351cccc13260e83bd358dec86926811458 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 6 May 2021 22:08:42 +0200 Subject: [PATCH 2/3] start to describe new metadata format --- docs/_writing_tool_metadata.rst | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/docs/_writing_tool_metadata.rst b/docs/_writing_tool_metadata.rst index 59104b407..622b5824d 100644 --- a/docs/_writing_tool_metadata.rst +++ b/docs/_writing_tool_metadata.rst @@ -19,7 +19,20 @@ to build a manifest file. A tool may also produce a file called ``galaxy.json`` during execution. If upon a job's completion this file is populated, Galaxy will expect to find metadata -about outputs in it. +about outputs in it. + +The current format of the metadata file -- which has been introduced in release 17.09 -- +is described in the following. The legacy format is described at the end of this section. + +---------------------------------------------------------------- +Metadata format +---------------------------------------------------------------- + +NEED INPUT HERE + +---------------------------------------------------------------- +Legacy metadata format +---------------------------------------------------------------- The format of this file is a bit quirky - each line of this file should be a JSON dictionary. Each such dictionary should contain a ``type`` attribute - this type From a38ef63b46140ba16ba878e626c922c7ae81ca30 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 5 Aug 2021 10:04:09 +0200 Subject: [PATCH 3/3] added some links --- docs/_writing_tool_metadata.rst | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/docs/_writing_tool_metadata.rst b/docs/_writing_tool_metadata.rst index 622b5824d..56090cfe1 100644 --- a/docs/_writing_tool_metadata.rst +++ b/docs/_writing_tool_metadata.rst @@ -28,7 +28,20 @@ is described in the following. The legacy format is described at the end of this Metadata format ---------------------------------------------------------------- -NEED INPUT HERE +Original PR https://github.com/galaxyproject/galaxy/pull/4437 + +Simple data sets: + +TODO + +Discovered data sets: + +TODO + +Collections: + +https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml +https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_dynamic_nested_from_json.xml ---------------------------------------------------------------- Legacy metadata format