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docs processes reordered sections and normalized language

ordering is a bit more in line with the order in which they are
encountered in a normal workflow
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tgbugs committed Jan 29, 2019
1 parent 5d8568b commit 1bc26744af1c2b173665b5a9c52a5c950892193c
Showing with 27 additions and 27 deletions.
  1. +27 −27 docs/processes.md
@@ -41,38 +41,19 @@ ttlfmt $(git status -s | grep ttl | grep M | cut -d' ' -f3)
qnamefix $(git status -s | grep ttl | grep M | cut -d' ' -f3)
```

### Adding a new external import
All external imports should be imported into NIFSTD via a bridge file.
### Adding a new remote import
All remote imports should be imported into NIFSTD via a bridge file.
This file will hold any local additions that we want to make.
1. Create a new bridge file by copying an existing bridge file and modifying
as needed to import the external file from its canonical iri, and to import
as needed to import the remote file from its canonical iri, and to import
`filename-dead.ttl`.
2. Add an entry in [catalog-extras](../catalog-extras) for the new import.
3. Create `ttl/generated/filename-dead.ttl` by running `necromancy http://myurl.org/filename.owl`.
4. Whenever there is a new release repeat step 3.

### Changing an ontology file
1. Edit your file and save.
2. If using protege `git diff` to make sure that any new triples
have landed in the correct file.
3. Execute prior to commit processes.

### Adding a new ontology file
```bash
touch filename.ttl
add filename.ttl
`make_catalog` # NOTE this is broken at the moment
```
1. Add an entry in [catalog-v001.xml](../ttl/catalog-v001.xml.example) by hand.
Note that you will need to make sure that `catalog-v001.xml` is copied from the
example order to make use of the new entry.

Before you run `make_catalog` make sure that the import chain is local (unpatched)
otherwise it will take an extremely long time to fetch files.

### Load remote imports from local copies
Sometimes we don't want to have to retrieve remote copies of files every time
we start protege, or we need to run tests for patches that are applied to external
we start protege, or we need to run tests for patches that are applied to remote
imports when loading the ontology into SciGraph.
```bash
cd ttl/
@@ -106,10 +87,24 @@ protege # can be launched as you see fit
Protege does not have to be run from `ttl/` in order to find `ttl/catalog-v001.xml`,
however the file opened must be in `ttl/`.

### Check for incorrect or unimported predicates
1. Remove `/tmp/ttlcmp.patch` if it exists
2. `ttlcmp.sh` (lives in `pyontutils/pyontutils`)
3. Review `/tmp/ttlcmp.patch` for annotation and object properties.
### Changing an ontology file
1. Edit your file and save.
2. If using protege `git diff` to make sure that any new triples
have landed in the correct file.
3. Execute prior to commit processes.

### Adding a new ontology file
```bash
touch filename.ttl
add filename.ttl
`make_catalog` # NOTE this is broken at the moment
```
1. Add an entry in [catalog-v001.xml](../ttl/catalog-v001.xml.example) by hand.
Note that you will need to make sure that `catalog-v001.xml` is copied from the
example order to make use of the new entry.

Before you run `make_catalog` make sure that the import chain is local (unpatched)
otherwise it will take an extremely long time to fetch files.

### Integrating a new set of terms
If there is an existing ttl file that has been formatted with ttlfmt as described above then
@@ -123,6 +118,11 @@ This does not need to be done if ttl file will become the source of truth once i
Any set of terms that requires more than direct transformation to ttl should also follow the process described in
[pyontutils/development/README.md](https://github.com/tgbugs/pyontutils/blob/master/development/README.md).

### Check for incorrect or unimported predicates
1. Remove `/tmp/ttlcmp.patch` if it exists
2. `ttlcmp.sh` (lives in `pyontutils/pyontutils`)
3. Review `/tmp/ttlcmp.patch` for annotation and object properties.

## External source synchronization
Full documentation of defaults and command line arguments can be found by running
`--help` for any of the commands listed in this section.

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