From 46c7461b9d504e7b3be33272848c4dcf794ee770 Mon Sep 17 00:00:00 2001 From: Gregory Jefferis Date: Tue, 9 Apr 2019 16:24:07 +0100 Subject: [PATCH] Bump version to 0.9.7 and redown --- DESCRIPTION | 2 +- NEWS.md | 10 ++++- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 15 ++++++- docs/reference/AV4b1.html | 2 +- docs/reference/as.catmaidmesh.html | 2 +- docs/reference/catmaid-package.html | 2 +- docs/reference/catmaid_add_volume.html | 2 +- docs/reference/catmaid_connection_setenv.html | 2 +- .../catmaid_entities_from_models.html | 2 +- docs/reference/catmaid_fetch.html | 4 +- .../reference/catmaid_get_annotationlist.html | 2 +- ...catmaid_get_annotations_for_skeletons.html | 2 +- .../catmaid_get_compact_skeleton.html | 2 +- .../catmaid_get_connector_table.html | 7 +-- docs/reference/catmaid_get_connectors.html | 2 +- .../catmaid_get_connectors_between.html | 2 +- .../catmaid_get_contributor_stats.html | 2 +- docs/reference/catmaid_get_label_stats.html | 2 +- docs/reference/catmaid_get_labels.html | 2 +- docs/reference/catmaid_get_neuronnames.html | 2 +- docs/reference/catmaid_get_node_count.html | 2 +- docs/reference/catmaid_get_review_status.html | 2 +- .../reference/catmaid_get_treenode_table.html | 2 +- .../catmaid_get_treenodes_detail.html | 2 +- docs/reference/catmaid_get_user_list.html | 8 ++-- docs/reference/catmaid_get_volume.html | 2 +- docs/reference/catmaid_get_volumelist.html | 2 +- docs/reference/catmaid_login.html | 44 ++++++++++++------- docs/reference/catmaid_parse_url.html | 2 +- docs/reference/catmaid_query_by_name.html | 2 +- docs/reference/catmaid_query_connected.html | 2 +- docs/reference/catmaid_rename_neuron.html | 2 +- docs/reference/catmaid_skids.html | 2 +- docs/reference/catmaid_user_history.html | 2 +- docs/reference/catmaid_version.html | 2 +- docs/reference/connectors.html | 2 +- docs/reference/copy_tags_connectors.html | 2 +- docs/reference/index.html | 2 +- docs/reference/nsoma.html | 2 +- docs/reference/plot3d.catmaidneuron.html | 2 +- docs/reference/read.neuron.catmaid.html | 2 +- docs/reference/read_catmaid_selection.html | 2 +- docs/reference/write_catmaid_selection.html | 2 +- 45 files changed, 99 insertions(+), 67 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0e55307..d56084f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: catmaid Type: Package Title: R access to the API for the CATMAID web image annotation tool -Version: 0.9.6 +Version: 0.9.7 Authors@R: person("Gregory","Jefferis", email="jefferis@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0587-9355")) Maintainer: Gregory Jefferis diff --git a/NEWS.md b/NEWS.md index 425da57..10485e7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,11 @@ +# catmaid 0.9.7 +* New `catmaid_userids()` function converts user login names to ids. +* `catmaid_connection()` gets a new `config` argument to allow curl options to + be set (#108). +* Return format and documentation fix: tree node ids in + `catmaid_get_connector_table()` always refer to the query skeleton and not + the partner neuron (#107) + # catmaid 0.9.6 * Give `read.neurons.catmaid()` an optional fetch.annotations argument that @@ -76,7 +84,7 @@ with nat >=1.8.12.900 from github. This is a major version update because of the new support (and recommendation) to use environment variables for login (.Rprofile is still supported). -* support fetching login informaion from environment variables (#80) +* support fetching login information from environment variables (#80) * catmaid_get_compact_skeleton now returns list of vectors (#79) (used to be a list of lists, but this was less convenient and not helpful) * fix query_by_neuron_or_annotation adding empty annotations attribute diff --git a/docs/authors.html b/docs/authors.html index b223c84..0165abf 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -60,7 +60,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/index.html b/docs/index.html index f0ab322..c3cd489 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/news/index.html b/docs/news/index.html index a53a97c..5ead727 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -60,7 +60,7 @@ catmaid - 0.9.6 + 0.9.7 @@ -103,6 +103,16 @@

Changelog

Source: NEWS.md +
+

+catmaid 0.9.7

+ +

catmaid 0.9.6

@@ -192,7 +202,7 @@

catmaid 0.8

This is a major version update because of the new support (and recommendation) to use environment variables for login (.Rprofile is still supported).

    -
  • support fetching login informaion from environment variables (#80)
    • +
  • support fetching login information from environment variables (#80)
  • catmaid_get_compact_skeleton now returns list of vectors (#79) (used to be a list of lists, but this was less convenient and not helpful)
  • fix query_by_neuron_or_annotation adding empty annotations attribute
@@ -307,6 +317,7 @@

Contents

    +
  • 0.9.7
  • 0.9.6
  • 0.9.5
  • 0.9.4
    • diff --git a/docs/reference/AV4b1.html b/docs/reference/AV4b1.html index dd0dcfa..1eabd4d 100644 --- a/docs/reference/AV4b1.html +++ b/docs/reference/AV4b1.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7
diff --git a/docs/reference/as.catmaidmesh.html b/docs/reference/as.catmaidmesh.html index f640f3d..1be6b78 100644 --- a/docs/reference/as.catmaidmesh.html +++ b/docs/reference/as.catmaidmesh.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7

diff --git a/docs/reference/catmaid-package.html b/docs/reference/catmaid-package.html index 4c1e635..7a895c2 100644 --- a/docs/reference/catmaid-package.html +++ b/docs/reference/catmaid-package.html @@ -68,7 +68,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_add_volume.html b/docs/reference/catmaid_add_volume.html index 275e75f..c8a87fe 100644 --- a/docs/reference/catmaid_add_volume.html +++ b/docs/reference/catmaid_add_volume.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_connection_setenv.html b/docs/reference/catmaid_connection_setenv.html index 3287084..9383ed9 100644 --- a/docs/reference/catmaid_connection_setenv.html +++ b/docs/reference/catmaid_connection_setenv.html @@ -68,7 +68,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_entities_from_models.html b/docs/reference/catmaid_entities_from_models.html index ec03945..65427aa 100644 --- a/docs/reference/catmaid_entities_from_models.html +++ b/docs/reference/catmaid_entities_from_models.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_fetch.html b/docs/reference/catmaid_fetch.html index 456d0d8..9ac7362 100644 --- a/docs/reference/catmaid_fetch.html +++ b/docs/reference/catmaid_fetch.html @@ -65,7 +65,7 @@ catmaid - 0.9.6 + 0.9.7 @@ -211,7 +211,7 @@

Examp group_by(name) %>% mutate(ccount = cumsum(count)) %>% filter(name %in% top10$name) %>% - ggplot(aes(date, ccount, col = name)) + geom_line() + ggplot(aes(date, ccount, col = name)) + geom_line() ## demonstrate that bad urls will result in an error catmaid_fetch("/1/rhubarb/crumble") diff --git a/docs/reference/catmaid_get_annotationlist.html b/docs/reference/catmaid_get_annotationlist.html index 22daa9e..23b852e 100644 --- a/docs/reference/catmaid_get_annotationlist.html +++ b/docs/reference/catmaid_get_annotationlist.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_annotations_for_skeletons.html b/docs/reference/catmaid_get_annotations_for_skeletons.html index c4d0d5a..7194aaa 100644 --- a/docs/reference/catmaid_get_annotations_for_skeletons.html +++ b/docs/reference/catmaid_get_annotations_for_skeletons.html @@ -68,7 +68,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_compact_skeleton.html b/docs/reference/catmaid_get_compact_skeleton.html index 82517c3..20babc5 100644 --- a/docs/reference/catmaid_get_compact_skeleton.html +++ b/docs/reference/catmaid_get_compact_skeleton.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_connector_table.html b/docs/reference/catmaid_get_connector_table.html index 839a6ab..9c0d42e 100644 --- a/docs/reference/catmaid_get_connector_table.html +++ b/docs/reference/catmaid_get_connector_table.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 @@ -173,7 +173,8 @@

Value

  • z

  • confidence

  • user_id

    • -

  • partner_treenode_id

    • +

  • treenode_id (NB this is always the treenode id of the query skeleton + whether or not incoming or outgoing connections are requested)

  • last_modified

  • partner_skid

    • @@ -189,7 +190,7 @@

    Value

  • tags

  • nodes_in_partner

  • username

    • -

  • partner_treenode_id

    • +

  • treenode_id

  • last_modified

    • diff --git a/docs/reference/catmaid_get_connectors.html b/docs/reference/catmaid_get_connectors.html index baa6a5e..06d8057 100644 --- a/docs/reference/catmaid_get_connectors.html +++ b/docs/reference/catmaid_get_connectors.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_connectors_between.html b/docs/reference/catmaid_get_connectors_between.html index 75f4c20..8d66283 100644 --- a/docs/reference/catmaid_get_connectors_between.html +++ b/docs/reference/catmaid_get_connectors_between.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_contributor_stats.html b/docs/reference/catmaid_get_contributor_stats.html index c033568..85875c7 100644 --- a/docs/reference/catmaid_get_contributor_stats.html +++ b/docs/reference/catmaid_get_contributor_stats.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_label_stats.html b/docs/reference/catmaid_get_label_stats.html index fd71c18..50d7913 100644 --- a/docs/reference/catmaid_get_label_stats.html +++ b/docs/reference/catmaid_get_label_stats.html @@ -65,7 +65,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_labels.html b/docs/reference/catmaid_get_labels.html index d83664b..7b516fd 100644 --- a/docs/reference/catmaid_get_labels.html +++ b/docs/reference/catmaid_get_labels.html @@ -68,7 +68,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_neuronnames.html b/docs/reference/catmaid_get_neuronnames.html index 1dd4f22..a9dc705 100644 --- a/docs/reference/catmaid_get_neuronnames.html +++ b/docs/reference/catmaid_get_neuronnames.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_node_count.html b/docs/reference/catmaid_get_node_count.html index 365bf54..a9afbfb 100644 --- a/docs/reference/catmaid_get_node_count.html +++ b/docs/reference/catmaid_get_node_count.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_review_status.html b/docs/reference/catmaid_get_review_status.html index c14dba5..90d59f6 100644 --- a/docs/reference/catmaid_get_review_status.html +++ b/docs/reference/catmaid_get_review_status.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_treenode_table.html b/docs/reference/catmaid_get_treenode_table.html index d2ab608..087c176 100644 --- a/docs/reference/catmaid_get_treenode_table.html +++ b/docs/reference/catmaid_get_treenode_table.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_treenodes_detail.html b/docs/reference/catmaid_get_treenodes_detail.html index c59cecf..5fe2b64 100644 --- a/docs/reference/catmaid_get_treenodes_detail.html +++ b/docs/reference/catmaid_get_treenodes_detail.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_user_list.html b/docs/reference/catmaid_get_user_list.html index c3179f4..f455a27 100644 --- a/docs/reference/catmaid_get_user_list.html +++ b/docs/reference/catmaid_get_user_list.html @@ -32,7 +32,7 @@ - + @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 @@ -109,7 +109,7 @@

    Fetch or translate catmaid users for current/specified connection/project -

    catmaid_users convert login names to numeric ids

    +

    catmaid_userids convert login names to numeric ids

    @@ -146,7 +146,7 @@

    Arg

    Value

    For catmaid_get_user_list a data.frame with

    -

    For catmaid_users an integer vector of numeric ids

    +

    For catmaid_userids an integer vector of numeric ids

    See also

    diff --git a/docs/reference/catmaid_get_volume.html b/docs/reference/catmaid_get_volume.html index 28ef6db..73ae84b 100644 --- a/docs/reference/catmaid_get_volume.html +++ b/docs/reference/catmaid_get_volume.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_get_volumelist.html b/docs/reference/catmaid_get_volumelist.html index 8dfaffa..5eccff4 100644 --- a/docs/reference/catmaid_get_volumelist.html +++ b/docs/reference/catmaid_get_volumelist.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_login.html b/docs/reference/catmaid_login.html index 100cdd1..c4a6431 100644 --- a/docs/reference/catmaid_login.html +++ b/docs/reference/catmaid_login.html @@ -40,9 +40,9 @@ The connection object returned by catmaid_login (or cached when Cache=TRUE, the default) can then be used for future requests to the CATMAID server by get/query/fetch functions. -catmaid_connection is a lower level function used by - catmaid_login to create a connection object. End users should not - need to call this directly, but it does document the arguments that can be +catmaid_connection is a lower level function used by + catmaid_login to create a connection object. End users should not + need to call this directly, but it does document the arguments that can be used to specify a connection to a CATMAID server." /> @@ -74,7 +74,7 @@ catmaid - 0.9.6 + 0.9.7 @@ -128,9 +128,9 @@

    Connect/authenticate to a CATMAID server, returning a connection object

    The connection object returned by catmaid_login (or cached when Cache=TRUE, the default) can then be used for future requests to the CATMAID server by get/query/fetch functions.

    -

    catmaid_connection is a lower level function used by - catmaid_login to create a connection object. End users should not - need to call this directly, but it does document the arguments that can be +

    catmaid_connection is a lower level function used by + catmaid_login to create a connection object. End users should not + need to call this directly, but it does document the arguments that can be used to specify a connection to a CATMAID server.

    @@ -139,7 +139,7 @@

    Connect/authenticate to a CATMAID server, returning a connection object

    catmaid_connection(server, username = NULL, password = NULL, authname = NULL, authpassword = NULL, token = NULL, - authtype = NULL) + authtype = NULL, config = NULL)

    Arguments

    @@ -172,19 +172,24 @@

    Arg

    - - - + + + +
    authname, authpassword

    The http username/password that optionally +

    The http username/password that optionally secures the CATMAID website. These are not the same as your CATMAID login details.
    token

    An API token (A modern alternative to providing your CATMAID +

    An API token (A modern alternative to providing your CATMAID username and password). See Token based authentication for details.
    authtype

    The http authentication scheme, see +

    The http authentication scheme, see authenticate for details.

    config

    Additional curl config options. See config +for details and the examples section below.
    @@ -203,11 +208,11 @@

    Details catmaid_login is called with enough information to indicate that the same server is desired OR (when no information about the server is passed to catmaid_login) the last opened connection will be used.

    -

    Note the difference between authname/authpassword and - username/password. The former are for generic web - authentication, which is sometimes used to protect a private catmaid site - from being accessible to general web traffic. The latter are used to - authenticate to the CATMAID web application itself - for example the +

    Note the difference between authname/authpassword and + username/password. The former are for generic web + authentication, which is sometimes used to protect a private catmaid site + from being accessible to general web traffic. The latter are used to + authenticate to the CATMAID web application itself - for example the username is the one that will be associated with any tracing carried out by you in CATMAID.

    @@ -292,8 +297,15 @@

    Examp conn = catmaid_login() conn = catmaid_login(server='https://someotherserver.org/catmaidroot') +## set additional curl options/headers +# This example will bypass an SSL certificate verification error on the +# remote host e.g. if it has expired. Don't this regularly of course! +conn = catmaid_login(config=httr::config(ssl_verifypeer=0)) + ## now do stuff with the connection like skel=catmaid_fetch("1/10418394/0/0/compact-skeleton", conn=conn) +# you can also omit the connecttion because it will be cached and reused +skel=catmaid_fetch("1/10418394/0/0/compact-skeleton") ## or for those who want to work at the lowest level skel2=GET("https://mycatmaidserver.org/catmaidroot/1/10418394/0/0/compact-skeleton", diff --git a/docs/reference/catmaid_parse_url.html b/docs/reference/catmaid_parse_url.html index 03adb82..53cf8b5 100644 --- a/docs/reference/catmaid_parse_url.html +++ b/docs/reference/catmaid_parse_url.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_query_by_name.html b/docs/reference/catmaid_query_by_name.html index 93e3ab1..1bd4033 100644 --- a/docs/reference/catmaid_query_by_name.html +++ b/docs/reference/catmaid_query_by_name.html @@ -74,7 +74,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_query_connected.html b/docs/reference/catmaid_query_connected.html index eb958f4..ba3a354 100644 --- a/docs/reference/catmaid_query_connected.html +++ b/docs/reference/catmaid_query_connected.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_rename_neuron.html b/docs/reference/catmaid_rename_neuron.html index 8b93ca6..428d903 100644 --- a/docs/reference/catmaid_rename_neuron.html +++ b/docs/reference/catmaid_rename_neuron.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_skids.html b/docs/reference/catmaid_skids.html index e894da7..68db9bb 100644 --- a/docs/reference/catmaid_skids.html +++ b/docs/reference/catmaid_skids.html @@ -64,7 +64,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_user_history.html b/docs/reference/catmaid_user_history.html index 7e83e90..4c64c8a 100644 --- a/docs/reference/catmaid_user_history.html +++ b/docs/reference/catmaid_user_history.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/catmaid_version.html b/docs/reference/catmaid_version.html index 35e49da..46da57b 100644 --- a/docs/reference/catmaid_version.html +++ b/docs/reference/catmaid_version.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/connectors.html b/docs/reference/connectors.html index bf06c4a..fe2d4c7 100644 --- a/docs/reference/connectors.html +++ b/docs/reference/connectors.html @@ -65,7 +65,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/copy_tags_connectors.html b/docs/reference/copy_tags_connectors.html index baa72ad..3943363 100644 --- a/docs/reference/copy_tags_connectors.html +++ b/docs/reference/copy_tags_connectors.html @@ -65,7 +65,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/index.html b/docs/reference/index.html index 6c4ed65..de63dfc 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/nsoma.html b/docs/reference/nsoma.html index 5f24598..c7075b8 100644 --- a/docs/reference/nsoma.html +++ b/docs/reference/nsoma.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/plot3d.catmaidneuron.html b/docs/reference/plot3d.catmaidneuron.html index 296fbd7..859a480 100644 --- a/docs/reference/plot3d.catmaidneuron.html +++ b/docs/reference/plot3d.catmaidneuron.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/read.neuron.catmaid.html b/docs/reference/read.neuron.catmaid.html index 7d2ea37..7294943 100644 --- a/docs/reference/read.neuron.catmaid.html +++ b/docs/reference/read.neuron.catmaid.html @@ -65,7 +65,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/read_catmaid_selection.html b/docs/reference/read_catmaid_selection.html index f01b2e4..479287c 100644 --- a/docs/reference/read_catmaid_selection.html +++ b/docs/reference/read_catmaid_selection.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7 diff --git a/docs/reference/write_catmaid_selection.html b/docs/reference/write_catmaid_selection.html index 7dc0da5..5be9bb2 100644 --- a/docs/reference/write_catmaid_selection.html +++ b/docs/reference/write_catmaid_selection.html @@ -63,7 +63,7 @@ catmaid - 0.9.6 + 0.9.7