From 292b2e8480a36282a836747455307115b55e854f Mon Sep 17 00:00:00 2001
From: B13nch3n <b13nch3n_01@theb-si.de>
Date: Sat, 7 May 2022 21:02:13 +0200
Subject: [PATCH] Explain associated dirs
---
validation/README.md | 37 ++++++++++++++++++++++++++++++++++---
1 file changed, 34 insertions(+), 3 deletions(-)
diff --git a/validation/README.md b/validation/README.md
index 93ea398..224ec96 100644
--- a/validation/README.md
+++ b/validation/README.md
@@ -51,10 +51,39 @@ $ validate-mmcif-file model.cif -e
$
```
-### Associated files...
+### Base directory for associated files
+
+For a ModelCIF file using the `_ma_entry_associated_files` category, the validation tool tries to merge associated data into the ModelCIF file, if `_ma_entry_associated_files.file_format` is `cif`. That way the outsourced data is validated, too.
+
+Command line argument `--associates-dir` (`-a`) is used to declare the base directory associated files are stored in. Inside the directory, the path must follow what is defined in `_ma_entry_associated_files.file_url`. If the URL is just the file name, the file must be stored right in the associates directory. The following example works for `_ma_entry_associated_files.file_url model_pae.cif`
+
+```bash
+$ grep _ma_entry_associated_files.file_url model.cif
+_ma_entry_associated_files.file_url model_pae.cif
+$ ls extra
+model_pae.cif
+$ validate-mmcif-file -a extra model.cif
+{"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.358","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.0","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/dist/mmcif_ma.dic"}]}
+$
+```
+
+If the URL points to a subdirectory, that must be reflected by the associates directory declared to the validation tool. The following example illustrates that the `extra` directory needs a `pae` directory storing the associated file as expected by `_ma_entry_associated_files.file_url`:
+
+```bash
+$ grep _ma_entry_associated_files.file_url model.cif
+_ma_entry_associated_files.file_url pae/model_pae.cif
+$ ls extra
+pae
+$ ls extra/pae
+model_pae.cif
+$ validate-mmcif-file -a extra model.cif
+{"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.358","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.0","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/dist/mmcif_ma.dic"}]}
+$
+```
+
+
- basic usage
-- add version of dict validated against
- remaining options
## How to run the container
@@ -65,5 +94,7 @@ $
# Files in this directory
-<!-- LocalWords: PDBx ModelCIF TOC JSON CifCheck RCSB mmcif cif pdbx dic
+<!-- LocalWords: PDBx ModelCIF TOC JSON CifCheck RCSB mmcif cif pdbx dic dir
+<!-- LocalWords: url pae
+ -->
-->
--
GitLab