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[INFRA] Use linkchecker (from a dedicated docker image) to check all URLs #293

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merged 13 commits into from
Aug 12, 2019
Merged

[INFRA] Use linkchecker (from a dedicated docker image) to check all URLs #293

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95a46d5
ENH: Neurodocker script to create docker container with patched linkc…
yarikoptic Aug 2, 2019
649e5ec
ENH: place built site/ into workspace and run linkchecker from a dedi…
yarikoptic Aug 2, 2019
5107ae0
BF: state that linkchecker requires build (otherwise workspace is emp…
yarikoptic Aug 5, 2019
64faa85
BF: add linkchecker command (entered image), and chmod entire ~ to be…
yarikoptic Aug 2, 2019
f795519
BF: fixed up #anchored references in two files
yarikoptic Aug 5, 2019
002c365
BF(workaround): run linkchecker in a single thread
yarikoptic Aug 5, 2019
7d329ff
BF: URL to mindboggle should have no www.
yarikoptic Aug 5, 2019
1d73e7b
BF: Cognitive atlas urls went from /term/ to /task/ for the rest stat…
yarikoptic Aug 5, 2019
f461c26
BF: Replaced dead link to fdt_dtifit with URL to FDT/UserGuide
yarikoptic Aug 5, 2019
e25ae72
BF: Replace dead link to download of ICBM 452T1 to some lame 1 page .…
yarikoptic Aug 5, 2019
ef6801c
ENH: add a separate call to check external URLs
yarikoptic Aug 5, 2019
54a3469
BF: fixed up introduced problems to tables alignment
yarikoptic Aug 5, 2019
4432d90
Merge remote-tracking branch 'origin/master' into bf-links-docker
yarikoptic Aug 8, 2019
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20 changes: 20 additions & 0 deletions .circleci/config.yml
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Expand Up @@ -25,6 +25,23 @@ jobs:
command: pipenv run mkdocs build --clean --strict --verbose
- store_artifacts:
path: site
- persist_to_workspace:
root: .
paths: site

linkchecker:
docker:
- image: yarikoptic/linkchecker:9.4.0.anchorfix1-1
steps:
- attach_workspace:
at: ~/build
- run:
command: |
chmod a+rX -R ~
linkchecker -t 1 ~/build/site/
# check external separately by pointing to all *html so no
# failures for local file:/// -- yoh found no better way,
linkchecker -t 1 --check-extern --ignore-url 'file:///.*' --ignore-url https://fonts.gstatic.com ~/build/site/*html ~/build/site/*/*.html

# Auto changelog collector
github-changelog-generator:
Expand Down Expand Up @@ -127,6 +144,9 @@ workflows:
search_build:
jobs:
- build
- linkchecker:
requires:
- build
- github-changelog-generator:
filters:
branches:
Expand Down
2 changes: 1 addition & 1 deletion src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
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Expand Up @@ -380,7 +380,7 @@ however the user is free to choose any other label than `singleband` and
`multiband` as long as they are consistent across subjects and sessions. For
multiband acquisitions, one can also save the single-band reference image as
type `sbref` (e.g. `dwi/sub-control01_sbref.nii[.gz]`) The bvec and bval files
are in the [FSL format](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_dtifit.html):
are in the [FSL format](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#DTIFIT):
The bvec files contain 3 rows with n space-delimited floating-point numbers
(corresponding to the n volumes in the relevant NIfTI file). The first row
contains the x elements, the second row contains the y elements and third row
Expand Down
2 changes: 1 addition & 1 deletion src/04-modality-specific-files/02-magnetoencephalography.md
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Expand Up @@ -75,7 +75,7 @@ Whenever possible, please avoid using ad-hoc wording.
| SoftwareVersions | RECOMMENDED. Manufacturer’s designation of the acquisition software. |
| TaskDescription | RECOMMENDED. Description of the task. |
| Instructions | RECOMMENDED. Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (e.g. to distinguish between eyes open and eyes closed). |
| CogAtlasID | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (e.g. Resting State with eyes closed "[http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b)") |
| CogAtlasID | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (e.g. Resting State with eyes closed "[http://www.cognitiveatlas.org/task/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/task/id/trm_54e69c642d89b)") |
| CogPOID | RECOMMENDED. URL of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (e.g. Rest "[http://wiki.cogpo.org/index.php?title=Rest](http://wiki.cogpo.org/index.php?title=Rest)") |
| DeviceSerialNumber | RECOMMENDED. The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |

Expand Down
6 changes: 3 additions & 3 deletions src/04-modality-specific-files/03-electroencephalography.md
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Expand Up @@ -104,7 +104,7 @@ Whenever possible, please avoid using ad hoc wording.
| SoftwareVersions | RECOMMENDED. Manufacturer's designation of the acquisition software. |
| TaskDescription | RECOMMENDED. Description of the task. |
| Instructions | RECOMMENDED. Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (e.g., to distinguish between eyes open and eyes closed). |
| CogAtlasID | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (e.g., Resting State with eyes closed "[http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b)"). |
| CogAtlasID | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (e.g., Resting State with eyes closed "[http://www.cognitiveatlas.org/task/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/task/id/trm_54e69c642d89b)"). |
| CogPOID | RECOMMENDED. URL of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (e.g., Rest "[http://wiki.cogpo.org/index.php?title=Rest](http://wiki.cogpo.org/index.php?title=Rest)") . |
| DeviceSerialNumber | RECOMMENDED. The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |

Expand Down Expand Up @@ -197,7 +197,7 @@ required columns are channel `name`, `type` and `units` in this specific order.
Channel names should furthermore appear in the table in the same order they do
in the EEG data file. Any number of additional columns may be provided to
provide additional information about the channels. Note that electrode
positions should not be added to this file, but to [`*_electrodes.tsv`](./03-electroencephalography.md#electrodes-description-electrodes-tsv).
positions should not be added to this file, but to [`*_electrodes.tsv`](./03-electroencephalography.md#electrodes-description-_electrodestsv).

The columns of the Channels description table stored in `*_channels.tsv` are:

Expand Down Expand Up @@ -272,7 +272,7 @@ sub-<label>/
File that gives the location of EEG electrodes. Note that coordinates are
expected in cartesian coordinates according to the `EEGCoordinateSystem` and
`EEGCoordinateSystemUnits` fields in `*_coordsystem.json`. **If an
`*_electrodes.tsv` file is specified, a [`*_coordsystem.json`](#coordinate-system-json-coordsystem-json)
`*_electrodes.tsv` file is specified, a [`*_coordsystem.json`](#coordinate-system-json-_coordsystemjson)
file MUST be specified as well**. The order of the required columns in the
`*_electrodes.tsv` file MUST be as listed below.

Expand Down
16 changes: 8 additions & 8 deletions src/04-modality-specific-files/04-intracranial-electroencephalography.md
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Expand Up @@ -390,13 +390,13 @@ General fields:

Fields relating to the iEEG electrode positions:

| Field name | Definition |
| :---------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| iEEGCoordinateSystem | REQUIRED. Defines the coordinate system for the iEEG electrodes. See [Appendix VIII](../99-appendices/08-coordinate-systems.md) for a list of restricted keywords. If positions correspond to pixel indices in a 2D image (of either a volume-rendering, surface-rendering, operative photo, or operative drawing), this must be "Pixels". For more information, see the section on [2D coordinate systems](../04-modality-specific-files/04-intracranial-electroencephalography.md#Allowed-2D-coordinate-systems). |
| iEEGCoordinateUnits | REQUIRED. Units of the \_electrodes.tsv, MUST be "m", "mm", "cm" or "pixels". |
| iEEGCoordinateSystemDescription | RECOMMENDED. Freeform text description or link to document describing the iEEG coordinate system system in detail (e.g., "Coordinate system with the origin at anterior commissure (AC), negative y-axis going through the posterior commissure (PC), z-axis going to a mid-hemisperic point which lies superior to the AC-PC line, x-axis going to the right"). |
| iEEGCoordinateProcessingDescription | RECOMMENDED. Has any post-processing (such as projection) been done on the electrode positions (e.g., "surface_projection", "none"). |
| iEEGCoordinateProcessingReference | RECOMMENDED. A reference to a paper that defines in more detail the method used to localize the electrodes and to post-process the electrode positions. . |
| Field name | Definition |
| :---------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| iEEGCoordinateSystem | REQUIRED. Defines the coordinate system for the iEEG electrodes. See [Appendix VIII](../99-appendices/08-coordinate-systems.md) for a list of restricted keywords. If positions correspond to pixel indices in a 2D image (of either a volume-rendering, surface-rendering, operative photo, or operative drawing), this must be "Pixels". For more information, see the section on [2D coordinate systems](#allowed-2d-coordinate-systems) |
| iEEGCoordinateUnits | REQUIRED. Units of the \_electrodes.tsv, MUST be "m", "mm", "cm" or "pixels". |
| iEEGCoordinateSystemDescription | RECOMMENDED. Freeform text description or link to document describing the iEEG coordinate system system in detail (e.g., "Coordinate system with the origin at anterior commissure (AC), negative y-axis going through the posterior commissure (PC), z-axis going to a mid-hemisperic point which lies superior to the AC-PC line, x-axis going to the right"). |
| iEEGCoordinateProcessingDescription | RECOMMENDED. Has any post-processing (such as projection) been done on the electrode positions (e.g., "surface_projection", "none"). |
| iEEGCoordinateProcessingReference | RECOMMENDED. A reference to a paper that defines in more detail the method used to localize the electrodes and to post-process the electrode positions. . |

### Recommended 3D coordinate systems

Expand All @@ -417,7 +417,7 @@ upper left pixel and (N,0) corresponding to the lower left pixel.

If electrode positions are known in multiple coordinate systems (e.g., MRI, CT
and MNI), these spaces can be distinguished by the optional `[_space-<label>]`
field, see the [`*_electrodes.tsv`-section](../04-modality-specific-files/04-intracranial-electroencephalography.md#electrode-description-space-label-electrodes-tsv)
field, see the [`*_electrodes.tsv`-section](#electrode-description-_electrodestsv)
for more information. Note that the `[_space-<label>]` fields must correspond
between `*_electrodes.tsv` and `*_coordsystem.json` if they refer to the same
data.
Expand Down
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