gitea ssh testing

This reverts commit 203d63c16a.

README.md

@@ -1,45 +1,27 @@
 ## biblio database test repo
 
-### datproject url test
+<div id="refs" class="references" role="doc-bibliography">
 
-Here is a link to a dat blob archive:
-
-<dat://cdbdaf1e57ddb7066be9c2bee940358b9fbcf779f557e329a4c322b2ef3ea912>
-
-Here is another version of that link:
-
-[The dat link](dat://cdbdaf1e57ddb7066be9c2bee940358b9fbcf779f557e329a4c322b2ef3ea912) is essentially a globally unique identifier (guid) url (using a common, public domain cryptographic hash functions to compute the identifier for your bytes of interest.
-
-If you are using the Beaker browser or Firefox with the decentralized link(s) plugin for dat or ipfs urls you may be able to click and navigate into the above link to see its content.
-
-To clone this repo do:
-
-    git clone https://git.ackmanlab.com/jackman/bibd-test.git
-
-Then within the cloned repo clone the dat archive (install dat first, see me for help or datproject.org):  
-
-    cd ~/Downloads/bibd-test/
-    dat clone dat://cdbdaf1e57ddb7066be9c2bee940358b9fbcf779f557e329a4c322b2ef3ea912 
-
-### ipfs url test
-
-Let's try ipfs instead. Here is an ipfs link for 'image4.jpeg':
-
-<ipfs://QmXYgnpqeS7Kh5i8xHXTc6u6DqKAJz7q8eZC9JSLZsj2Af>
-
-Another version of that link:
-
-[The ipfs link](ipfs://QmXYgnpqeS7Kh5i8xHXTc6u6DqKAJz7q8eZC9JSLZsj2Af)
-
-
-A retinal wave movie:  
-
-<ipfs://QmUZgMkKkQBYV3QYkyBEZEtsFWr8t6afFdQmu4i7Zyjpq3>
-
-Another movie:  
-
-<ipfs://QmNuf4ZNF7kJchMP7FsRPtMt7YHAzJxqeo9jP7wEbMesdS>
-
-140509_10.tif:  
-<ipfs://QmQHod49MoCynfSiuzG4RMg7T23ZYyCs252qsf6zE12Rm3> 
+<div id="ref-Belanger:2011a">
+<p>1. Bélanger M, Allaman I, Magistretti PJ. Brain energy metabolism: Focus on astrocyte-neuron metabolic cooperation. Cell Metab. 2011;14: 724–38. doi:<a href="https://doi.org/10.1016/j.cmet.2011.08.016">10.1016/j.cmet.2011.08.016</a> pmid:<a href="https://www.ncbi.nlm.nih.gov/pubmed/22152301">22152301</a> <a href="ipfs://QmUmByy9faKDj3Uwzbs7rY8kuQQJVnMCPxrTTAaUbcANK2">ipfs://QmUmByy9faKDj3Uwzbs7rY8kuQQJVnMCPxrTTAaUbcANK2</a></p>
+</div>
+<div id="ref-Joshi:2008">
+<p>2. Joshi PS, Molyneaux BJ, Feng L, Xie X, Macklis JD, Gan L. Bhlhb5 regulates the postmitotic acquisition of area identities in layers ii-v of the developing neocortex. Neuron. 2008;60: 258–72. doi:<a href="https://doi.org/10.1016/j.neuron.2008.08.006">10.1016/j.neuron.2008.08.006</a> pmid:<a href="https://www.ncbi.nlm.nih.gov/pubmed/18957218">18957218</a> <a href="ipfs://QmZ4uURSGkysTeEp4y5nm7abSyrWBkoQ67Mx9K4uQshYRa">ipfs://QmZ4uURSGkysTeEp4y5nm7abSyrWBkoQ67Mx9K4uQshYRa</a></p>
+</div>
+<div id="ref-Strange:2014">
+<p>3. Strange BA, Witter MP, Lein ES, Moser EI. Functional organization of the hippocampal longitudinal axis. Nat Rev Neurosci. 2014;15: 655–69. doi:<a href="https://doi.org/10.1038/nrn3785">10.1038/nrn3785</a> pmid:<a href="https://www.ncbi.nlm.nih.gov/pubmed/25234264">25234264</a> <a href="ipfs://QmYwhmRJUA7aCtnRyD4CjYaiiMakrRVP9w4TXdwwiKr9RP">ipfs://QmYwhmRJUA7aCtnRyD4CjYaiiMakrRVP9w4TXdwwiKr9RP</a></p>
+</div>
+<div id="ref-Lisman:2017">
+<p>4. Lisman J, Buzsáki G, Eichenbaum H, Nadel L, Ranganath C, Redish AD. Viewpoints: How the hippocampus contributes to memory, navigation and cognition. Nat Neurosci. 2017;20: 1434–1447. doi:<a href="https://doi.org/10.1038/nn.4661">10.1038/nn.4661</a> pmid:<a href="https://www.ncbi.nlm.nih.gov/pubmed/29073641">29073641</a> <a href="ipfs://QmTaYzsXwpbBbDQxKVXruRa5N21PJdHQazAbcXvbhQXWY3">ipfs://QmTaYzsXwpbBbDQxKVXruRa5N21PJdHQazAbcXvbhQXWY3</a></p>
+</div>
+<div id="ref-Cullen:2017">
+<p>5. Cullen KE, Taube JS. Our sense of direction: Progress, controversies and challenges. Nat Neurosci. 2017;20: 1465–1473. doi:<a href="https://doi.org/10.1038/nn.4658">10.1038/nn.4658</a> pmid:<a href="https://www.ncbi.nlm.nih.gov/pubmed/29073639">29073639</a> <a href="ipfs://QmQj4Sw6BLLH6yQyVHJV8nHibk1fPtwLwXVkBc5namBZRR">ipfs://QmQj4Sw6BLLH6yQyVHJV8nHibk1fPtwLwXVkBc5namBZRR</a></p>
+</div>
+<div id="ref-Moser:2017">
+<p>6. Moser EI, Moser M-B, McNaughton BL. Spatial representation in the hippocampal formation: A history. Nat Neurosci. 2017;20: 1448–1464. doi:<a href="https://doi.org/10.1038/nn.4653">10.1038/nn.4653</a> pmid:<a href="https://www.ncbi.nlm.nih.gov/pubmed/29073644">29073644</a> <a href="ipfs://QmbVyq4TRBPBZcPdxxA59JYcZAi29Q7Wb7HAufhqwjwoY3">ipfs://QmbVyq4TRBPBZcPdxxA59JYcZAi29Q7Wb7HAufhqwjwoY3</a></p>
+</div>
+<div id="ref-Kim:2014">
+<p>7. Kim CK, Miri A, Leung LC, Berndt A, Mourrain P, Tank DW, et al. Prolonged, brain-wide expression of nuclear-localized gcamp3 for functional circuit mapping. Front Neural Circuits. 2014;8: 138. doi:<a href="https://doi.org/10.3389/fncir.2014.00138">10.3389/fncir.2014.00138</a> pmid:<a href="https://www.ncbi.nlm.nih.gov/pubmed/25505384">25505384</a> <a href="ipfs://QmQ5DfsGQMHyt61u8YShp1vMAfUPbjVVGiGNGRUdEpouDW">ipfs://QmQ5DfsGQMHyt61u8YShp1vMAfUPbjVVGiGNGRUdEpouDW</a></p>
+</div>
+</div>
 

urlconv.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+if [ "$1" == "-h" ] ; then
+    echo "
+         urlconv - add blob to ipfs and convert corresponding referring url in a bibtex database file
+    
+              Usage: urlconv preprint.pdf references.bib
+   "
+    #echo "$(tput setaf 6)$EDITOR $(tput setaf 7)is currently set as editor"
+    exit 0
+fi
+
+fn=$1
+bibFile=$2
+relPath="ipfs://"
+
+hashid=$(ipfs add $fn | grep $fn | cut --delimiter=" " -f 2)
+
+sed -i -E "s|(\W*Url = \{).*$fn(\}.*)|\1$relPath$hashid\2|" $bibFile

wave.bib

@@ -16,7 +16,7 @@
 	Title = {Brain energy metabolism: focus on astrocyte-neuron metabolic cooperation},
 	Volume = {14},
 	Year = {2011},
-	File = {papers/Bélanger_CellMetab2011a.pdf}}
+	Url = {ipfs://QmUmByy9faKDj3Uwzbs7rY8kuQQJVnMCPxrTTAaUbcANK2}}
 
 @article{Joshi:2008,
 	Abstract = {While progenitor-restricted factors broadly specify area identities in developing neocortex, the downstream regulatory elements involved in acquisition of those identities in postmitotic neurons are largely unknown. Here, we identify Bhlhb5, a transcription factor expressed in layers II-V, as a postmitotic regulator of area identity. Bhlhb5 is initially expressed in a high caudomedial to low rostrolateral gradient that transforms into a sharp border between sensory and rostral motor cortices. Bhlhb5 null mice exhibit aberrant expression of area-specific genes and structural organization in the somatosensory and caudal motor cortices. In somatosensory cortex, Bhlhb5 null mice display postsynaptic disorganization of vibrissal barrels. In caudal motor cortex, Bhlhb5 null mice exhibit anomalous differentiation of corticospinal motor neurons, accompanied by failure of corticospinal tract formation. Together, these results demonstrate Bhlhb5's function as an area-specific transcription factor that regulates the postmitotic acquisition of area identities and elucidate the genetic hierarchy between progenitors and postmitotic neurons driving neocortical arealization.},
@@ -36,7 +36,7 @@
 	Title = {Bhlhb5 regulates the postmitotic acquisition of area identities in layers II-V of the developing neocortex},
 	Volume = {60},
 	Year = {2008},
-	File = {papers/Joshi_Neuron2008.pdf}}
+	Url = {ipfs://QmZ4uURSGkysTeEp4y5nm7abSyrWBkoQ67Mx9K4uQshYRa}}
 
 @article{Strange:2014,
 	Abstract = {The precise functional role of the hippocampus remains a topic of much debate. The dominant view is that the dorsal (or posterior) hippocampus is implicated in memory and spatial navigation and the ventral (or anterior) hippocampus mediates anxiety-related behaviours. However, this 'dichotomy view' may need revision. Gene expression studies demonstrate multiple functional domains along the hippocampal long axis, which often exhibit sharply demarcated borders. By contrast, anatomical studies and electrophysiological recordings in rodents suggest that the long axis is organized along a gradient. Together, these observations suggest a model in which functional long-axis gradients are superimposed on discrete functional domains. This model provides a potential framework to explain and test the multiple functions ascribed to the hippocampus. },
@@ -55,7 +55,7 @@
 	Title = {Functional organization of the hippocampal longitudinal axis},
 	Volume = {15},
 	Year = {2014},
-	File = {papers/Strange_NatRevNeurosci2014.pdf},
+	Url = {ipfs://QmYwhmRJUA7aCtnRyD4CjYaiiMakrRVP9w4TXdwwiKr9RP},
 	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn3785}}
 
 @article{Lisman:2017,
@@ -74,7 +74,7 @@
 	Title = {Viewpoints: how the hippocampus contributes to memory, navigation and cognition},
 	Volume = {20},
 	Year = {2017},
-	File = {papers/Lisman_NatNeurosci2017.pdf},
+	Url = {ipfs://QmTaYzsXwpbBbDQxKVXruRa5N21PJdHQazAbcXvbhQXWY3},
 	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.4661}}
 
 @article{Cullen:2017,
@@ -93,7 +93,7 @@
 	Title = {Our sense of direction: progress, controversies and challenges},
 	Volume = {20},
 	Year = {2017},
-	File = {papers/Cullen_NatNeurosci2017.pdf},
+	Url = {ipfs://QmQj4Sw6BLLH6yQyVHJV8nHibk1fPtwLwXVkBc5namBZRR},
 	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.4658}}
 
 @article{Moser:2017,
@@ -113,7 +113,7 @@
 	Title = {Spatial representation in the hippocampal formation: a history},
 	Volume = {20},
 	Year = {2017},
-	File = {papers/Moser_NatNeurosci2017.pdf},
+	Url = {ipfs://QmbVyq4TRBPBZcPdxxA59JYcZAi29Q7Wb7HAufhqwjwoY3},
 	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.4653}}
 
 @article{Kim:2014,
@@ -133,5 +133,5 @@
 	Title = {Prolonged, brain-wide expression of nuclear-localized GCaMP3 for functional circuit mapping},
 	Volume = {8},
 	Year = {2014},
-	File = {papers/Kim_FrontNeuralCircuits2014.pdf}}
+	Url = {ipfs://QmQ5DfsGQMHyt61u8YShp1vMAfUPbjVVGiGNGRUdEpouDW}}