2d0f1f1f85b147f9176abe594f56106b364229e8
angie
  Mon Sep 12 14:09:52 2022 -0700
trackHubOpen doesn't actually connect the hub; use hubConnectLoadHubs so if/when the user selects the hub, it is connected.

diff --git src/hg/hgPhyloPlace/phyloPlace.h src/hg/hgPhyloPlace/phyloPlace.h
index 399edee..cd0fb2a 100644
--- src/hg/hgPhyloPlace/phyloPlace.h
+++ src/hg/hgPhyloPlace/phyloPlace.h
@@ -1,21 +1,22 @@
 /* Place SARS-CoV-2 sequences in phylogenetic tree using add_missing_samples program. */
 
 #ifndef _PHYLO_PLACE_H_
 #define _PHYLO_PLACE_H_
 
 #include "common.h"
+#include "cart.h"
 #include "dnaseq.h"
 #include "hash.h"
 #include "linefile.h"
 #include "parsimonyProto.h"
 #include "phyloTree.h"
 #include "seqWindow.h"
 #include "trashDir.h"
 
 #define PHYLOPLACE_DATA_DIR "hgPhyloPlaceData"
 
 // Allow users to upload a lot of sequences, but put limits on how much detail we'll show and
 // how many custom tracks we'll create.
 #define MAX_SUBTREE_BUTTONS 5
 #define MAX_SEQ_DETAILS 100
 #define MAX_SUBTREE_CTS 10
@@ -189,31 +190,31 @@
  * (https://github.com/nextstrain/augur/blob/master/augur/data/schema-export-v2.json). */
 
 struct tempName *writeCustomTracks(char *db, struct tempName *vcfTn, struct usherResults *ur,
                                    struct slName *sampleIds, struct mutationAnnotatedTree *bigTree,
                                    char *source, int fontHeight,
                                    struct phyloTree **retSampleTree, int *pStartTime);
 /* Write one custom track per subtree, and one custom track with just the user's uploaded samples. */
 
 
 struct sampleMetadata *metadataForSample(struct hash *sampleMetadata, char *sampleId);
 /* Look up sampleId in sampleMetadata, by accession if sampleId seems to include an accession. */
 
 struct phyloTree *phyloPruneToIds(struct phyloTree *node, struct slName *sampleIds);
 /* Prune all descendants of node that have no leaf descendants in sampleIds. */
 
-struct slName *phyloPlaceDbList();
+struct slName *phyloPlaceDbList(struct cart *cart);
 /* Each subdirectory of PHYLOPLACE_DATA_DIR that contains a config.ra file is a supported db
  * or track hub name (without the hub_number_ prefix).  Return a list of them, or NULL if none
  * are found. */
 
 char *phyloPlaceDbSetting(char *db, char *settingName);
 /* Return a setting from hgPhyloPlaceData/<db>/config.ra or NULL if not found. */
 
 char *phyloPlaceDbSettingPath(char *db, char *settingName);
 /* Return path to a file named by a setting from hgPhyloPlaceData/<db>/config.ra,
  * or NULL if not found.  (Append hgPhyloPlaceData/<db>/ to the beginning of relative path) */
 
 struct treeChoices *loadTreeChoices(char *db);
 /* If <db>/config.ra specifies a treeChoices file, load it up, else return NULL. */
 
 boolean isInternalNodeName(char *nodeName, int minNewNode);